Fink

Recent Package Updates

2020-01-16: cran-fmri-r31-1.7-2-1 (Analysis of fMRI experiments)
The package contains R-functions to perform an fmri analysis as described
in K. Tabelow, J. Polzehl, H.U. Voss, and V. Spokoiny, Analysing fMRI
experiments with structure adaptive smoothing procedures, NeuroImage,
33:55-62 (2006), J. Polzehl, H.U. Voss, K. Tabelow, Structural adaptive
segmentation for statistical parametric mapping, NeuroImage, 52:515-513
(2010) and K. Tabelow, J. Polzehl, Statistical Parametric Maps for
Functional MRI Experiments in {R}: The Package {fmri}}, Journal of
Statistical Software, 44(11):1-21 (2011).

commit log from Daniel Macks (dmacks@netspace.org):

    Fix distribution restriction f some -r31 variants
2020-01-16: importlib-metadata-py35-1.1.3-1 (Read metadata from Python packages)
Read metadata from Python packages

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: packaging-py37-19.1-1 (Core utilities for Python packages)
This module includes APIs for
-  Version handling (`.version.Version`)
-  Specifiers (`.specifiers.SpecifierSet`)
-  Markers (`.markers.Marker`)
-  Requirements (`.requirements.Requirement`)
-  Utilities (`.utils`)

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: pytest-cov-py38-2.6.1-1 (Coverage plugin for pytest)
This plugin produces coverage reports. Compared to just using coverage
run this plugin does some extras:

    * Subprocess support: you can fork or run stuff in a subprocess and
    will get covered without any fuss.
    * Xdist support: you can use all of pytest-xdist's features and still
    get coverage.
    * Consistent pytest behavior. If you run coverage run -m pytest you
    will have slightly different sys.path (CWD will be in it, unlike
    when running pytest).

All features offered by the coverage package should work, either through
pytest-cov's command line options or through coverage's config file.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: html5lib-py36-1.0.1-3 (Python implementation of HTML5 parser)
html5lib is a pure-python library for parsing HTML. It is designed to conform
to the WHATWG HTML 5 specification, which has formalized the error handling
algorithms of popular web browsers and is implemented by all major browsers.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: wcwidth-py36-0.1.7-1 (Measure number of Terminal column cells)
This library measures the number of Terminal column cells of wide-character
codes. It is mainly intended for those implementing a Terminal Emulator,
or programs that carefully produce output to be interpreted by one.

Problem Statement: When printed to the screen, the length of the string is
usually equal to the number of cells it occupies. However, there are categories
of characters that occupy 2 cells (full-wide), and others that occupy 0.

Solution: POSIX.1-2001 and POSIX.1-2008 conforming systems provide wcwidth(3)
and wcswidth(3) C functions of which this python module's functions precisely
copy. These functions return the number of cells a unicode string is expected
to occupy.

This library aims to be forward-looking, portable, and most correct. The most
current release of this API is based on the Unicode Standard release files.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: pytest-py35-5.1.2-1 (Cross-project testing tool for Python)
py.test is a command line tool to collect, run and report about
automated tests. It runs well on Linux, Windows and OSX and on Python
2.4 through to 3.1 versions. It is used in many projects, ranging from
running 10 thousands of tests to a few inlined tests on a command line
script. As of version 1.2 you can also generate a no-dependency
py.test-equivalent standalone script that you can distribute along with
your application.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: metaboanalyst-tomcat8-r32-2.0-6 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: html5lib-py37-1.0.1-3 (Python implementation of HTML5 parser)
html5lib is a pure-python library for parsing HTML. It is designed to conform
to the WHATWG HTML 5 specification, which has formalized the error handling
algorithms of popular web browsers and is implemented by all major browsers.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: chardet-py37-3.0.4-2 (Universal Character Encoding Detector)
Previously maintained by Jrabbit 

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: pluggy-py37-0.13.0-1 (Python plugin and hook mechanism)
This is the plugin manager as used by pytest but stripped of pytest 
specific details.

Previously maintained by Hanspeter Niederstrasser
<mailto:nieder@users.sourceforge.net>

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: metaboanalyst-tomcat8-r34-2.0-6 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: chardet-py38-3.0.4-2 (Universal Character Encoding Detector)
Previously maintained by Jrabbit 

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: genshi-py36-0.7-1 (Toolkit for generation of output for the web)
Genshi is a Python library that provides an integrated set of
components for parsing, generating, and processing HTML, XML or other
textual content for output generation on the web.

The main feature is a template language that is smart about markup:
unlike conventional template languages that only deal with bytes and
(if you're lucky) characters, Genshi knows the difference between
tags, attributes, and actual text nodes, and uses that knowledge to
your advantage. For example:

    * Intelligent automatic escaping greatly reduces the risk of
      opening up your site to cross-site scripting attacks (XSS).

    * Template directives are often less verbose than those in most
      other template languages, as they can be attached directly to
      the elements they act upon.

    * Independence from a specific serialization format lets you
      instantly switch between generating well-formed HTML 4.01 and
      XHTML 1.0 (or other formats).

    * Stream-based filtering allows you to apply various
      transformations as a template is being processed, without having
      to parse and serialize the output again.

    * Match templates let you enforce a common structure on template
      output, and more. This, in combination with XInclude support, is
      used instead of the more rigid inheritance feature commonly
      found in other template languages.

For those cases where you don't want to generate markup, Genshi also
provides a simple text-based template language.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: coverage-py27-4.5.1-1 (Python code coverage for testing)
Coverage.py measures code coverage, typically during test
execution. It uses the code analysis tools and tracing hooks provided
in the Python standard library to determine which lines are
executable, and which have been executed.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: chardet-py35-3.0.4-2 (Universal Character Encoding Detector)
Previously maintained by Jrabbit 

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: metaboanalyst-tomcat8-r33-2.0-6 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: pluggy-py38-0.13.0-1 (Python plugin and hook mechanism)
This is the plugin manager as used by pytest but stripped of pytest 
specific details.

Previously maintained by Hanspeter Niederstrasser
<mailto:nieder@users.sourceforge.net>

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: importlib-metadata-py36-1.1.3-1 (Read metadata from Python packages)
Read metadata from Python packages

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: packaging-py36-19.1-1 (Core utilities for Python packages)
This module includes APIs for
-  Version handling (`.version.Version`)
-  Specifiers (`.specifiers.SpecifierSet`)
-  Markers (`.markers.Marker`)
-  Requirements (`.requirements.Requirement`)
-  Utilities (`.utils`)

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: coverage-py34-4.5.1-1 (Python code coverage for testing)
Coverage.py measures code coverage, typically during test
execution. It uses the code analysis tools and tracing hooks provided
in the Python standard library to determine which lines are
executable, and which have been executed.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: metaboanalyst-tomcat7-r33-2.0-6 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: beautifulsoup-py36-4.7.1-1 (Python HTML/XML parser)
Beautiful Soup is a Python HTML/XML parser designed for quick 
  turnaround projects like screen-scraping. Three features make 
  it powerful:
  1. Beautiful Soup won't choke if you give it bad markup. 
     It yields a parse tree that makes approximately as much 
     sense as your original document. This is usually good enough 
     to collect the data you need and run away.
  2. Beautiful Soup provides a few simple methods and Pythonic
     idioms for navigating, searching, and modifying a parse 
     tree: a toolkit for dissecting a document and extracting 
     what you need. You don't have to create a custom parser 
     for each application.
  3. Beautiful Soup automatically converts incoming documents 
     to Unicode and outgoing documents to UTF-8. You don't have 
     to think about encodings, unless the document doesn't specify 
     an encoding and Beautiful Soup can't autodetect one. Then you 
     just have to specify the original encoding.
     
  For documentation, see:
  http://www.crummy.com/software/BeautifulSoup/bs4/doc/

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: coverage-py35-4.5.1-1 (Python code coverage for testing)
Coverage.py measures code coverage, typically during test
execution. It uses the code analysis tools and tracing hooks provided
in the Python standard library to determine which lines are
executable, and which have been executed.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: chardet-py34-3.0.4-2 (Universal Character Encoding Detector)
Previously maintained by Jrabbit 

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: beautifulsoup-py34-4.7.1-1 (Python HTML/XML parser)
Beautiful Soup is a Python HTML/XML parser designed for quick 
  turnaround projects like screen-scraping. Three features make 
  it powerful:
  1. Beautiful Soup won't choke if you give it bad markup. 
     It yields a parse tree that makes approximately as much 
     sense as your original document. This is usually good enough 
     to collect the data you need and run away.
  2. Beautiful Soup provides a few simple methods and Pythonic
     idioms for navigating, searching, and modifying a parse 
     tree: a toolkit for dissecting a document and extracting 
     what you need. You don't have to create a custom parser 
     for each application.
  3. Beautiful Soup automatically converts incoming documents 
     to Unicode and outgoing documents to UTF-8. You don't have 
     to think about encodings, unless the document doesn't specify 
     an encoding and Beautiful Soup can't autodetect one. Then you 
     just have to specify the original encoding.
     
  For documentation, see:
  http://www.crummy.com/software/BeautifulSoup/bs4/doc/

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: cran-evtree-r34-1.0-7-1 (Evolutionary Learning)
Commonly used classification and regression tree methods like the
CART algorithm are recursive partitioning methods that build the
model in a forward stepwise search. Although this approach is known
to be an efficient heuristic, the results of recursive tree methods
are only locally optimal, as splits are chosen to maximize homogeneity
at the next step only. An alternative way to search over the parameter
space of trees is to use global optimization methods like evolutionary
algorithms. The evtree package implements an evolutionary algorithm
for learning globally optimal classification and regression trees in R.
CPU and memory-intensive tasks are fully computed in C++ while the
partykit package is leveraged to represent the resulting trees in R,
providing unified infrastructure for summaries, visualizations, and
predictions.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix distribution restriction f some -r31 variants
2020-01-16: lxml-py36-4.2.5-1 (Binding for the libxml2 and libxslt)
The C libraries libxml2 and libxslt have huge benefits:

    * Standards-compliant XML support.
    * Full-featured.  (e.g. supports XPath)
    * Actively maintained by XML experts.
    * fast

lxml is a new Python binding for libxml2 and libxslt, completely
independent from these existing Python bindings. Its aim:

    * Pythonic API.
    * Documented.
    * Use Python unicode strings in API.
    * Safe (no segfaults).
    * No manual memory management!

lxml aims to provide a Pythonic API by following as much as possible
the ElementTree API. We're trying to avoid having to invent too many
new APIs, or you having to learn new things -- XML is complicated
enough.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: cran-fmri-r33-1.7-2-1 (Analysis of fMRI experiments)
The package contains R-functions to perform an fmri analysis as described
in K. Tabelow, J. Polzehl, H.U. Voss, and V. Spokoiny, Analysing fMRI
experiments with structure adaptive smoothing procedures, NeuroImage,
33:55-62 (2006), J. Polzehl, H.U. Voss, K. Tabelow, Structural adaptive
segmentation for statistical parametric mapping, NeuroImage, 52:515-513
(2010) and K. Tabelow, J. Polzehl, Statistical Parametric Maps for
Functional MRI Experiments in {R}: The Package {fmri}}, Journal of
Statistical Software, 44(11):1-21 (2011).

commit log from Daniel Macks (dmacks@netspace.org):

    Fix distribution restriction f some -r31 variants
2020-01-16: metaboanalyst-tomcat6-r33-2.0-6 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: pytest-expect-py34-1.1.0-1 (Test expectations plugin for pytest)
Test expectations plugin for pytest

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: pytest-expect-py36-1.1.0-1 (Test expectations plugin for pytest)
Test expectations plugin for pytest

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: coverage-py37-4.5.1-1 (Python code coverage for testing)
Coverage.py measures code coverage, typically during test
execution. It uses the code analysis tools and tracing hooks provided
in the Python standard library to determine which lines are
executable, and which have been executed.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: chardet-py36-3.0.4-2 (Universal Character Encoding Detector)
Previously maintained by Jrabbit 

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: genshi-py38-0.7-1 (Toolkit for generation of output for the web)
Genshi is a Python library that provides an integrated set of
components for parsing, generating, and processing HTML, XML or other
textual content for output generation on the web.

The main feature is a template language that is smart about markup:
unlike conventional template languages that only deal with bytes and
(if you're lucky) characters, Genshi knows the difference between
tags, attributes, and actual text nodes, and uses that knowledge to
your advantage. For example:

    * Intelligent automatic escaping greatly reduces the risk of
      opening up your site to cross-site scripting attacks (XSS).

    * Template directives are often less verbose than those in most
      other template languages, as they can be attached directly to
      the elements they act upon.

    * Independence from a specific serialization format lets you
      instantly switch between generating well-formed HTML 4.01 and
      XHTML 1.0 (or other formats).

    * Stream-based filtering allows you to apply various
      transformations as a template is being processed, without having
      to parse and serialize the output again.

    * Match templates let you enforce a common structure on template
      output, and more. This, in combination with XInclude support, is
      used instead of the more rigid inheritance feature commonly
      found in other template languages.

For those cases where you don't want to generate markup, Genshi also
provides a simple text-based template language.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: bioconductor-vsn-r34-3.54.0-1 (Variance stabilization for microarray data)
The package implements a method for normalising microarray intensities, 
and works for single- and multiple-color arrays. It can also be used for 
data from other technologies, as long as they have similar format. The 
method uses a robust variant of the maximum-likelihood estimator for an 
additive-multiplicative error model and affine calibration. The model 
incorporates data calibration step (a.k.a. normalization), a model for 
the dependence of the variance on the mean intensity and a variance 
stabilizing data transformation. Differences between transformed intensities 
are analogous to "normalized log-ratios". However, in contrast to the 
latter, their variance is independent of the mean, and they are usually 
more sensitive and specific in detecting differential transcription.

commit log from Daniel Macks (dmacks@netspace.org):

    Add some missing -rXX variants
2020-01-16: lxml-py34-4.2.5-1 (Binding for the libxml2 and libxslt)
The C libraries libxml2 and libxslt have huge benefits:

    * Standards-compliant XML support.
    * Full-featured.  (e.g. supports XPath)
    * Actively maintained by XML experts.
    * fast

lxml is a new Python binding for libxml2 and libxslt, completely
independent from these existing Python bindings. Its aim:

    * Pythonic API.
    * Documented.
    * Use Python unicode strings in API.
    * Safe (no segfaults).
    * No manual memory management!

lxml aims to provide a Pythonic API by following as much as possible
the ElementTree API. We're trying to avoid having to invent too many
new APIs, or you having to learn new things -- XML is complicated
enough.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: lxml-py35-4.2.5-1 (Binding for the libxml2 and libxslt)
The C libraries libxml2 and libxslt have huge benefits:

    * Standards-compliant XML support.
    * Full-featured.  (e.g. supports XPath)
    * Actively maintained by XML experts.
    * fast

lxml is a new Python binding for libxml2 and libxslt, completely
independent from these existing Python bindings. Its aim:

    * Pythonic API.
    * Documented.
    * Use Python unicode strings in API.
    * Safe (no segfaults).
    * No manual memory management!

lxml aims to provide a Pythonic API by following as much as possible
the ElementTree API. We're trying to avoid having to invent too many
new APIs, or you having to learn new things -- XML is complicated
enough.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: pluggy-py36-0.13.0-1 (Python plugin and hook mechanism)
This is the plugin manager as used by pytest but stripped of pytest 
specific details.

Previously maintained by Hanspeter Niederstrasser
<mailto:nieder@users.sourceforge.net>

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: metaboanalyst3-tomcat7-r33-3.0-4 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: packaging-py34-19.1-1 (Core utilities for Python packages)
This module includes APIs for
-  Version handling (`.version.Version`)
-  Specifiers (`.specifiers.SpecifierSet`)
-  Markers (`.markers.Marker`)
-  Requirements (`.requirements.Requirement`)
-  Utilities (`.utils`)

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: atomicwrites-py34-1.3.0-1 (Python library for atomic file writes)
Atomic file writes.

        from atomicwrites import atomic_write
        with atomic_write('foo.txt', overwrite=True) as f:
                f.write('Hello world.')
                # "foo.txt" doesn't exist yet.

        # Now it does.

Features that distinguish it from other similar libraries:

Race-free assertion that the target file doesn't yet exist.
This can be controlled with the overwrite parameter.

Windows support, although not well-tested.

Simple high-level API that wraps a very flexible class-based API.

Consistent error handling across platforms.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: metaboanalyst-tomcat7-r32-2.0-6 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: wcwidth-py37-0.1.7-1 (Measure number of Terminal column cells)
This library measures the number of Terminal column cells of wide-character
codes. It is mainly intended for those implementing a Terminal Emulator,
or programs that carefully produce output to be interpreted by one.

Problem Statement: When printed to the screen, the length of the string is
usually equal to the number of cells it occupies. However, there are categories
of characters that occupy 2 cells (full-wide), and others that occupy 0.

Solution: POSIX.1-2001 and POSIX.1-2008 conforming systems provide wcwidth(3)
and wcswidth(3) C functions of which this python module's functions precisely
copy. These functions return the number of cells a unicode string is expected
to occupy.

This library aims to be forward-looking, portable, and most correct. The most
current release of this API is based on the Unicode Standard release files.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: coverage-py36-4.5.1-1 (Python code coverage for testing)
Coverage.py measures code coverage, typically during test
execution. It uses the code analysis tools and tracing hooks provided
in the Python standard library to determine which lines are
executable, and which have been executed.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: cran-evtree-r33-1.0-7-1 (Evolutionary Learning)
Commonly used classification and regression tree methods like the
CART algorithm are recursive partitioning methods that build the
model in a forward stepwise search. Although this approach is known
to be an efficient heuristic, the results of recursive tree methods
are only locally optimal, as splits are chosen to maximize homogeneity
at the next step only. An alternative way to search over the parameter
space of trees is to use global optimization methods like evolutionary
algorithms. The evtree package implements an evolutionary algorithm
for learning globally optimal classification and regression trees in R.
CPU and memory-intensive tasks are fully computed in C++ while the
partykit package is leveraged to represent the resulting trees in R,
providing unified infrastructure for summaries, visualizations, and
predictions.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix distribution restriction f some -r31 variants
2020-01-16: pytest-cov-py34-2.6.1-1 (Coverage plugin for pytest)
This plugin produces coverage reports. Compared to just using coverage
run this plugin does some extras:

    * Subprocess support: you can fork or run stuff in a subprocess and
    will get covered without any fuss.
    * Xdist support: you can use all of pytest-xdist's features and still
    get coverage.
    * Consistent pytest behavior. If you run coverage run -m pytest you
    will have slightly different sys.path (CWD will be in it, unlike
    when running pytest).

All features offered by the coverage package should work, either through
pytest-cov's command line options or through coverage's config file.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: cran-cocorresp-r32-0.3-0-1 (Co-correspondence analysis methods)
Fits predictive and symmetric co-correspondence analysis (CoCA) model
to relate one data matrix to another data matrix. More specifically,
CoCA maximises the weighted covariance between the weighted averaged
species scores of one community and the weighted averaged species
scores of another community. CoCA attempts to find patterns that are
common to both communitities.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix distribution restriction f some -r31 variants
2020-01-16: genshi-py37-0.7-1 (Toolkit for generation of output for the web)
Genshi is a Python library that provides an integrated set of
components for parsing, generating, and processing HTML, XML or other
textual content for output generation on the web.

The main feature is a template language that is smart about markup:
unlike conventional template languages that only deal with bytes and
(if you're lucky) characters, Genshi knows the difference between
tags, attributes, and actual text nodes, and uses that knowledge to
your advantage. For example:

    * Intelligent automatic escaping greatly reduces the risk of
      opening up your site to cross-site scripting attacks (XSS).

    * Template directives are often less verbose than those in most
      other template languages, as they can be attached directly to
      the elements they act upon.

    * Independence from a specific serialization format lets you
      instantly switch between generating well-formed HTML 4.01 and
      XHTML 1.0 (or other formats).

    * Stream-based filtering allows you to apply various
      transformations as a template is being processed, without having
      to parse and serialize the output again.

    * Match templates let you enforce a common structure on template
      output, and more. This, in combination with XInclude support, is
      used instead of the more rigid inheritance feature commonly
      found in other template languages.

For those cases where you don't want to generate markup, Genshi also
provides a simple text-based template language.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: metaboanalyst-tomcat6-r31-2.0-6 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: importlib-metadata-py34-1.1.3-1 (Read metadata from Python packages)
Read metadata from Python packages

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: metaboanalyst3-tomcat8-r31-3.0-4 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: bioconductor-vsn-r35-3.54.0-1 (Variance stabilization for microarray data)
The package implements a method for normalising microarray intensities, 
and works for single- and multiple-color arrays. It can also be used for 
data from other technologies, as long as they have similar format. The 
method uses a robust variant of the maximum-likelihood estimator for an 
additive-multiplicative error model and affine calibration. The model 
incorporates data calibration step (a.k.a. normalization), a model for 
the dependence of the variance on the mean intensity and a variance 
stabilizing data transformation. Differences between transformed intensities 
are analogous to "normalized log-ratios". However, in contrast to the 
latter, their variance is independent of the mean, and they are usually 
more sensitive and specific in detecting differential transcription.

commit log from Daniel Macks (dmacks@netspace.org):

    Add some missing -rXX variants
2020-01-16: lxml-py27-4.2.5-1 (Binding for the libxml2 and libxslt)
The C libraries libxml2 and libxslt have huge benefits:

    * Standards-compliant XML support.
    * Full-featured.  (e.g. supports XPath)
    * Actively maintained by XML experts.
    * fast

lxml is a new Python binding for libxml2 and libxslt, completely
independent from these existing Python bindings. Its aim:

    * Pythonic API.
    * Documented.
    * Use Python unicode strings in API.
    * Safe (no segfaults).
    * No manual memory management!

lxml aims to provide a Pythonic API by following as much as possible
the ElementTree API. We're trying to avoid having to invent too many
new APIs, or you having to learn new things -- XML is complicated
enough.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: html5lib-py34-1.0.1-3 (Python implementation of HTML5 parser)
html5lib is a pure-python library for parsing HTML. It is designed to conform
to the WHATWG HTML 5 specification, which has formalized the error handling
algorithms of popular web browsers and is implemented by all major browsers.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: html5lib-py35-1.0.1-3 (Python implementation of HTML5 parser)
html5lib is a pure-python library for parsing HTML. It is designed to conform
to the WHATWG HTML 5 specification, which has formalized the error handling
algorithms of popular web browsers and is implemented by all major browsers.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: wcwidth-py38-0.1.7-1 (Measure number of Terminal column cells)
This library measures the number of Terminal column cells of wide-character
codes. It is mainly intended for those implementing a Terminal Emulator,
or programs that carefully produce output to be interpreted by one.

Problem Statement: When printed to the screen, the length of the string is
usually equal to the number of cells it occupies. However, there are categories
of characters that occupy 2 cells (full-wide), and others that occupy 0.

Solution: POSIX.1-2001 and POSIX.1-2008 conforming systems provide wcwidth(3)
and wcswidth(3) C functions of which this python module's functions precisely
copy. These functions return the number of cells a unicode string is expected
to occupy.

This library aims to be forward-looking, portable, and most correct. The most
current release of this API is based on the Unicode Standard release files.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: metaboanalyst3-tomcat8-r34-3.0-4 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: wcwidth-py35-0.1.7-1 (Measure number of Terminal column cells)
This library measures the number of Terminal column cells of wide-character
codes. It is mainly intended for those implementing a Terminal Emulator,
or programs that carefully produce output to be interpreted by one.

Problem Statement: When printed to the screen, the length of the string is
usually equal to the number of cells it occupies. However, there are categories
of characters that occupy 2 cells (full-wide), and others that occupy 0.

Solution: POSIX.1-2001 and POSIX.1-2008 conforming systems provide wcwidth(3)
and wcswidth(3) C functions of which this python module's functions precisely
copy. These functions return the number of cells a unicode string is expected
to occupy.

This library aims to be forward-looking, portable, and most correct. The most
current release of this API is based on the Unicode Standard release files.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: wcwidth-py34-0.1.7-1 (Measure number of Terminal column cells)
This library measures the number of Terminal column cells of wide-character
codes. It is mainly intended for those implementing a Terminal Emulator,
or programs that carefully produce output to be interpreted by one.

Problem Statement: When printed to the screen, the length of the string is
usually equal to the number of cells it occupies. However, there are categories
of characters that occupy 2 cells (full-wide), and others that occupy 0.

Solution: POSIX.1-2001 and POSIX.1-2008 conforming systems provide wcwidth(3)
and wcswidth(3) C functions of which this python module's functions precisely
copy. These functions return the number of cells a unicode string is expected
to occupy.

This library aims to be forward-looking, portable, and most correct. The most
current release of this API is based on the Unicode Standard release files.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: metaboanalyst3-tomcat7-r32-3.0-4 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: importlib-metadata-py38-1.1.3-1 (Read metadata from Python packages)
Read metadata from Python packages

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: html5lib-py27-1.0.1-3 (Python implementation of HTML5 parser)
html5lib is a pure-python library for parsing HTML. It is designed to conform
to the WHATWG HTML 5 specification, which has formalized the error handling
algorithms of popular web browsers and is implemented by all major browsers.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: cran-cocorresp-r33-0.3-0-1 (Co-correspondence analysis methods)
Fits predictive and symmetric co-correspondence analysis (CoCA) model
to relate one data matrix to another data matrix. More specifically,
CoCA maximises the weighted covariance between the weighted averaged
species scores of one community and the weighted averaged species
scores of another community. CoCA attempts to find patterns that are
common to both communitities.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix distribution restriction f some -r31 variants
2020-01-16: genshi-py34-0.7-1 (Toolkit for generation of output for the web)
Genshi is a Python library that provides an integrated set of
components for parsing, generating, and processing HTML, XML or other
textual content for output generation on the web.

The main feature is a template language that is smart about markup:
unlike conventional template languages that only deal with bytes and
(if you're lucky) characters, Genshi knows the difference between
tags, attributes, and actual text nodes, and uses that knowledge to
your advantage. For example:

    * Intelligent automatic escaping greatly reduces the risk of
      opening up your site to cross-site scripting attacks (XSS).

    * Template directives are often less verbose than those in most
      other template languages, as they can be attached directly to
      the elements they act upon.

    * Independence from a specific serialization format lets you
      instantly switch between generating well-formed HTML 4.01 and
      XHTML 1.0 (or other formats).

    * Stream-based filtering allows you to apply various
      transformations as a template is being processed, without having
      to parse and serialize the output again.

    * Match templates let you enforce a common structure on template
      output, and more. This, in combination with XInclude support, is
      used instead of the more rigid inheritance feature commonly
      found in other template languages.

For those cases where you don't want to generate markup, Genshi also
provides a simple text-based template language.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: lxml-py38-4.2.5-1 (Binding for the libxml2 and libxslt)
The C libraries libxml2 and libxslt have huge benefits:

    * Standards-compliant XML support.
    * Full-featured.  (e.g. supports XPath)
    * Actively maintained by XML experts.
    * fast

lxml is a new Python binding for libxml2 and libxslt, completely
independent from these existing Python bindings. Its aim:

    * Pythonic API.
    * Documented.
    * Use Python unicode strings in API.
    * Safe (no segfaults).
    * No manual memory management!

lxml aims to provide a Pythonic API by following as much as possible
the ElementTree API. We're trying to avoid having to invent too many
new APIs, or you having to learn new things -- XML is complicated
enough.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: cran-evtree-r31-1.0-7-1 (Evolutionary Learning)
Commonly used classification and regression tree methods like the
CART algorithm are recursive partitioning methods that build the
model in a forward stepwise search. Although this approach is known
to be an efficient heuristic, the results of recursive tree methods
are only locally optimal, as splits are chosen to maximize homogeneity
at the next step only. An alternative way to search over the parameter
space of trees is to use global optimization methods like evolutionary
algorithms. The evtree package implements an evolutionary algorithm
for learning globally optimal classification and regression trees in R.
CPU and memory-intensive tasks are fully computed in C++ while the
partykit package is leveraged to represent the resulting trees in R,
providing unified infrastructure for summaries, visualizations, and
predictions.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix distribution restriction f some -r31 variants
2020-01-16: importlib-metadata-py27-1.1.3-1 (Read metadata from Python packages)
Read metadata from Python packages

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: wcwidth-py27-0.1.7-1 (Measure number of Terminal column cells)
This library measures the number of Terminal column cells of wide-character
codes. It is mainly intended for those implementing a Terminal Emulator,
or programs that carefully produce output to be interpreted by one.

Problem Statement: When printed to the screen, the length of the string is
usually equal to the number of cells it occupies. However, there are categories
of characters that occupy 2 cells (full-wide), and others that occupy 0.

Solution: POSIX.1-2001 and POSIX.1-2008 conforming systems provide wcwidth(3)
and wcswidth(3) C functions of which this python module's functions precisely
copy. These functions return the number of cells a unicode string is expected
to occupy.

This library aims to be forward-looking, portable, and most correct. The most
current release of this API is based on the Unicode Standard release files.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: genshi-py35-0.7-1 (Toolkit for generation of output for the web)
Genshi is a Python library that provides an integrated set of
components for parsing, generating, and processing HTML, XML or other
textual content for output generation on the web.

The main feature is a template language that is smart about markup:
unlike conventional template languages that only deal with bytes and
(if you're lucky) characters, Genshi knows the difference between
tags, attributes, and actual text nodes, and uses that knowledge to
your advantage. For example:

    * Intelligent automatic escaping greatly reduces the risk of
      opening up your site to cross-site scripting attacks (XSS).

    * Template directives are often less verbose than those in most
      other template languages, as they can be attached directly to
      the elements they act upon.

    * Independence from a specific serialization format lets you
      instantly switch between generating well-formed HTML 4.01 and
      XHTML 1.0 (or other formats).

    * Stream-based filtering allows you to apply various
      transformations as a template is being processed, without having
      to parse and serialize the output again.

    * Match templates let you enforce a common structure on template
      output, and more. This, in combination with XInclude support, is
      used instead of the more rigid inheritance feature commonly
      found in other template languages.

For those cases where you don't want to generate markup, Genshi also
provides a simple text-based template language.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: metaboanalyst-tomcat6-r34-2.0-6 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: cran-cocorresp-r31-0.3-0-1 (Co-correspondence analysis methods)
Fits predictive and symmetric co-correspondence analysis (CoCA) model
to relate one data matrix to another data matrix. More specifically,
CoCA maximises the weighted covariance between the weighted averaged
species scores of one community and the weighted averaged species
scores of another community. CoCA attempts to find patterns that are
common to both communitities.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix distribution restriction f some -r31 variants
2020-01-16: metaboanalyst-tomcat8-r31-2.0-6 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: genshi-py27-0.7-1 (Toolkit for generation of output for the web)
Genshi is a Python library that provides an integrated set of
components for parsing, generating, and processing HTML, XML or other
textual content for output generation on the web.

The main feature is a template language that is smart about markup:
unlike conventional template languages that only deal with bytes and
(if you're lucky) characters, Genshi knows the difference between
tags, attributes, and actual text nodes, and uses that knowledge to
your advantage. For example:

    * Intelligent automatic escaping greatly reduces the risk of
      opening up your site to cross-site scripting attacks (XSS).

    * Template directives are often less verbose than those in most
      other template languages, as they can be attached directly to
      the elements they act upon.

    * Independence from a specific serialization format lets you
      instantly switch between generating well-formed HTML 4.01 and
      XHTML 1.0 (or other formats).

    * Stream-based filtering allows you to apply various
      transformations as a template is being processed, without having
      to parse and serialize the output again.

    * Match templates let you enforce a common structure on template
      output, and more. This, in combination with XInclude support, is
      used instead of the more rigid inheritance feature commonly
      found in other template languages.

For those cases where you don't want to generate markup, Genshi also
provides a simple text-based template language.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: packaging-py38-19.1-1 (Core utilities for Python packages)
This module includes APIs for
-  Version handling (`.version.Version`)
-  Specifiers (`.specifiers.SpecifierSet`)
-  Markers (`.markers.Marker`)
-  Requirements (`.requirements.Requirement`)
-  Utilities (`.utils`)

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: metaboanalyst3-tomcat8-r32-3.0-4 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: atomicwrites-py36-1.3.0-1 (Python library for atomic file writes)
Atomic file writes.

        from atomicwrites import atomic_write
        with atomic_write('foo.txt', overwrite=True) as f:
                f.write('Hello world.')
                # "foo.txt" doesn't exist yet.

        # Now it does.

Features that distinguish it from other similar libraries:

Race-free assertion that the target file doesn't yet exist.
This can be controlled with the overwrite parameter.

Windows support, although not well-tested.

Simple high-level API that wraps a very flexible class-based API.

Consistent error handling across platforms.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: metaboanalyst-tomcat7-r31-2.0-6 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: atomicwrites-py38-1.3.0-1 (Python library for atomic file writes)
Atomic file writes.

        from atomicwrites import atomic_write
        with atomic_write('foo.txt', overwrite=True) as f:
                f.write('Hello world.')
                # "foo.txt" doesn't exist yet.

        # Now it does.

Features that distinguish it from other similar libraries:

Race-free assertion that the target file doesn't yet exist.
This can be controlled with the overwrite parameter.

Windows support, although not well-tested.

Simple high-level API that wraps a very flexible class-based API.

Consistent error handling across platforms.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: pytest-expect-py27-1.1.0-1 (Test expectations plugin for pytest)
Test expectations plugin for pytest

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: lxml-py37-4.2.5-1 (Binding for the libxml2 and libxslt)
The C libraries libxml2 and libxslt have huge benefits:

    * Standards-compliant XML support.
    * Full-featured.  (e.g. supports XPath)
    * Actively maintained by XML experts.
    * fast

lxml is a new Python binding for libxml2 and libxslt, completely
independent from these existing Python bindings. Its aim:

    * Pythonic API.
    * Documented.
    * Use Python unicode strings in API.
    * Safe (no segfaults).
    * No manual memory management!

lxml aims to provide a Pythonic API by following as much as possible
the ElementTree API. We're trying to avoid having to invent too many
new APIs, or you having to learn new things -- XML is complicated
enough.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: coverage-py38-4.5.1-1 (Python code coverage for testing)
Coverage.py measures code coverage, typically during test
execution. It uses the code analysis tools and tracing hooks provided
in the Python standard library to determine which lines are
executable, and which have been executed.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: metaboanalyst-tomcat7-r34-2.0-6 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: metaboanalyst3-tomcat7-r31-3.0-4 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: pytest-cov-py36-2.6.1-1 (Coverage plugin for pytest)
This plugin produces coverage reports. Compared to just using coverage
run this plugin does some extras:

    * Subprocess support: you can fork or run stuff in a subprocess and
    will get covered without any fuss.
    * Xdist support: you can use all of pytest-xdist's features and still
    get coverage.
    * Consistent pytest behavior. If you run coverage run -m pytest you
    will have slightly different sys.path (CWD will be in it, unlike
    when running pytest).

All features offered by the coverage package should work, either through
pytest-cov's command line options or through coverage's config file.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: metaboanalyst3-tomcat8-r33-3.0-4 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: cran-fmri-r32-1.7-2-1 (Analysis of fMRI experiments)
The package contains R-functions to perform an fmri analysis as described
in K. Tabelow, J. Polzehl, H.U. Voss, and V. Spokoiny, Analysing fMRI
experiments with structure adaptive smoothing procedures, NeuroImage,
33:55-62 (2006), J. Polzehl, H.U. Voss, K. Tabelow, Structural adaptive
segmentation for statistical parametric mapping, NeuroImage, 52:515-513
(2010) and K. Tabelow, J. Polzehl, Statistical Parametric Maps for
Functional MRI Experiments in {R}: The Package {fmri}}, Journal of
Statistical Software, 44(11):1-21 (2011).

commit log from Daniel Macks (dmacks@netspace.org):

    Fix distribution restriction f some -r31 variants
2020-01-16: beautifulsoup-py35-4.7.1-1 (Python HTML/XML parser)
Beautiful Soup is a Python HTML/XML parser designed for quick 
  turnaround projects like screen-scraping. Three features make 
  it powerful:
  1. Beautiful Soup won't choke if you give it bad markup. 
     It yields a parse tree that makes approximately as much 
     sense as your original document. This is usually good enough 
     to collect the data you need and run away.
  2. Beautiful Soup provides a few simple methods and Pythonic
     idioms for navigating, searching, and modifying a parse 
     tree: a toolkit for dissecting a document and extracting 
     what you need. You don't have to create a custom parser 
     for each application.
  3. Beautiful Soup automatically converts incoming documents 
     to Unicode and outgoing documents to UTF-8. You don't have 
     to think about encodings, unless the document doesn't specify 
     an encoding and Beautiful Soup can't autodetect one. Then you 
     just have to specify the original encoding.
     
  For documentation, see:
  http://www.crummy.com/software/BeautifulSoup/bs4/doc/

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: bioconductor-vsn-r36-3.54.0-1 (Variance stabilization for microarray data)
The package implements a method for normalising microarray intensities, 
and works for single- and multiple-color arrays. It can also be used for 
data from other technologies, as long as they have similar format. The 
method uses a robust variant of the maximum-likelihood estimator for an 
additive-multiplicative error model and affine calibration. The model 
incorporates data calibration step (a.k.a. normalization), a model for 
the dependence of the variance on the mean intensity and a variance 
stabilizing data transformation. Differences between transformed intensities 
are analogous to "normalized log-ratios". However, in contrast to the 
latter, their variance is independent of the mean, and they are usually 
more sensitive and specific in detecting differential transcription.

commit log from Daniel Macks (dmacks@netspace.org):

    Add some missing -rXX variants
2020-01-16: pytest-py36-5.1.2-1 (Cross-project testing tool for Python)
py.test is a command line tool to collect, run and report about
automated tests. It runs well on Linux, Windows and OSX and on Python
2.4 through to 3.1 versions. It is used in many projects, ranging from
running 10 thousands of tests to a few inlined tests on a command line
script. As of version 1.2 you can also generate a no-dependency
py.test-equivalent standalone script that you can distribute along with
your application.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: pytest-cov-py27-2.6.1-1 (Coverage plugin for pytest)
This plugin produces coverage reports. Compared to just using coverage
run this plugin does some extras:

    * Subprocess support: you can fork or run stuff in a subprocess and
    will get covered without any fuss.
    * Xdist support: you can use all of pytest-xdist's features and still
    get coverage.
    * Consistent pytest behavior. If you run coverage run -m pytest you
    will have slightly different sys.path (CWD will be in it, unlike
    when running pytest).

All features offered by the coverage package should work, either through
pytest-cov's command line options or through coverage's config file.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: metaboanalyst3-tomcat7-r34-3.0-4 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: packaging-py35-19.1-1 (Core utilities for Python packages)
This module includes APIs for
-  Version handling (`.version.Version`)
-  Specifiers (`.specifiers.SpecifierSet`)
-  Markers (`.markers.Marker`)
-  Requirements (`.requirements.Requirement`)
-  Utilities (`.utils`)

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: pytest-expect-py37-1.1.0-1 (Test expectations plugin for pytest)
Test expectations plugin for pytest

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: pytest-expect-py38-1.1.0-1 (Test expectations plugin for pytest)
Test expectations plugin for pytest

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: atomicwrites-py35-1.3.0-1 (Python library for atomic file writes)
Atomic file writes.

        from atomicwrites import atomic_write
        with atomic_write('foo.txt', overwrite=True) as f:
                f.write('Hello world.')
                # "foo.txt" doesn't exist yet.

        # Now it does.

Features that distinguish it from other similar libraries:

Race-free assertion that the target file doesn't yet exist.
This can be controlled with the overwrite parameter.

Windows support, although not well-tested.

Simple high-level API that wraps a very flexible class-based API.

Consistent error handling across platforms.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: metaboanalyst-tomcat6-r32-2.0-6 (Tool suite for metabolomic data analysis)
Provide a user-friendly, web-based analytical pipeline for high-throughput
metabolomics studies. In particular, MetaboAnalyst aims to offer a variety
of commonly used procedures for metabolomic data processing, normalization,
multivariate statistical analysis, as well as data annotation. The current
implementation focuses on exploratory statistical analysis and functional
interpretation for quantitative metabolomics studies.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix typo in dependency
2020-01-16: chardet-py27-3.0.4-2 (Universal Character Encoding Detector)
Previously maintained by Jrabbit 

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: atomicwrites-py37-1.3.0-1 (Python library for atomic file writes)
Atomic file writes.

        from atomicwrites import atomic_write
        with atomic_write('foo.txt', overwrite=True) as f:
                f.write('Hello world.')
                # "foo.txt" doesn't exist yet.

        # Now it does.

Features that distinguish it from other similar libraries:

Race-free assertion that the target file doesn't yet exist.
This can be controlled with the overwrite parameter.

Windows support, although not well-tested.

Simple high-level API that wraps a very flexible class-based API.

Consistent error handling across platforms.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: pytest-py37-5.1.2-1 (Cross-project testing tool for Python)
py.test is a command line tool to collect, run and report about
automated tests. It runs well on Linux, Windows and OSX and on Python
2.4 through to 3.1 versions. It is used in many projects, ranging from
running 10 thousands of tests to a few inlined tests on a command line
script. As of version 1.2 you can also generate a no-dependency
py.test-equivalent standalone script that you can distribute along with
your application.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: beautifulsoup-py38-4.7.1-1 (Python HTML/XML parser)
Beautiful Soup is a Python HTML/XML parser designed for quick 
  turnaround projects like screen-scraping. Three features make 
  it powerful:
  1. Beautiful Soup won't choke if you give it bad markup. 
     It yields a parse tree that makes approximately as much 
     sense as your original document. This is usually good enough 
     to collect the data you need and run away.
  2. Beautiful Soup provides a few simple methods and Pythonic
     idioms for navigating, searching, and modifying a parse 
     tree: a toolkit for dissecting a document and extracting 
     what you need. You don't have to create a custom parser 
     for each application.
  3. Beautiful Soup automatically converts incoming documents 
     to Unicode and outgoing documents to UTF-8. You don't have 
     to think about encodings, unless the document doesn't specify 
     an encoding and Beautiful Soup can't autodetect one. Then you 
     just have to specify the original encoding.
     
  For documentation, see:
  http://www.crummy.com/software/BeautifulSoup/bs4/doc/

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: beautifulsoup-py37-4.7.1-1 (Python HTML/XML parser)
Beautiful Soup is a Python HTML/XML parser designed for quick 
  turnaround projects like screen-scraping. Three features make 
  it powerful:
  1. Beautiful Soup won't choke if you give it bad markup. 
     It yields a parse tree that makes approximately as much 
     sense as your original document. This is usually good enough 
     to collect the data you need and run away.
  2. Beautiful Soup provides a few simple methods and Pythonic
     idioms for navigating, searching, and modifying a parse 
     tree: a toolkit for dissecting a document and extracting 
     what you need. You don't have to create a custom parser 
     for each application.
  3. Beautiful Soup automatically converts incoming documents 
     to Unicode and outgoing documents to UTF-8. You don't have 
     to think about encodings, unless the document doesn't specify 
     an encoding and Beautiful Soup can't autodetect one. Then you 
     just have to specify the original encoding.
     
  For documentation, see:
  http://www.crummy.com/software/BeautifulSoup/bs4/doc/

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: pytest-py38-5.1.2-1 (Cross-project testing tool for Python)
py.test is a command line tool to collect, run and report about
automated tests. It runs well on Linux, Windows and OSX and on Python
2.4 through to 3.1 versions. It is used in many projects, ranging from
running 10 thousands of tests to a few inlined tests on a command line
script. As of version 1.2 you can also generate a no-dependency
py.test-equivalent standalone script that you can distribute along with
your application.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: pytest-expect-py35-1.1.0-1 (Test expectations plugin for pytest)
Test expectations plugin for pytest

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: packaging-py27-19.1-1 (Core utilities for Python packages)
This module includes APIs for
-  Version handling (`.version.Version`)
-  Specifiers (`.specifiers.SpecifierSet`)
-  Markers (`.markers.Marker`)
-  Requirements (`.requirements.Requirement`)
-  Utilities (`.utils`)

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: atomicwrites-py27-1.3.0-1 (Python library for atomic file writes)
Atomic file writes.

        from atomicwrites import atomic_write
        with atomic_write('foo.txt', overwrite=True) as f:
                f.write('Hello world.')
                # "foo.txt" doesn't exist yet.

        # Now it does.

Features that distinguish it from other similar libraries:

Race-free assertion that the target file doesn't yet exist.
This can be controlled with the overwrite parameter.

Windows support, although not well-tested.

Simple high-level API that wraps a very flexible class-based API.

Consistent error handling across platforms.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: pytest-cov-py35-2.6.1-1 (Coverage plugin for pytest)
This plugin produces coverage reports. Compared to just using coverage
run this plugin does some extras:

    * Subprocess support: you can fork or run stuff in a subprocess and
    will get covered without any fuss.
    * Xdist support: you can use all of pytest-xdist's features and still
    get coverage.
    * Consistent pytest behavior. If you run coverage run -m pytest you
    will have slightly different sys.path (CWD will be in it, unlike
    when running pytest).

All features offered by the coverage package should work, either through
pytest-cov's command line options or through coverage's config file.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: beautifulsoup-py27-4.7.1-1 (Python HTML/XML parser)
Beautiful Soup is a Python HTML/XML parser designed for quick 
  turnaround projects like screen-scraping. Three features make 
  it powerful:
  1. Beautiful Soup won't choke if you give it bad markup. 
     It yields a parse tree that makes approximately as much 
     sense as your original document. This is usually good enough 
     to collect the data you need and run away.
  2. Beautiful Soup provides a few simple methods and Pythonic
     idioms for navigating, searching, and modifying a parse 
     tree: a toolkit for dissecting a document and extracting 
     what you need. You don't have to create a custom parser 
     for each application.
  3. Beautiful Soup automatically converts incoming documents 
     to Unicode and outgoing documents to UTF-8. You don't have 
     to think about encodings, unless the document doesn't specify 
     an encoding and Beautiful Soup can't autodetect one. Then you 
     just have to specify the original encoding.
     
  For documentation, see:
  http://www.crummy.com/software/BeautifulSoup/bs4/doc/

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: pluggy-py27-0.13.0-1 (Python plugin and hook mechanism)
This is the plugin manager as used by pytest but stripped of pytest 
specific details.

Previously maintained by Hanspeter Niederstrasser
<mailto:nieder@users.sourceforge.net>

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: html5lib-py38-1.0.1-3 (Python implementation of HTML5 parser)
html5lib is a pure-python library for parsing HTML. It is designed to conform
to the WHATWG HTML 5 specification, which has formalized the error handling
algorithms of popular web browsers and is implemented by all major browsers.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: cran-evtree-r35-1.0-7-1 (Evolutionary Learning)
Commonly used classification and regression tree methods like the
CART algorithm are recursive partitioning methods that build the
model in a forward stepwise search. Although this approach is known
to be an efficient heuristic, the results of recursive tree methods
are only locally optimal, as splits are chosen to maximize homogeneity
at the next step only. An alternative way to search over the parameter
space of trees is to use global optimization methods like evolutionary
algorithms. The evtree package implements an evolutionary algorithm
for learning globally optimal classification and regression trees in R.
CPU and memory-intensive tasks are fully computed in C++ while the
partykit package is leveraged to represent the resulting trees in R,
providing unified infrastructure for summaries, visualizations, and
predictions.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix distribution restriction f some -r31 variants
2020-01-16: pluggy-py35-0.13.0-1 (Python plugin and hook mechanism)
This is the plugin manager as used by pytest but stripped of pytest 
specific details.

Previously maintained by Hanspeter Niederstrasser
<mailto:nieder@users.sourceforge.net>

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: importlib-metadata-py37-1.1.3-1 (Read metadata from Python packages)
Read metadata from Python packages

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: pytest-cov-py37-2.6.1-1 (Coverage plugin for pytest)
This plugin produces coverage reports. Compared to just using coverage
run this plugin does some extras:

    * Subprocess support: you can fork or run stuff in a subprocess and
    will get covered without any fuss.
    * Xdist support: you can use all of pytest-xdist's features and still
    get coverage.
    * Consistent pytest behavior. If you run coverage run -m pytest you
    will have slightly different sys.path (CWD will be in it, unlike
    when running pytest).

All features offered by the coverage package should work, either through
pytest-cov's command line options or through coverage's config file.

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: cran-evtree-r32-1.0-7-1 (Evolutionary Learning)
Commonly used classification and regression tree methods like the
CART algorithm are recursive partitioning methods that build the
model in a forward stepwise search. Although this approach is known
to be an efficient heuristic, the results of recursive tree methods
are only locally optimal, as splits are chosen to maximize homogeneity
at the next step only. An alternative way to search over the parameter
space of trees is to use global optimization methods like evolutionary
algorithms. The evtree package implements an evolutionary algorithm
for learning globally optimal classification and regression trees in R.
CPU and memory-intensive tasks are fully computed in C++ while the
partykit package is leveraged to represent the resulting trees in R,
providing unified infrastructure for summaries, visualizations, and
predictions.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix distribution restriction f some -r31 variants
2020-01-16: pluggy-py34-0.13.0-1 (Python plugin and hook mechanism)
This is the plugin manager as used by pytest but stripped of pytest 
specific details.

Previously maintained by Hanspeter Niederstrasser
<mailto:nieder@users.sourceforge.net>

commit log from Daniel Macks (dmacks@netspace.org):

    +py38 to fix dep-tree holes
2020-01-16: cran-simcomp-r35-3.3-1 (Simultaneous Comparisons for Mult. Endpoints)
Simultaneous tests and confidence intervals for one-way experimental
designs with one or many normally distributed, primary response
variables (endpoints). The procedure of Hasler and Hothorn (2011,2012)
is applied for differences or ratios of means. Various contrasts can
be chosen, unbalanced sample sizes are allowed as well as heterogeneous
variances or covariance matrices.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sandwich-r33-2.5-1-1 (GNU R std err estimators for time-series data)
sandwich: Robust Covariance Matrix Estimators
Model-robust standard error estimators for cross-sectional, 
time series, and longitudinal data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-proxy-r34-0.4-23-1 (Distance and Similarity Measures)
Provides an extensible framework for the efficient calculation of
auto- and cross-proximities, along with implementations of the
most popular ones.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rjava-r33-0.9-8-2 (Low-level R to Java interface)
Low-level interface to Java VM very much like .C/.Call and friends.
Allows creation of objects, calling methods and accessing fields.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-vgamdata-r31-1.0-3-1 (Data supporting the VGAM package)
Data sets to accompany the VGAM package. These are used to illustrate
vector generalized linear and additive models, and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column Interaction Models,
and constrained ordination models in ecology.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rootsolve-r35-1.7-2 (Analysis of ordinary differential equations)
Routines to find the root of nonlinear functions, and to perform
steady-state and equilibrium analysis of ordinary differential
equations (ODE). Includes routines that: (1) generate gradient
and Jacobian matrices (full and banded), (2) find roots of
non-linear equations by the Newton-Raphson method, (3) estimate
steady-state conditions of a system of (differential) equations
in full, banded or sparse form, using the Newton-Raphson method,
or by dynamically running, (4) solve the steady-state conditions
for uni-and multicomponent 1-D, 2-D, and 3-D partial differential
equations, that have been converted to ODEs by numerical differencing
(using the method-of-lines approach). Includes fortran code.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rcdk-r32-3.4.7.1-1 (Interface to the CDK Libraries)
This package allows the user to access functionality in the CDK,
a Java framework for cheminformatics. This allows the user to load
molecules, evaluate fingerprints, calculate molecular descriptors
and so on. In addition the CDK API allows the user to view structures
in 2D.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rpanel-r36-1.1-4-1 (Simple interactive controls)
rpanel provides a set of functions to build simple GUI controls for
R functions. These are built on the tcltk package. Uses could include
changing a parameter on a graph by animating it with a slider or a
"doublebutton", up to more sophisticated control panels. Some functions
for specific graphical tasks, referred to as 'cartoons', are provided.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-proto-r33-1.0.0-1 (Prototype object-based programming)
An object oriented system using object-based, also called
prototype-based, rather than class-based object oriented ideas.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rastervis-r32-0.46-1 (Visualization methods for raster)
The raster package defines classes and methods for spatial raster
data access and manipulation. The rasterVis package complements
raster providing a set of methods for enhanced visualization and
interaction.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-spatialnp-r31-1.1-3-1 (Spatial Multivariate nonparametric methods)
This package contains test and estimates of location, tests of independence,
tests of sphericity and several estimates of shape all based on spatial signs,
symmetrized signs, ranks and signed ranks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-svunit-r34-0.7-12-1 (SciViews GUI API - Unit testing)
A complete unit test system and functions to implement its GUI part

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcompression-r32-0.93-2-1 (R Package for in-memory compression)
This package is a basic R interface to the zlib and bzip2 facilities for 
compressing and uncompressing data that are in memory rather than in files.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rootsolve-r31-1.7-2 (Analysis of ordinary differential equations)
Routines to find the root of nonlinear functions, and to perform
steady-state and equilibrium analysis of ordinary differential
equations (ODE). Includes routines that: (1) generate gradient
and Jacobian matrices (full and banded), (2) find roots of
non-linear equations by the Newton-Raphson method, (3) estimate
steady-state conditions of a system of (differential) equations
in full, banded or sparse form, using the Newton-Raphson method,
or by dynamically running, (4) solve the steady-state conditions
for uni-and multicomponent 1-D, 2-D, and 3-D partial differential
equations, that have been converted to ODEs by numerical differencing
(using the method-of-lines approach). Includes fortran code.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-selectr-r32-0.4-1-1 (Translate CSS Selectors to XPath Expressions)
Translates a CSS3 selector into an equivalent XPath expression. This
allows us to use CSS selectors when working with the XML package as it
can only evaluate XPath expressions. Also provided are convenience
functions useful for using CSS selectors on XML nodes. This package is a
port of the Python package 'cssselect'
(<https://cssselect.readthedocs.io/>).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-simecol-r34-0.8-13-1 (Simulation of ecological dynamic systems)
simecol is an object oriented framework to simulate ecological (and other)
dynamic systems. It can be used for differential equations, individual-based
(or agent-based) and other models as well. The package helps to organize
scenarios (avoids copy and paste) and improves readability and usability of
code.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-ps-r33-1.3.0-1 (List, Query, Manipulate System Processes)
List, query and manipulate all system processes, on 'Windows', 'Linux'
and 'macOS'.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-statip-r34-0.2.0-1 (Functions for Distributions and Regression)
A collection of miscellaneous statistical functions for probability
distributions: dbern(), pbern(), qbern(), rbern() for the Bernoulli
distribution, and distr2name(), name2distr() for distribution names;
probability density estimation: densityfun(); most frequent value
estimation: mfv(), mfv1(); calculation of the Hellinger distance:
hellinger(); use of classical kernels: kernelfun(), kernel_properties();
univariate piecewise-constant regression: picor().

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-spatialnp-r35-1.1-3-1 (Spatial Multivariate nonparametric methods)
This package contains test and estimates of location, tests of independence,
tests of sphericity and several estimates of shape all based on spatial signs,
symmetrized signs, ranks and signed ranks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-relaimpo-r36-2.2-3-1 (Relative importance of regressors)
relaimpo provides several metrics for assessing relative importance
in linear models. These can be printed, plotted and bootstrapped.
The recommended metric is lmg, which provides a decomposition of
the model explained variance into non-negative contributions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcppeigen-r34-0.3.3.5.0-2 (Rcpp Eigen templated linear algebra library)
R and Eigen integration using Rcpp. Eigen is a C++ template library
for linear algebra: matrices, vectors, numerical solvers and related
algorithms. It supports dense and sparse matrices on integer,
floating point and complex numbers, decompositions of such matrices,
and solutions of linear systems. Its performance on many algorithms
is comparable with some of the best implementations based on Lapack
and level-3 BLAS. The RcppEigen package includes the header files
from the Eigen C++ template library (currently version 3.2.0).
Thus users do not need to install Eigen itself in order to use
RcppEigen. Since version 3.1.1, Eigen is licensed under the
Mozilla Public License (version 2); earlier version were licensed
under the GNU LGPL version 3 or later. RcppEigen (the Rcpp
bindings/bridge to Eigen) is licensed under the GNU GPL version 2
 or later, as is the rest of Rcpp.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rocr-r35-1.0-7-1 (Visualizing scoring classifier performance)
ROC graphs, sensitivity/specificity curves, lift charts, and
precision/recall plots are popular examples of trade-off
visualizations for specific pairs of performance measures. ROCR
is a flexible tool for creating cutoff-parameterized 2D
performance curves by freely combining two from over 25
performance measures (new performance measures can be added
using a standard interface). Curves from different cross-
alidation or bootstrapping runs can be averaged by different
methods, and standard deviations, standard errors or box plots
can be used to visualize the variability across the runs. The
parameterization can be visualized by printing cutoff values
at the corresponding curve positions, or by coloring the curve
according to cutoff. All components of a performance plot can
be quickly adjusted using a flexible parameter dispatching
mechanism. Despite its flexibility, ROCR is easy to use, with
only three commands and reasonable default values for all
optional parameters.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r.utils-r32-2.9.0-1 (Various programming utilities)
This package provides utility methods useful when programming
and developing R packages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-vgamdata-r34-1.0-3-1 (Data supporting the VGAM package)
Data sets to accompany the VGAM package. These are used to illustrate
vector generalized linear and additive models, and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column Interaction Models,
and constrained ordination models in ecology.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-strucchange-r32-1.5-1-1 (Structural Changes)
Testing, monitoring and dating structural changes in (linear) regression
models. strucchange features tests/methods from the generalized fluctuation
test framework as well as from the F test (Chow test) framework.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-questionr-r32-0.7.0-1 (Functions to Make Surveys Processing Easier)
Set of functions to make the processing and analysis of surveys easier :
interactive shiny apps and addins for data recoding, contingency tables,
dataset metadata handling, and several convenience functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-yaletoolkit-r32-4.2.2-1 (Data exploration tools from Yale University)
This collection of data exploration tools was developed at Yale University
for the graphical exploration of complex multivariate data; barcode and
gpairs now have their own packages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sfsmisc-r34-1.1-4-1 (Utilities from Statistik ETH Zurich seminar)
Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich,
quite a few related to graphics; many ported from S-plus times.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-remotes-r32-2.1.0-1 (R Pkg Installation from Remote Repositories)
Run 'R CMD check' from 'R' programmatically, and capture the results of
the individual checks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rpart-r35-4.1-15-1 (GNU R Tools for recursive partitioning)
Recursive partitioning and regression trees

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2020-01-16: cran-rcppeigen-r36-0.3.3.5.0-2 (Rcpp Eigen templated linear algebra library)
R and Eigen integration using Rcpp. Eigen is a C++ template library
for linear algebra: matrices, vectors, numerical solvers and related
algorithms. It supports dense and sparse matrices on integer,
floating point and complex numbers, decompositions of such matrices,
and solutions of linear systems. Its performance on many algorithms
is comparable with some of the best implementations based on Lapack
and level-3 BLAS. The RcppEigen package includes the header files
from the Eigen C++ template library (currently version 3.2.0).
Thus users do not need to install Eigen itself in order to use
RcppEigen. Since version 3.1.1, Eigen is licensed under the
Mozilla Public License (version 2); earlier version were licensed
under the GNU LGPL version 3 or later. RcppEigen (the Rcpp
bindings/bridge to Eigen) is licensed under the GNU GPL version 2
 or later, as is the rest of Rcpp.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-viridislite-r32-0.3.0-1 (Default Color Maps from 'matplotlib')
Port of the new 'matplotlib' color maps ('viridis' - the default -, 
'magma', plasma' and 'inferno') to 'R'. 'matplotlib' 
http://matplotlib.org/  is a popular plotting library for 'python'. 
These color maps are designed in such a way that they will analytically be 
perfectly perceptually-uniform, both in regular form and also when 
converted to black-and-white. They are also designed to be perceived by 
readers with the most common form of color blindness. This is the 'lite' 
version of the more complete 'viridis' package that can be found at 
<https://cran.r-project.org/package=viridis>.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-psych-r31-1.8.12-1 (Procedures for Psychological Research)
A number of routines for personality, psychometrics and experimental
psychology. Functions are primarily for scale construction using
factor analysis, cluster analysis and reliability analysis, although
others provide basic descriptive statistics. Item Response Theory is
done using factor analysis of tetrachoric and polychoric correlations.
Functions for simulating particular item and test structures are
included. Several functions serve as a useful front end for structural
equation modeling. Graphical displays of path diagrams, factor analysis
and structural equation models are created using basic graphics. Some
of the functions are written to support a book on psychometrics as well
as publications in personality research. For more information, see the
personality-project.org/r webpage.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-ttr-r35-0.23-5-1 (Technical Trading Rules)
Technical analysis and other functions to construct technical trading 
rules with R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-registry-r31-0.5-1-1 (Infrastructure for R Package Registries)
Provides a generic infrastructure for creating and using registries.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rggobi-r33-2.1.22-1 (Interface between R and GGobi)
The rggobi package provides a command-line interface to GGobi, an
interactive and dynamic graphics package. Rggobi complements GGobi's
graphical user interface, providing a way to fluidly transition
between analysis and exploration, as well as automating common tasks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-st-r34-1.2.5-1 (Shrinkage t Statistic and CAT Score)
This package implements the "shrinkage t" statistic introduced in
Opgen-Rhein and Strimmer (2007) and a shrinkage estimate of the
"correlation-adjusted t-score" (CAT score) described in Zuber
and Strimmer (2009). It also offers a convenient interface to
a number of other regularized t-statistics commonly employed in
high-dimensional case-control studies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rattle-r31-5.2.0-1 (Graphical user interface for data mining in R)
Rattle (the R Analytic Tool To Learn Easily) provides a Gnome
(RGtk2) based interface to R functionality for data mining.
The aim is to provide a simple and intuitive interface that
allows a user to quickly load data from a CSV file (or via ODBC),
transform and explore the data, build and evaluate models, and
export models as PMML (predictive modelling markup language) or
as scores. All of this with knowing little about R. All R
commands are logged and commented through the log tab. Thus
they are available to the user as a script file or as an aide
for the user to learn R or to copy-and-paste directly into R
itself. Rattle also exports a number of utility functions and
the graphical user interface, invoked as rattle(), does not
need to be run to deploy these.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-survival-r33-2.44-1.1-1 (GNU R Tools for survival analysis)
survival analysis: descriptive statistics, two-sample tests,
parametric accelerated failure models, Cox model.
Delayed entry (truncation) allowed for all models;
interval censoring for parametric models. Case-cohort designs.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tcltk2-r35-1.2-11-1 (Tcl/Tk Additions)
A series of additional Tcl commands and Tk widgets with style and
various functions (under Windows: DDE exchange, access to the
registry and icon manipulation) to supplement the tcltk package

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sna-r35-2.4-1 (Tools for Social Network Analysis)
A range of tools for social network analysis, including node and graph-level
indices, structural distance and covariance methods, structural equivalence
detection, network regression, random graph generation, and 2D/3D network
visualization.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-turner-r34-0.1.7-1 (Turn lists of vectors into indexed structures)
Package designed for working with vectors and lists of vectors,
mainly for turning them into other indexed data structures.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-randomforestsrc-r36-2.9.1-1 (Random Forests for Survival)
A unified treatment of Breiman's random forests for survival, regression
and classification problems based on Ishwaran and Kogalur's random survival
forests (RSF) package. The package runs in both serial and parallel
(OpenMP) modes.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-selectr-r35-0.4-1-1 (Translate CSS Selectors to XPath Expressions)
Translates a CSS3 selector into an equivalent XPath expression. This
allows us to use CSS selectors when working with the XML package as it
can only evaluate XPath expressions. Also provided are convenience
functions useful for using CSS selectors on XML nodes. This package is a
port of the Python package 'cssselect'
(<https://cssselect.readthedocs.io/>).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-zcompositions-r32-1.3.2-1-1 (Treatment of Zero/Missing Values in Data Sets)
Principled methods for the imputation of zeros, left-censored and
missing data in compositional data sets.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-polspline-r31-1.1.16-2 (Polynomial spline routines)
Routines for the polynomial spline fitting routines hazard regression,
hazard estimation with flexible tails, logspline, lspec, polyclass,
and polymars, by C. Kooperberg and co-authors

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-tensor-r33-1.5-1 (Tensor product of arrays)
The tensor product of two arrays is notionally an outer product
of the arrays collapsed in specific extents by summing along
the appropriate diagonals.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rsvgdevice-r35-0.6.4.4-2 (R SVG graphics device)
A graphics device for R that uses the w3.org xml standard
for Scalable Vector Graphics.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-remotes-r35-2.1.0-1 (R Pkg Installation from Remote Repositories)
Run 'R CMD check' from 'R' programmatically, and capture the results of
the individual checks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rocr-r34-1.0-7-1 (Visualizing scoring classifier performance)
ROC graphs, sensitivity/specificity curves, lift charts, and
precision/recall plots are popular examples of trade-off
visualizations for specific pairs of performance measures. ROCR
is a flexible tool for creating cutoff-parameterized 2D
performance curves by freely combining two from over 25
performance measures (new performance measures can be added
using a standard interface). Curves from different cross-
alidation or bootstrapping runs can be averaged by different
methods, and standard deviations, standard errors or box plots
can be used to visualize the variability across the runs. The
parameterization can be visualized by printing cutoff values
at the corresponding curve positions, or by coloring the curve
according to cutoff. All components of a performance plot can
be quickly adjusted using a flexible parameter dispatching
mechanism. Despite its flexibility, ROCR is easy to use, with
only three commands and reasonable default values for all
optional parameters.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-r.utils-r35-2.9.0-1 (Various programming utilities)
This package provides utility methods useful when programming
and developing R packages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-seriation-r32-1.2-8-2 (Infrastructure for seriation)
Infrastructure for seriation with an implementation of several
seriation/sequencing techniques to reorder matrices, dissimilarity
matrices, and dendrograms. Also contains some visualizations
techniques based on seriation.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-trust-r35-0.1-7-1 (Trust Region Optimization)
local optimization using two derivatives and trust regions

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-simcomp-r32-3.3-1 (Simultaneous Comparisons for Mult. Endpoints)
Simultaneous tests and confidence intervals for one-way experimental
designs with one or many normally distributed, primary response
variables (endpoints). The procedure of Hasler and Hothorn (2011,2012)
is applied for differences or ratios of means. Various contrasts can
be chosen, unbalanced sample sizes are allowed as well as heterogeneous
variances or covariance matrices.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-randomforest-r32-4.6-12-1 (GNU R Tools for random forest class/regress)
Classification and regression based on a forest of trees using random inputs.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-speaq-r36-2.6.0-1 (NMR Spectrum Alignment Tools)
We introduce a novel suite of informatics tools for the quantitative analysis
of NMR metabolomic profile data. The core of the processing cascade is a novel
peak alignment algorithm, called hierarchical Cluster-based Peak Alignment
(CluPA). The algorithm aligns a target spectrum to the reference spectrum in
a top-down fashion by building a hierarchical cluster tree from peak lists of
reference and target spectra and then dividing the spectra into smaller
segments based on the most distant clusters of the tree. To reduce the
computational time to estimate the spectral misalignment, the method makes
use of Fast Fourier Transformation (FFT) cross-correlation. Since the method
returns a high-quality alignment, we can propose a simple methodology to study
the variability of the NMR spectra. For each aligned NMR data point the ratio
of the between-group and within-group sum of squares (BW-ratio) is calculated
to quantify the difference in variability between and within predefined groups
of NMR spectra. This differential analysis is related to the calculation of
the F-statistic or a one-way ANOVA, but without distributional assumptions.
Statistical inference based on the BW-ratio is achieved by bootstrapping the
null distribution from the experimental data. Related publication is
available at http://www.biomedcentral.com/1471-2105/12/405/.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rda-r35-1.0.2-2.1-1 (Shrunken Centroids RDA)
Shrunken Centroids Regularized Discriminant Analysis
for the classification purpose in high dimensional data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-registry-r34-0.5-1-1 (Infrastructure for R Package Registries)
Provides a generic infrastructure for creating and using registries.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sm-r34-2.2-5.6-2 (Smoothing methods)
This is software linked to the book 'Applied Smoothing Techniques for
Data Analysis - The Kernel Approach with S-Plus Illustrations' Oxford
University Press.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-polspline-r35-1.1.16-2 (Polynomial spline routines)
Routines for the polynomial spline fitting routines hazard regression,
hazard estimation with flexible tails, logspline, lspec, polyclass,
and polymars, by C. Kooperberg and co-authors

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-ttr-r34-0.23-5-1 (Technical Trading Rules)
Technical analysis and other functions to construct technical trading 
rules with R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-vim-r33-4.8.0-1 (Missing Values Visualization and Imputation)
This package introduces new tools for the visualization of missing and/or
imputed values, which can be used for exploring the data and the structure
of the missing and/or imputed values. Depending on this structure of the
missing values, the corresponding methods may help to identify the
mechanism generating the missing values and allows to explore the data
including missing values. In addition, the quality of imputation can be
visually explored using various univariate, bivariate, multiple and
multivariate plot methods. A graphical user interface available in the
separate package VIMGUI allows an easy handling of the implemented plot
methods.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcppziggurat-r33-0.1.5-1 (Integration of Ziggurat RNG Implementations)
The Ziggurat generator for normally distributed random numbers,
originally proposed by Marsaglia and Tsang (2000,
) has been improved upon a few times starting
with Leong et al (2005, ). This package
provides an aggregation in order to compare different implementations in
order to provide an 'faster but good enough' alternative for use with R
and C++ code.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-png-r33-0.1-7-2 (Read and write PNG images)
This package provides an easy and simple way to read, write and
display bitmap images stored in the PNG format. It can read and
write both files and in-memory raw vectors.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcmdrplugin.ma-r34-0.0-2-1 (GUI for Conducting Meta-Analyses in R)
This is an R-Commander plug-in for meta-analysis. This package enables
the user to conduct a meta-analysis in a menu-driven, graphical user
interface environment (e.g., SPSS). It uses recommended procedures as
described in The Handbook of Research Synthesis and Meta-Analysis
(Cooper, Hedges, & Valentine, 2009).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sna-r34-2.4-1 (Tools for Social Network Analysis)
A range of tools for social network analysis, including node and graph-level
indices, structural distance and covariance methods, structural equivalence
detection, network regression, random graph generation, and 2D/3D network
visualization.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-viridis-r35-0.5.1-2 (Default Color Maps from 'matplotlib')
Port of the new 'matplotlib' color maps ('viridis' - the default -,
'magma', plasma' and 'inferno') to 'R'. 'matplotlib'
http://matplotlib.org/  is a popular plotting library for 'python'.
These color maps are designed in such a way that they will analytically be
perfectly perceptually-uniform, both in regular form and also when
converted to black-and-white. They are also designed to be perceived by
readers with the most common form of color blindness. This is the 'lite'
version of the more complete 'viridis' package that can be found at
<https://cran.r-project.org/package=viridis>.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcppgsl-r35-0.3.4-1 (Rcpp Integration for 'GNU GSL')
'Rcpp' integration for 'GNU GSL' vectors and matrices The 'GNU
Scientific Library' (or 'GSL') is a collection of numerical routines for
scientific computing. It is particularly useful for C and C++ programs
as it provides a standard C interface to a wide range of mathematical
routines. There are over 1000 functions in total with an extensive test
suite. The 'RcppGSL' package provides an easy-to-use interface between
'GSL' data structures and R using concepts from 'Rcpp' which is itself a
package that eases the interfaces between R and C++. This package also
serves as a prime example of how to build a package that uses 'Rcpp' to
connect to another third-party library. The 'autoconf' script, 'inline'
plugin and example package can all be used as a stanza to write a
similar package against another library.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tkrplot-r36-0.0-24-1 (TK Rplot)
simple mechanism for placing R graphics in a Tk widget

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-qvcalc-r36-1.0.1-1 (Quasi Variances for Effects in Stat Models)
Functions to compute quasi variances and associated measures of
approximation error.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-st-r35-1.2.5-1 (Shrinkage t Statistic and CAT Score)
This package implements the "shrinkage t" statistic introduced in
Opgen-Rhein and Strimmer (2007) and a shrinkage estimate of the
"correlation-adjusted t-score" (CAT score) described in Zuber
and Strimmer (2009). It also offers a convenient interface to
a number of other regularized t-statistics commonly employed in
high-dimensional case-control studies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-spls-r34-2.2-3-1 (Sparse Partial Least Squares Regression)
This package provides functions for fitting a Sparse Partial
Least Squares Regression and Classification

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rstudioapi-r35-0.10-1 (Safely access the RStudio API)
This package provides functions to make it easy to access the RStudio
API when available, and provide informative error messages when not.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rmpi-r36-0.6-9-1 (R Interface Wrapper to MPI)
Rmpi provides an interface (wrapper) to MPI APIs. It also provides
an interactive R slave environment.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-zip-r32-2.0.4-1 (Cross-Platform 'zip' Compression)
Cross-Platform 'zip' Compression Library. A replacement for the 'zip'
function, that does not require any additional external tools on any
platform.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-som-r31-0.3-5.1-1 (Self-Organizing Map)
Self-Organizing Map (with application in gene clustering)

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcppprogress-r35-0.4.1-1 (Interruptible Progress Bar)
Allows to display a progress bar in the R console for long running
computations taking place in c++ code, and support for interrupting
those computations even in multithreaded code, typically using OpenMP.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rgdal-r34-1.4-6-1 (GNU R Bindings for GDAL)
GNU R Bindings for GDAL

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tsfa-r35-2014.10-1-1 (Time Series Factor Analysis)
Extraction of Factors from Multivariate Time Series.
See ?00tsfa-Intro for more details.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-prettyunits-r35-1.0.2-3 (Human Readable Formatting of Quantities)
Pretty, human readable formatting of quantities.
Time intervals: 1337000 -> 15d 11h 23m 20s.
Vague time intervals: 2674000 -> about a month ago.
Bytes: 1337 -> 1.34 kB.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcmdcheck-r34-1.3.3-1 (Run 'R CMD check' from 'R')
Run 'R CMD check' from 'R' programmatically, and capture the results of
the individual checks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-prabclus-r35-2.3-1-1 (Functions for Clustering)
Distance-based parametric bootstrap tests for clustering with spatial
neighborhood information. Some distance measures, Clustering of
presence-absence, abundance and multilocus genetical data for
species delimitation, nearest neighbor based noise detection.
Try package?prabclus for on overview.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sm-r35-2.2-5.6-2 (Smoothing methods)
This is software linked to the book 'Applied Smoothing Techniques for
Data Analysis - The Kernel Approach with S-Plus Illustrations' Oxford
University Press.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rcmdcheck-r36-1.3.3-1 (Run 'R CMD check' from 'R')
Run 'R CMD check' from 'R' programmatically, and capture the results of
the individual checks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-timp-r31-1.13.2-1 (Fitting separable nonlinear models)
TIMP is a problem solving environment for fitting separable nonlinear
models to measurements arising in physics and chemistry experiments,
and has been extensively applied to time-resolved spectroscopy and
FLIM-FRET data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sessioninfo-r33-1.1.1-1 (R Session Information)
Query and print information about the current R session. It is similar
to 'utils::sessionInfo()', but includes more information about packages,
and where they were installed from.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rmpfr-r31-0.6-1-1 (Multiple Precision Floating-Point Reliable)
Rmpfr provides (S4 classes and methods for) arithmetic including transcendental
("special") functions for arbitrary precision floating point numbers. To this
end, it interfaces to the LGPL'ed MPFR (Multiple Precision Floating-Point
Reliable) Library which itself is based on the GMP (GNU Multiple Precision)
Library.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tcltk2-r32-1.2-11-1 (Tcl/Tk Additions)
A series of additional Tcl commands and Tk widgets with style and
various functions (under Windows: DDE exchange, access to the
registry and icon manipulation) to supplement the tcltk package

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rda-r34-1.0.2-2.1-1 (Shrunken Centroids RDA)
Shrunken Centroids Regularized Discriminant Analysis
for the classification purpose in high dimensional data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tidyr-r33-1.0.0-2 (Easily Tidy Data)
An evolution of 'reshape2'. It's designed specifically for data 
tidying (not general reshaping or aggregating) and works well 
with 'dplyr' data pipelines.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-runit-r36-0.4.32-1 (R Unit test framework)
R functions implementing a standard Unit Testing framework,
with additional code inspection and report generation tools

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-som-r36-0.3-5.1-1 (Self-Organizing Map)
Self-Organizing Map (with application in gene clustering)

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcgmin-r36-2013-2.21-1 (Conjugate Gradient Minimization)
Conjugate gradient minimization of nonlinear functions with box constraints
incorporating the Dai/Yuan update. This implementation should be used in
place of the "CG" algorithm of the optim() function.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rdpack-r31-0.8-0-1 (Update/Manipulate Rd Documentation Objects)
Functions for manipulation of R documentation objects, including
functions reprompt() and ereprompt() for updating 'Rd' documentation for
functions, methods and classes; 'Rd' macros for citations and import of
references from 'bibtex' files for use in 'Rd' files and 'roxygen2'
comments; 'Rd' macros for evaluating and inserting snippets of 'R' code
and the results of its evaluation or creating graphics on the fly; and
many functions for manipulation of references and Rd files.

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2020-01-16: cran-truncnorm-r36-1.0-8-1 (Truncated Normal Distribution)
Density, probability, quantile and random number generation functions
for the truncated normal distribution.

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2020-01-16: cran-setrng-r33-2013.9-1-1 (Random Number Generator and Seed)
SetRNG provides utilities to help set and record the setting of
the seed and the uniform and normal generators used when a random
experiment is run. The utilities can be used in other functions
that do random experiments to simplify recording and/or setting
all the necessary information for reproducibility.

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2020-01-16: cran-rcmdr-r32-2.4-2-1 (R Commander)
A platform-independent basic-statistics GUI (graphical user
interface) for R, based on the tcltk package.

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2020-01-16: cran-progress-r32-1.2.2-1 (Statnet project common scripts and utilities)

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2020-01-16: cran-resemble-r32-1.2.2-3 (Similarity/dissimilarity and MBL analysis)
This package implements functions for spectral similarity/dissimilarity
analysis and memory-based learning (MBL) for non-linear modelling in
complex spectral datasets. MBL is also known as local modelling in the
chemometrics literature.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-tsfa-r34-2014.10-1-1 (Time Series Factor Analysis)
Extraction of Factors from Multivariate Time Series.
See ?00tsfa-Intro for more details.

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2020-01-16: cran-rmpi-r33-0.6-9-1 (R Interface Wrapper to MPI)
Rmpi provides an interface (wrapper) to MPI APIs. It also provides
an interactive R slave environment.

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2020-01-16: cran-xopen-r31-1.0.0-1 (Open System Files, 'URLs', Anything)
Cross platform solution to open files, directories or 'URLs' with their
associated programs.

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2020-01-16: cran-profilemodel-r34-0.6.0-1 (Inference functions profiling tools)
profileModel provides tools that can be used to calculate, evaluate, plot
and use for inference the profiles of *arbitrary* inference functions for
for *arbitrary* 'glm'-like fitted models with linear predictors.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-truncnorm-r34-1.0-8-1 (Truncated Normal Distribution)
Density, probability, quantile and random number generation functions
for the truncated normal distribution.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-simpleboot-r35-1.1-7-1 (GNU R Tools for simple bootstrap)
Simple bootstrap routines

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2020-01-16: cran-rcppgsl-r32-0.3.4-1 (Rcpp Integration for 'GNU GSL')
'Rcpp' integration for 'GNU GSL' vectors and matrices The 'GNU
Scientific Library' (or 'GSL') is a collection of numerical routines for
scientific computing. It is particularly useful for C and C++ programs
as it provides a standard C interface to a wide range of mathematical
routines. There are over 1000 functions in total with an extensive test
suite. The 'RcppGSL' package provides an easy-to-use interface between
'GSL' data structures and R using concepts from 'Rcpp' which is itself a
package that eases the interfaces between R and C++. This package also
serves as a prime example of how to build a package that uses 'Rcpp' to
connect to another third-party library. The 'autoconf' script, 'inline'
plugin and example package can all be used as a stanza to write a
similar package against another library.

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2020-01-16: cran-spls-r35-2.2-3-1 (Sparse Partial Least Squares Regression)
This package provides functions for fitting a Sparse Partial
Least Squares Regression and Classification

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2020-01-16: cran-viridis-r32-0.5.1-2 (Default Color Maps from 'matplotlib')
Port of the new 'matplotlib' color maps ('viridis' - the default -,
'magma', plasma' and 'inferno') to 'R'. 'matplotlib'
http://matplotlib.org/  is a popular plotting library for 'python'.
These color maps are designed in such a way that they will analytically be
perfectly perceptually-uniform, both in regular form and also when
converted to black-and-white. They are also designed to be perceived by
readers with the most common form of color blindness. This is the 'lite'
version of the more complete 'viridis' package that can be found at
<https://cran.r-project.org/package=viridis>.

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2020-01-16: cran-robustrankaggreg-r34-1.1-2 (Methods for robust rank aggregation)
Methods for aggregating ranked lists, especially lists of genes. It 
implements the Robust Rank Aggregation (Kolde et. al in preparation) 
and some other simple algorithms for the task. RRA method uses a 
probabilistic model for aggregation that is robust to noise and also 
facilitates the calculation of significance probabilities for all the 
elements in the final ranking.

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2020-01-16: cran-r2stats-r36-0.68-39-1 (GTK GUI for fitting and comparing GLM and GLM)
R2STATS is a gWidgetsRGtk2 GUI for fitting and comparing GLM or GLMM (based
on Douglas Bates' lme4 package) in R. It is designed to make comparisons
between numerous models easy, both numerically and graphically, which may
be useful for teaching. Relevant plots are automatically produced for each
model family. R2STATS is *not* a generic graphical interface for R, but a
GUI for statistical modelling in a model comparison approach.

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2020-01-16: cran-psy-r32-1.1-1 (Various procedures used in psychometry)
Kappa, ICC, Cronbach alpha, screeplot, mtmm

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2020-01-16: cran-sessioninfo-r36-1.1.1-1 (R Session Information)
Query and print information about the current R session. It is similar
to 'utils::sessionInfo()', but includes more information about packages,
and where they were installed from.

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2020-01-16: cran-sn-r31-1.5-4-1 (Skew-normal and skew-t distributions)
Define and manipulate probability distributions of the skew-normal
family and some related ones (notably the skew-t family) and provide
related statistical methods for data fitting and diagnostics, in the
univariate and in the multivariate case.

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2020-01-16: cran-scarabee-r32-1.1-3-2 (R port of the Scarabee toolkit)
scaRabee is a port of the Scarabee toolkit originally written as a Matlab-based
application. It provides a framework for simulation and optimization of
pharmacokinetic-pharmacodynamic models at the individual and population level.
It is built on top of the neldermead package, which provides the direct search
algorithm proposed by Nelder and Mead for model optimization.

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2020-01-16: cran-r.matlab-r32-3.6.2-1 (Read and write of MAT files)
This package provides methods readMat() and writeMat() to read
and write MAT files. It also makes it possible to communicate
(evaluate code, send and retrieve objects etc.) with MATLAB v6
or higher running locally or on a remote host.

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2020-01-16: cran-subplex-r33-1.5-4-2 (Subplex optimization algorithm)
The subplex algorithm for unconstrained optimization, developed by Tom Rowan.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-sp-r35-1.3-1-1 (GNU R classes and methods for spatial data)
GNU R classes and methods for spatial data

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-stabledist-r34-0.7-1-1 (Stable Distribution Functions)
Density, Probability and Quantile functions, and random number
generation for (skew) stable distributions, using the
parametrizations of Nolan.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-quadprog-r36-1.5-7-2 (Functionss for Quadratic Programming Problems)
This package contains routines and documentation for solving
quadratic programming problems.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-pryr-r36-0.1.4-1 (Tools for Computing on the Language)
Useful tools to pry back the covers of R and understand the language at
a deeper level.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-readjdx-r31-0.3.250-1 (Import Data in the JCAMP-DX Format)
Import data written in the JCAMP-DX format. This is an
instrument-independent format used in the field of spectroscopy.
Examples include IR, NMR, and Raman spectroscopy. See the vignette for
background and supported formats. The official JCAMP-DX site is
http://www.jcamp-dx.org/.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-pmmltransformations-r33-1.3.3-1 (Transforms input data from a PMML perspective)
Allows for data to be transformed before using it to construct models.
Builds structures to allow functions in the PMML package to output
transformation details in addition to the model in the resulting PMML file.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sda-r31-1.3.7-1 (Shrinkage Discriminant Analysis)
This package provides an efficient framework for high-dimensional
linear and diagonal discriminant analysis with variable selection.
The classifier is trained using James-Stein-type shrinkage estimators
and predictor variables are ranked using correlation-adjusted t-scores
(CAT scores). Variable selection error is controlled using false
non-discovery rates or higher criticism.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tseries-r33-0.10-47-2 (Time series analysis and finance)
Package for time series analysis and computational finance

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-prim-r31-1.0.16-1 (Patient Rule Induction Method)
PRIM for bump hunting in high-dimensional data

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-promises-r31-1.1.0-1 (Promise-Based Asynchronous Programming)
Provides fundamental abstractions for doing asynchronous programming in
R using promises. Asynchronous programming is useful for allowing a
single R process to orchestrate multiple tasks in the background while
also attending to something else. Semantics are similar to 'JavaScript'
promises, but with a syntax that is idiomatic R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-xlsx-r32-0.6.1-1 (Excel 2007 and Excel 97/2000/XP/2003 support)
Provide R functions to read/write/format Excel 2007 and
Excel 97/2000/XP/2003 file formats.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-readjdx-r34-0.3.250-1 (Import Data in the JCAMP-DX Format)
Import data written in the JCAMP-DX format. This is an
instrument-independent format used in the field of spectroscopy.
Examples include IR, NMR, and Raman spectroscopy. See the vignette for
background and supported formats. The official JCAMP-DX site is
http://www.jcamp-dx.org/.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tframe-r35-2015.12-1.1-1 (Time Frame coding kernel)
The tframe package provides a kernel of functions for programming
time series methods in a way that is relatively independently of
the representation of time. It also provides plotting, time
windowing, and some other utility functions which are specifically
intended for time series. See the Guide distributed as a vignette,
or ?tframe.Intro for more details. (User utilities other than the
programming kernel have been moved into package tfplot.)

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2020-01-16: cran-r6-r33-2.4.0-1 (Classes with reference semantics)
The R6 package allows the creation of classes with reference semantics,
similar to R's built-in reference classes. Compared to reference classes,
R6 classes are simpler and lighter-weight, and they are not built on S4
classes so they do not require the methods package. These classes allow
public and private members, and they support inheritance, even when the
classes are defined in different packages.

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2020-01-16: cran-rsclient-r35-0.7-3-2 (RSclient: Client for Rserve)
Client for Rserve, allowing to connect to Rserve instances
and issue commands.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rex-r35-1.1.2-1 (Friendly Regular Expressions)
A friendly interface for the construction of regular expressions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-whisker-r33-0.4-1 ({{mustache}} for R, logicless templating)
logicless templating, reuse templates in many programming
languages including R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-praise-r32-1.0.0-1 (Praise Users)
Build friendly R packages that praise their users if they have 
done something good, or they just need it to feel better.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-promises-r34-1.1.0-1 (Promise-Based Asynchronous Programming)
Provides fundamental abstractions for doing asynchronous programming in
R using promises. Asynchronous programming is useful for allowing a
single R process to orchestrate multiple tasks in the background while
also attending to something else. Semantics are similar to 'JavaScript'
promises, but with a syntax that is idiomatic R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rodbc-r31-1.3-16-1 (ODBC Database Access for R)
An ODBC database interface

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcpparmadillo-r34-0.9.800.1.0-2 (Rcpp integration for Armadillo)
R and Armadillo integration using Rcpp Armadillo is a templated
C++ linear algebra library (by Conrad Sanderson) that aims towards
a good balance between speed and ease of use. Integer, floating
point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions
are provided through optional integration with LAPACK and ATLAS
libraries. A delayed evaluation approach is employed (during compile
time) to combine several operations into one, and to reduce (or
eliminate) the need for temporaries. This is accomplished through
recursive templates and template meta-programming. This library is
useful if C++ has been decided as the language of choice (due
to speed and/or integration capabilities), rather than another
language. The RcppArmadillo package includes the header files
from the templated Armadillo library. Thus users do not need to
install Armadillo itself in order to use RcppArmadillo. This
Armadillo integration provides a nice illustration of the
capabilities of the Rcpp package for seamless R and C++
integration. Armadillo is licensed under the MPL 2.0, while
RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is
licensed under the GNU GPL version 2 or later, as is the
rest of Rcpp.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-polynomf-r32-2.0-2-1 (Polynomials in R)
Implements univariate polynomial operations in R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-timeseries-r34-3042.102-1 (Rmetrics - Financial Time Series Objects)
Environment for teaching "Financial Engineering and Computational Finance"

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcolorbrewer-r35-1.1-2-1 (GNU R Tools for variable-dependent palettes)
The packages provides palettes for drawing nice maps shaded 
according to a variable.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-qtl-r36-1.44-9-1 (Quantitative trait loci)
Analysis of experimental crosses to identify genes 
(called quantitative trait loci, QTLs) contributing 
to variation in quantitative traits.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-pmmltransformations-r34-1.3.3-1 (Transforms input data from a PMML perspective)
Allows for data to be transformed before using it to construct models.
Builds structures to allow functions in the PMML package to output
transformation details in addition to the model in the resulting PMML file.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rgtk2extras-r34-0.6.1-1 (Data frame editor and dialog RGtk2 wrapper)

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-smatr-r34-3.4-8-1 (Major Axis Estimation and Testing Routines)
s package provides methods of fitting bivariate lines in allometry using
the major axis (MA) or standardised major axis (SMA), and for making
inferences about such lines. The available methods of inference include
confidence intervals and one-sample tests for slope and elevation, testing
for a common slope or elevation amongst several allometric lines,
constructing a confidence interval for a common slope or elevation, and
testing for no shift along a common axis, amongst several samples.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-pryr-r33-0.1.4-1 (Tools for Computing on the Language)
Useful tools to pry back the covers of R and understand the language at
a deeper level.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-shiny-r33-1.3.2-1 (Web Application Framework for R)
Makes it incredibly easy to build interactive web applications with R. 
Automatic "reactive" binding between inputs and outputs and extensive 
pre-built widgets make it possible to build beautiful, responsive, 
and powerful applications with minimal effort.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-stringr-r34-1.4.0-1 (GNU R Tools for string function wrappers)
stringr is a set of simple wrappers that make R's string functions more 
consistent, simpler and easier to use. It does this by ensuring that: 
function and argument names (and positions) are consistent, all functions 
deal with NA's and zero length character appropriately, and the output 
data structures from each function matches the input data structures of 
other functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-raster-r36-3.0-7-1 (Geographic data analysis and modeling)
Reading, writing, manipulating, analyzing and modeling of gridded spatial
data. The package implements basic and high-level functions. Processing of
very large files is supported.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tsp-r33-1.1-7-1 (Traveling Salesperson Problem)
Basic infrastructure and some algorithms for the traveling salesperson
problem (also traveling salesman problem; TSP). The package provides
some simple algorithms and an interface to Concorde, the currently
fastest TSP solver. Concorde itself is not included in the package
and has to be obtained separately.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-wilcoxcv-r34-1.0-2-1 (Wilcoxon-based variable selection in cv)
This package provides functions to perform fast variable selection
based on the Wilcoxon rank sum test in the cross-validation or
Monte-Carlo cross-validation settings, for use in microarray-based
binary classification.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sda-r36-1.3.7-1 (Shrinkage Discriminant Analysis)
This package provides an efficient framework for high-dimensional
linear and diagonal discriminant analysis with variable selection.
The classifier is trained using James-Stein-type shrinkage estimators
and predictor variables are ranked using correlation-adjusted t-scores
(CAT scores). Variable selection error is controlled using false
non-discovery rates or higher criticism.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-v8-r33-2.3-2 (Embedded JavaScript Engine for R)
An R interface to Google's open source JavaScript engine.
V8 is written in C++ and implements ECMAScript as specified in ECMA-262,
5th edition. In addition, this package implements typed arrays as specified
in ECMA 6 used for high-performance computing and libraries compiled
with 'emscripten'.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rcmdr-r35-2.6-0-1 (R Commander)
A platform-independent basic-statistics GUI (graphical user
interface) for R, based on the tcltk package.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-stringr-r31-1.4.0-1 (GNU R Tools for string function wrappers)
stringr is a set of simple wrappers that make R's string functions more 
consistent, simpler and easier to use. It does this by ensuring that: 
function and argument names (and positions) are consistent, all functions 
deal with NA's and zero length character appropriately, and the output 
data structures from each function matches the input data structures of 
other functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-statmod-r36-1.4.32-2 (Statistical Modeling)
Various statistical modeling functions including growth curve comparisons,
limiting dilution analysis, mixed linear models, heteroscedastic regression,
Tweedie family generalized linear models, the inverse-Gaussian distribution
and Gauss quadrature.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-randomfieldsutils-r33-0.5.3-2 (Utilities for Random Fields)
Various utilities are provided that might be used in 
spatial statistics and elsewhere. It delivers a method 
for solving linear equations that checks the sparsity 
of the matrix before any algorithm is used. Furthermore, 
it includes the Struve functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-spgrass6-r35-0.8-9-1 (Interface between GRASS 6+ and R)
Interface between GRASS 6+ and R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-processx-r32-3.4.1-1 (Execute and Control System Processes)
Tools to run system processes in the background. It can check if a
background process is running; wait on a background process to finish;
get the exit status of finished processes; kill background processes. It
can read the standard output and error of the processes, using
non-blocking connections. 'processx' can poll a process for standard
output or error, with a timeout. It can also poll several processes at
once.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-utf8-r32-1.1.4-1 (Unicode Text Processing)
Process and print 'UTF-8' encoded international text (Unicode). Input,
validate, normalize, encode, format, and display.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-qtl-r31-1.44-9-1 (Quantitative trait loci)
Analysis of experimental crosses to identify genes 
(called quantitative trait loci, QTLs) contributing 
to variation in quantitative traits.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-squarem-r33-2017.10-1-1 (Squared Extrapolation Methods For Algorithms)
Algorithms for accelerating the convergence of slow, monotone sequences
from smooth, contraction mapping such as the EM algorithm. It can be
used to accelerate any smooth, linearly convergent acceleration scheme.
A tutorial style introduction to this package is available in a vignette
on the CRAN download page or, when the package is loaded in an R
session, with vignette("SQUAREM").

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tester-r35-0.1.7-1 (Tests and checks characteristics of R objects)
tester allows you to test characteristics of common R objects.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tsa-r32-1.2-1 (Time Series Analysis)
Contains R functions and datasets detailed in the book "Time
Series Analysis with Applications in R (second edition)" by
Jonathan Cryer and Kung-Sik Chan

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-wilcoxcv-r31-1.0-2-1 (Wilcoxon-based variable selection in cv)
This package provides functions to perform fast variable selection
based on the Wilcoxon rank sum test in the cross-validation or
Monte-Carlo cross-validation settings, for use in microarray-based
binary classification.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-webshot-r36-0.5.1-1 (Shiny UI Widgets for Small Screens)
Provides UI widget and layout functions for writing Shiny apps that work
well on small screens.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rsvgdevice-r32-0.6.4.4-2 (R SVG graphics device)
A graphics device for R that uses the w3.org xml standard
for Scalable Vector Graphics.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-ranger-r32-0.11.2-1 (Manage Life Cycle of Package)
This package can be used to solve Linear Programming / Linear 
Optimization problems by using the simplex algorithm.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sessioninfo-r32-1.1.1-1 (R Session Information)
Query and print information about the current R session. It is similar
to 'utils::sessionInfo()', but includes more information about packages,
and where they were installed from.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-setrng-r34-2013.9-1-1 (Random Number Generator and Seed)
SetRNG provides utilities to help set and record the setting of
the seed and the uniform and normal generators used when a random
experiment is run. The utilities can be used in other functions
that do random experiments to simplify recording and/or setting
all the necessary information for reproducibility.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-reshapegui-r34-0.1.0-1 (GUI for the reshape2 and plyr packages)
A tool for learning how to use the functions, melt, acast/dcast, and ddply.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcpparmadillo-r33-0.9.800.1.0-2 (Rcpp integration for Armadillo)
R and Armadillo integration using Rcpp Armadillo is a templated
C++ linear algebra library (by Conrad Sanderson) that aims towards
a good balance between speed and ease of use. Integer, floating
point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions
are provided through optional integration with LAPACK and ATLAS
libraries. A delayed evaluation approach is employed (during compile
time) to combine several operations into one, and to reduce (or
eliminate) the need for temporaries. This is accomplished through
recursive templates and template meta-programming. This library is
useful if C++ has been decided as the language of choice (due
to speed and/or integration capabilities), rather than another
language. The RcppArmadillo package includes the header files
from the templated Armadillo library. Thus users do not need to
install Armadillo itself in order to use RcppArmadillo. This
Armadillo integration provides a nice illustration of the
capabilities of the Rcpp package for seamless R and C++
integration. Armadillo is licensed under the MPL 2.0, while
RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is
licensed under the GNU GPL version 2 or later, as is the
rest of Rcpp.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rlang-r34-0.4.0-2 (Functions for Base Types and Core R)
A toolbox for working with base types, core R features like 
the condition system, and core `Tidyverse' features like tidy evaluation.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-ranger-r35-0.11.2-1 (Manage Life Cycle of Package)
This package can be used to solve Linear Programming / Linear 
Optimization problems by using the simplex algorithm.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-statip-r33-0.2.0-1 (Functions for Distributions and Regression)
A collection of miscellaneous statistical functions for probability
distributions: dbern(), pbern(), qbern(), rbern() for the Bernoulli
distribution, and distr2name(), name2distr() for distribution names;
probability density estimation: densityfun(); most frequent value
estimation: mfv(), mfv1(); calculation of the Hellinger distance:
hellinger(); use of classical kernels: kernelfun(), kernel_properties();
univariate piecewise-constant regression: picor().

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-subselect-r35-0.14-2 (Selecting variable subsets)
A collection of functions which (i) assess the quality of variable
subsets as surrogates for a full data set, in either an exploratory
data analysis or in the context of a multivariate linear model, and
(ii) search for subsets which are optimal under various criteria.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-vegan-r31-2.4-3-1 (Community Ecology Package)
Ordination methods, diversity analysis and other functions
for community and vegetation ecologists.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rsqlite-r31-2.1.1-2 (SQLite interface for R)
Database Interface R driver for SQLite. This package embeds the SQLite
database engine in R and provides an interface compliant with the DBI
package. The source for the SQLite engine (version 3.7.17) is included.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    New upstream Bioconductor versions (bioc 3.10)
2020-01-16: cran-sde-r33-2.0.15-1 (Stochastic Differential Equations)
Companion package to the book Simulation and Inference for Stochastic
Differential Equations With R Examples, ISBN 978-0-387-75838-1, Springer, NY.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rsqlite-r34-2.1.1-2 (SQLite interface for R)
Database Interface R driver for SQLite. This package embeds the SQLite
database engine in R and provides an interface compliant with the DBI
package. The source for the SQLite engine (version 3.7.17) is included.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    New upstream Bioconductor versions (bioc 3.10)
2020-01-16: cran-vimgui-r36-0.10.0-1 (Visualization & Imputation of Missing Values)
This package introduces new tools for the visualization of missing and/or
imputed values, which can be used for exploring the data and the structure
of the missing and/or imputed values. Depending on this structure of the
missing values, the corresponding methods may help to identify the mechanism
generating the missings and allows to explore the data including missing
values. In addition, the quality of imputation can be visually explored
using various univariate, bivariate, multiple and multivariate plot methods.
A graphical user interface allows an easy handling of the implemented plot
methods.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-polynom-r33-1.4-0-1 (Univariate polynomial manipulations in R)
A collection of functions to implement a class for univariate
polynomial manipulations.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-psm-r33-0.8-12-2 (Non-Linear Mixed-Effects modelling)
This package provides functions for estimation of linear and non-linear
mixed-effects models using stochastic differential equations. Moreover
it provides functions for finding smoothed estimates of model states
and for simulation. The package allows for any multivariate non-linear
time-variant model to be specified, and it also handles multidimensional
input, co-variates, missing observations and specification of dosage regimen.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-roxygen2-r35-6.1.1-1 (In-source documentation for R)
A Doxygen-like in-source documentation system for Rd, collation,
and NAMESPACE.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tester-r32-0.1.7-1 (Tests and checks characteristics of R objects)
tester allows you to test characteristics of common R objects.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-pmmltransformations-r36-1.3.3-1 (Transforms input data from a PMML perspective)
Allows for data to be transformed before using it to construct models.
Builds structures to allow functions in the PMML package to output
transformation details in addition to the model in the resulting PMML file.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sys-r31-3.3-1 (Tools for Running System Commands in R)
Drop-in replacements for the base system2() function with fine control
and consistent behavior across platforms. Supports clean interruption,
timeout, background tasks, and streaming STDIN / STDOUT / STDERR over
binary or text connections. Arguments on Windows automatically get
encoded and quoted to work on different locales.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-xtable-r31-1.8-4-1 (Export tables to LaTeX or HTML)
Coerce data to LaTeX and HTML tables

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-yaletoolkit-r36-4.2.2-1 (Data exploration tools from Yale University)
This collection of data exploration tools was developed at Yale University
for the graphical exploration of complex multivariate data; barcode and
gpairs now have their own packages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rglwidget-r32-0.2.1-1 (Rgl in htmlwidgets Framework)
Provides an 'htmlwidgets' framework for the 'rgl' package.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-viridislite-r36-0.3.0-1 (Default Color Maps from 'matplotlib')
Port of the new 'matplotlib' color maps ('viridis' - the default -, 
'magma', plasma' and 'inferno') to 'R'. 'matplotlib' 
http://matplotlib.org/  is a popular plotting library for 'python'. 
These color maps are designed in such a way that they will analytically be 
perfectly perceptually-uniform, both in regular form and also when 
converted to black-and-white. They are also designed to be perceived by 
readers with the most common form of color blindness. This is the 'lite' 
version of the more complete 'viridis' package that can be found at 
<https://cran.r-project.org/package=viridis>.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-svunit-r33-0.7-12-1 (SciViews GUI API - Unit testing)
A complete unit test system and functions to implement its GUI part

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-subselect-r31-0.14-2 (Selecting variable subsets)
A collection of functions which (i) assess the quality of variable
subsets as surrogates for a full data set, in either an exploratory
data analysis or in the context of a multivariate linear model, and
(ii) search for subsets which are optimal under various criteria.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rwekajars-r32-3.9.3-1-1 (R/Weka interface jars)
External jars required for package RWeka.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rstudioapi-r32-0.10-1 (Safely access the RStudio API)
This package provides functions to make it easy to access the RStudio
API when available, and provide informative error messages when not.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-pscl-r33-1.5.2-1 (Political Science Computational Laboratory)
Bayesian analysis of item-response theory (IRT) models, roll call analysis;
computing highest density regions; maximum likelihood estimation of zero-
inflated and hurdle models for count data; goodness-of-fit measures for
GLMs; data sets used in writing and teaching at the Political Science
Computational Laboratory; seats-votes curves.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rpart-r32-4.1-15-1 (GNU R Tools for recursive partitioning)
Recursive partitioning and regression trees

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-strucchange-r36-1.5-1-1 (Structural Changes)
Testing, monitoring and dating structural changes in (linear) regression
models. strucchange features tests/methods from the generalized fluctuation
test framework as well as from the F test (Chow test) framework.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-simpleboot-r32-1.1-7-1 (GNU R Tools for simple bootstrap)
Simple bootstrap routines

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-reactran-r35-1.4.3.1-2 (Reactive transport modelling in 1D, 2D and 3D)
Routines for developing models that describe reaction and
advective-diffusive transport in one, two or three dimensions.
Includes transport routines in porous media, in estuaries, and
in bodies with variable shape.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rsnns-r36-0.4-12-1 (Stuttgart Neural Network Simulator in R)
The Stuttgart Neural Network Simulator (SNNS) is a library containing many
standard implementations of neural networks. This package wraps the SNNS
functionality to make it available from within R. Using the RSNNS low-level
interface, all of the algorithmic functionality and flexibility of SNNS can
be accessed. Furthermore, the package contains a convenient high-level
interface, so that the most common neural network topologies and learning
algorithms integrate seamlessly into R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-quantmod-r31-0.4-10-1 (Quantitative Financial Modelling Framework)
Specify, build, trade, and analyse quantitative financial trading strategies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r2winbugs-r36-2.1-21-1 (Running WinBUGS and OpenBUGS from R / S-PLUS)
Using this package, it is possible to call a BUGS model, summarize
inferences and convergence in a table and graph, and save the
simulations in arrays for easy access in R / S-PLUS. In S-PLUS,
the openbugs functionality and the windows emulation functionality
is not yet available.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-xml-r33-3.98-1.20-1 (Tools for parsing and generating XML within R)
Tools for parsing and generating XML within R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tripack-r33-1.3-8-2 (Triangulation of irregularly spaced data)
A constrained two-dimensional Delaunay triangulation package

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-sp-r34-1.3-1-1 (GNU R classes and methods for spatial data)
GNU R classes and methods for spatial data

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-yaml-r31-2.2.0-1 (Libyaml YAML 1.1 parser and emitter for R)
This package implements the libyaml YAML 1.1 parser and emitter 
(http://pyyaml.org/wiki/LibYAML) for R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r2winbugs-r34-2.1-21-1 (Running WinBUGS and OpenBUGS from R / S-PLUS)
Using this package, it is possible to call a BUGS model, summarize
inferences and convergence in a table and graph, and save the
simulations in arrays for easy access in R / S-PLUS. In S-PLUS,
the openbugs functionality and the windows emulation functionality
is not yet available.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rex-r34-1.1.2-1 (Friendly Regular Expressions)
A friendly interface for the construction of regular expressions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-trust-r32-0.1-7-1 (Trust Region Optimization)
local optimization using two derivatives and trust regions

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-turner-r33-0.1.7-1 (Turn lists of vectors into indexed structures)
Package designed for working with vectors and lists of vectors,
mainly for turning them into other indexed data structures.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tframe-r32-2015.12-1.1-1 (Time Frame coding kernel)
The tframe package provides a kernel of functions for programming
time series methods in a way that is relatively independently of
the representation of time. It also provides plotting, time
windowing, and some other utility functions which are specifically
intended for time series. See the Guide distributed as a vignette,
or ?tframe.Intro for more details. (User utilities other than the
programming kernel have been moved into package tfplot.)

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rggobi-r34-2.1.22-1 (Interface between R and GGobi)
The rggobi package provides a command-line interface to GGobi, an
interactive and dynamic graphics package. Rggobi complements GGobi's
graphical user interface, providing a way to fluidly transition
between analysis and exploration, as well as automating common tasks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-praise-r35-1.0.0-1 (Praise Users)
Build friendly R packages that praise their users if they have 
done something good, or they just need it to feel better.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-viridislite-r33-0.3.0-1 (Default Color Maps from 'matplotlib')
Port of the new 'matplotlib' color maps ('viridis' - the default -, 
'magma', plasma' and 'inferno') to 'R'. 'matplotlib' 
http://matplotlib.org/  is a popular plotting library for 'python'. 
These color maps are designed in such a way that they will analytically be 
perfectly perceptually-uniform, both in regular form and also when 
converted to black-and-white. They are also designed to be perceived by 
readers with the most common form of color blindness. This is the 'lite' 
version of the more complete 'viridis' package that can be found at 
<https://cran.r-project.org/package=viridis>.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-quantmod-r34-0.4-15-2 (Quantitative Financial Modelling Framework)
Specify, build, trade, and analyse quantitative financial trading strategies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-sys-r36-3.3-1 (Tools for Running System Commands in R)
Drop-in replacements for the base system2() function with fine control
and consistent behavior across platforms. Supports clean interruption,
timeout, background tasks, and streaming STDIN / STDOUT / STDERR over
binary or text connections. Arguments on Windows automatically get
encoded and quoted to work on different locales.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-yaletoolkit-r33-4.2.2-1 (Data exploration tools from Yale University)
This collection of data exploration tools was developed at Yale University
for the graphical exploration of complex multivariate data; barcode and
gpairs now have their own packages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rpubchem-r36-1.5.10-1 (Interface to the PubChem Collection)
Access PubChem data (compounds, substance, assays). Structural information
is provided in the form of SMILES strings. This package only provides
access to a subset of the precalculated data stored by PubChem. Bio-assay
data can be accessed to obtain descriptions as well as the actual data.
It is also possible to search for assay ID's by keyword. Currently the main
limitation is that only 1000 molecules can be downloaded at a time from the
PubChem servers

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-pscl-r36-1.5.2-1 (Political Science Computational Laboratory)
Bayesian analysis of item-response theory (IRT) models, roll call analysis;
computing highest density regions; maximum likelihood estimation of zero-
inflated and hurdle models for count data; goodness-of-fit measures for
GLMs; data sets used in writing and teaching at the Political Science
Computational Laboratory; seats-votes curves.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-strucchange-r33-1.5-1-1 (Structural Changes)
Testing, monitoring and dating structural changes in (linear) regression
models. strucchange features tests/methods from the generalized fluctuation
test framework as well as from the F test (Chow test) framework.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-stable-r31-1.1.4-1 (Functions and Models for Stable Distributions)
Density, distribution, quantile and hazard functions of a stable
variate; generalized regression models for the parameters of a stable
distribution. See the README for how to make equivalent calls to those
of 'stabledist'. See github for Journal article.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tensor-r34-1.5-1 (Tensor product of arrays)
The tensor product of two arrays is notionally an outer product
of the arrays collapsed in specific extents by summing along
the appropriate diagonals.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-superpc-r31-1.09-1 (Supervised principal components)
Supervised principal components for regression and survival analsysis.
Especially useful for high-dimnesional data, including microarray data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcmdrplugin.survival-r35-1.2-0-1 (R Commander Plug-in for the survival Package)
This package provides an R Commander plug-in for the survival package,
with dialogs for Cox models, parametric survival regression models,
estimation of survival curves, and testing for differences in survival
curves, along with data-management facilities and a variety of tests,
and graphs.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-ps-r35-1.3.0-1 (List, Query, Manipulate System Processes)
List, query and manipulate all system processes, on 'Windows', 'Linux'
and 'macOS'.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcurl-r34-1.95-4.12-1 (Network client (HTTP/FTP/...) R interface)
The package allows one to compose general HTTP requests and provides
convenient functions to fetch URIs, get & post forms, etc. and process
the results returned by the Web server. This provides a great deal of
control over the HTTP/FTP/... connection and the form of the request 
while providing a higher-level interface than is available just using
R socket connections. Additionally, the underlying implementation is
robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads),
SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects,
authentication, etc.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-questionr-r33-0.7.0-1 (Functions to Make Surveys Processing Easier)
Set of functions to make the processing and analysis of surveys easier :
interactive shiny apps and addins for data recoding, contingency tables,
dataset metadata handling, and several convenience functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcmdrplugin.doby-r32-0.1-3-1 (Rcmdr doBy Plug-In)
This package provides an Rcmdr "plug-in" for the core doBy functions
in the doBy package, which helps with computing groupwise summary statistics.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-randomforestsrc-r33-2.8.0-1 (Random Forests for Survival)
A unified treatment of Breiman's random forests for survival, regression
and classification problems based on Ishwaran and Kogalur's random survival
forests (RSF) package. The package runs in both serial and parallel
(OpenMP) modes.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-robustbase-r32-0.93-5-2 (GNU R Tools for robust methods)
"Essential" Robust Statistics.
The goal is to provide tools allowing to analyze data with robust methods.
This includes regression methodology including model selections and
multivariate statistics where we strive to cover the book
"Robust Statistics, Theory and Methods" by Maronna, Martin and Yohai;
Wiley 2006.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-superpc-r34-1.09-1 (Supervised principal components)
Supervised principal components for regression and survival analsysis.
Especially useful for high-dimnesional data, including microarray data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rweka-r36-0.4-40-1 (R/Weka interface)
An R interface to Weka (Version 3.7.11). Weka is a collection of machine
learning algorithms for data mining tasks written in Java, containing
tools for data pre-processing, classification, regression, clustering,
association rules, and visualization. Package RWeka contains the interface
code, the Weka jar is in a separate package RWekajars. For more information
on Weka see http://www.cs.waikato.ac.nz/~ml/weka/.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-pmmltransformations-r35-1.3.3-1 (Transforms input data from a PMML perspective)
Allows for data to be transformed before using it to construct models.
Builds structures to allow functions in the PMML package to output
transformation details in addition to the model in the resulting PMML file.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-slam-r32-0.1-37-1 (Sparse Lightweight Arrays and Matrices)
Data structures and algorithms for sparse arrays and matrices,
based on index arrays and simple triplet representations, respectively.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rgtk2extras-r35-0.6.1-1 (Data frame editor and dialog RGtk2 wrapper)

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2020-01-16: cran-rastervis-r33-0.46-1 (Visualization methods for raster)
The raster package defines classes and methods for spatial raster
data access and manipulation. The rasterVis package complements
raster providing a set of methods for enhanced visualization and
interaction.

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2020-01-16: cran-sca-r33-0.9-0-1 (Simple Component Analysis)
Simple Component Analysis (SCA) often provides much more interpretable
components than Principal Components (PCA) while still representing
much of the variability in the data.

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2020-01-16: cran-r.oo-r33-1.22.0-1 (R object-oriented programming)
Methods and classes for object-oriented programming in R
with or without references.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-th.data-r31-1.0-10-1 (TH's Data Archive)
Contains data sets used in other packages Torsten Hothorn maintains.

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2020-01-16: cran-ucminf-r33-1.1-4-2 (Unconstrained non-linear optimization)
An algorithm for general-purpose unconstrained non-linear optimization.
The algorithm is of quasi-Newton type with BFGS updating of the inverse
Hessian and soft line search with a trust region type monitoring of the
input to the line search algorithm. The interface of 'ucminf' is designed
for easy interchange with 'optim'.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rmpfr-r35-0.7-2-1 (Multiple Precision Floating-Point Reliable)
Rmpfr provides (S4 classes and methods for) arithmetic including transcendental
("special") functions for arbitrary precision floating point numbers. To this
end, it interfaces to the LGPL'ed MPFR (Multiple Precision Floating-Point
Reliable) Library which itself is based on the GMP (GNU Multiple Precision)
Library.

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2020-01-16: cran-simcomp-r33-3.3-1 (Simultaneous Comparisons for Mult. Endpoints)
Simultaneous tests and confidence intervals for one-way experimental
designs with one or many normally distributed, primary response
variables (endpoints). The procedure of Hasler and Hothorn (2011,2012)
is applied for differences or ratios of means. Various contrasts can
be chosen, unbalanced sample sizes are allowed as well as heterogeneous
variances or covariance matrices.

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2020-01-16: cran-vgam-r33-1.0-3-1 (Vector Generalized Linear and Additive Models)
Vector generalized linear and additive models, and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Reduced-Rank VGAMs). This
package fits many models and distribution by maximum likelihood
estimation (MLE) or penalized MLE. Also fits constrained ordination
models in ecology.

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2020-01-16: cran-stepplr-r36-0.93-2 (L2 penalized logistic regression)
L2 penalized logistic regression for both continuous and discrete
predictors, with forward stagewise/forward stepwise variable
selection procedure.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-raster-r31-3.0-7-1 (Geographic data analysis and modeling)
Reading, writing, manipulating, analyzing and modeling of gridded spatial
data. The package implements basic and high-level functions. Processing of
very large files is supported.

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2020-01-16: cran-sets-r36-1.0-18-1 (Generalized and Customizable Sets)
Data structures and basic operations for ordinary sets, generalizations
such as fuzzy sets, multisets, and fuzzy multisets, customizable sets,
and intervals.

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2020-01-16: cran-rwave-r33-2.4-8-1 (Time-Frequency analysis of 1-D signals)
Rwave is a library of R functions which provide an environment for
the Time-Frequency analysis of 1-D signals (and especially for the
wavelet and Gabor transforms of noisy signals). It was originally
written for Splus by Rene Carmona, Bruno Torresani, and Wen L. 
wang, first at the University of California at Irvine and then
at Princeton University. Credit should also be given to Andrea
Wang whose functions on the dyadic wavelet transform are included.
Rwave is based on the book: "Practical Time-Frequency Analysis:
Gabor and Wavelet Transforms with an Implementation in S", by Rene
Carmona, Wen L. Hwang and Bruno Torresani, Academic Press, 1998.

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2020-01-16: cran-rcppprogress-r34-0.4.1-1 (Interruptible Progress Bar)
Allows to display a progress bar in the R console for long running
computations taking place in c++ code, and support for interrupting
those computations even in multithreaded code, typically using OpenMP.

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2020-01-16: cran-survival-r32-2.44-1.1-1 (GNU R Tools for survival analysis)
survival analysis: descriptive statistics, two-sample tests,
parametric accelerated failure models, Cox model.
Delayed entry (truncation) allowed for all models;
interval censoring for parametric models. Case-cohort designs.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-pracma-r33-2.2.5-1 (Practical Numerical Math Functions)
Functions from numerical analysis and linear algebra, numerical optimization,
differential equations, plus some special functions. Uses Matlab function names
where appropriate to simplify porting.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-th.data-r34-1.0-10-1 (TH's Data Archive)
Contains data sets used in other packages Torsten Hothorn maintains.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-shape-r33-1.4.4-1 (Plotting graphical shapes, colors)
Functions for plotting graphical shapes such as ellipses,
circles, cylinders, arrows, ...

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rodbc-r32-1.3-16-1 (ODBC Database Access for R)
An ODBC database interface

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-relimp-r34-1.0-5-1 (Relative Contribution of Effects)
Functions to facilitate inference on the relative importance
of predictors in a linear or generalized linear model, and
a couple of useful Tcl/Tk widgets.

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2020-01-16: cran-rbenchmark-r34-1.0.0-1 (Benchmarking routine for R)
rbenchmark is inspired by the Perl module Benchmark, and is intended
to facilitate benchmarking of arbitrary R code. The library consists
of just one function, benchmark, which is a simple wrapper around
system.time. Given a specification of the benchmarking process
(counts of replications, evaluation environment) and an arbitrary
number of expressions, benchmark evaluates each of the expressions
in the specified environment, replicating the evaluation as many
times as specified, and returning the results conveniently wrapped
into a data frame.

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2020-01-16: cran-rvest-r33-0.3.4-1 (Easily harvest web pages)
Wrappers around the 'xml2' and 'httr' packages to make it easy to
download, then manipulate, HTML and XML.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-xopen-r35-1.0.0-1 (Open System Files, 'URLs', Anything)
Cross platform solution to open files, directories or 'URLs' with their
associated programs.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-yaletoolkit-r31-4.2.2-1 (Data exploration tools from Yale University)
This collection of data exploration tools was developed at Yale University
for the graphical exploration of complex multivariate data; barcode and
gpairs now have their own packages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-viridislite-r31-0.3.0-1 (Default Color Maps from 'matplotlib')
Port of the new 'matplotlib' color maps ('viridis' - the default -, 
'magma', plasma' and 'inferno') to 'R'. 'matplotlib' 
http://matplotlib.org/  is a popular plotting library for 'python'. 
These color maps are designed in such a way that they will analytically be 
perfectly perceptually-uniform, both in regular form and also when 
converted to black-and-white. They are also designed to be perceived by 
readers with the most common form of color blindness. This is the 'lite' 
version of the more complete 'viridis' package that can be found at 
<https://cran.r-project.org/package=viridis>.

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2020-01-16: cran-strucchange-r31-1.5-1-1 (Structural Changes)
Testing, monitoring and dating structural changes in (linear) regression
models. strucchange features tests/methods from the generalized fluctuation
test framework as well as from the F test (Chow test) framework.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-r.oo-r36-1.22.0-1 (R object-oriented programming)
Methods and classes for object-oriented programming in R
with or without references.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-remotes-r33-2.1.0-1 (R Pkg Installation from Remote Repositories)
Run 'R CMD check' from 'R' programmatically, and capture the results of
the individual checks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-seriation-r33-1.2-8-2 (Infrastructure for seriation)
Infrastructure for seriation with an implementation of several
seriation/sequencing techniques to reorder matrices, dissimilarity
matrices, and dendrograms. Also contains some visualizations
techniques based on seriation.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-xfun-r32-0.10-1 (Misc. functions by Yihui Xie)
Miscellaneous functions commonly used in other packages maintained
by 'Yihui Xie'.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sem-r32-3.1-9-2 (Structural Equation Models)
This package contains functions for fitting general linear
structural equation models (with observed and unobserved
variables) using the RAM approach, and for fitting structural
equations in observed-variable models by two-stage least squares.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-scales-r35-1.0.0-1 (Scale functions for graphics)
Scales map data to aesthetics, and provide methods for automatically
determining breaks and labels for axes and legends.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-r.utils-r33-2.9.0-1 (Various programming utilities)
This package provides utility methods useful when programming
and developing R packages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sroc-r32-0.1-2-3 (Nonparametric Smooth ROC Curves)
This package contains a collection of functions to perform
 nonparametric estimation of receiver operating 
 characteristic (ROC) curves for continuous data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-vrmlgen-r36-1.4.9-1 (Generate 3D visualizations)
vrmlgen creates 3D scatter and bar plots, visualizations of 3D meshes,
parametric functions and height maps in web-formats like the Virtual
Reality Markup Language (VRML, filetype .wrl) and the LiveGraphics3D format.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rocr-r31-1.0-7-1 (Visualizing scoring classifier performance)
ROC graphs, sensitivity/specificity curves, lift charts, and
precision/recall plots are popular examples of trade-off
visualizations for specific pairs of performance measures. ROCR
is a flexible tool for creating cutoff-parameterized 2D
performance curves by freely combining two from over 25
performance measures (new performance measures can be added
using a standard interface). Curves from different cross-
alidation or bootstrapping runs can be averaged by different
methods, and standard deviations, standard errors or box plots
can be used to visualize the variability across the runs. The
parameterization can be visualized by printing cutoff values
at the corresponding curve positions, or by coloring the curve
according to cutoff. All components of a performance plot can
be quickly adjusted using a flexible parameter dispatching
mechanism. Despite its flexibility, ROCR is easy to use, with
only three commands and reasonable default values for all
optional parameters.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-vgam-r36-1.1-1-2 (Vector Generalized Linear and Additive Models)
Vector generalized linear and additive models, and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Reduced-Rank VGAMs). This
package fits many models and distribution by maximum likelihood
estimation (MLE) or penalized MLE. Also fits constrained ordination
models in ecology.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-profilemodel-r35-0.6.0-1 (Inference functions profiling tools)
profileModel provides tools that can be used to calculate, evaluate, plot
and use for inference the profiles of *arbitrary* inference functions for
for *arbitrary* 'glm'-like fitted models with linear predictors.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sets-r33-1.0-18-1 (Generalized and Customizable Sets)
Data structures and basic operations for ordinary sets, generalizations
such as fuzzy sets, multisets, and fuzzy multisets, customizable sets,
and intervals.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-teachingdemos-r34-2.10-2 (Demonstrations for Teaching and Learning)
Demonstration functions that can be used in a classroom to 
demonstrate statistical concepts, or on your own to better 
understand the concepts or the programming.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-prabclus-r36-2.3-1-1 (Functions for Clustering)
Distance-based parametric bootstrap tests for clustering with spatial
neighborhood information. Some distance measures, Clustering of
presence-absence, abundance and multilocus genetical data for
species delimitation, nearest neighbor based noise detection.
Try package?prabclus for on overview.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sandwich-r32-2.5-1-1 (GNU R std err estimators for time-series data)
sandwich: Robust Covariance Matrix Estimators
Model-robust standard error estimators for cross-sectional, 
time series, and longitudinal data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcmdrplugin.survival-r33-1.2-0-1 (R Commander Plug-in for the survival Package)
This package provides an R Commander plug-in for the survival package,
with dialogs for Cox models, parametric survival regression models,
estimation of survival curves, and testing for differences in survival
curves, along with data-management facilities and a variety of tests,
and graphs.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-scrime-r35-1.3.5-1 (Analysis of High-Dimensional Categorical Data)
Tools for the analysis of high-dimensional data developed/implemented 
at the group "Statistical Complexity Reduction In Molecular Epidemiology" 
(SCRIME). Main focus is on SNP data. But most of the functions can also 
be applied to other types of categorical data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    New upstream Bioconductor versions (bioc 3.10)
2020-01-16: cran-selectr-r33-0.4-1-1 (Translate CSS Selectors to XPath Expressions)
Translates a CSS3 selector into an equivalent XPath expression. This
allows us to use CSS selectors when working with the XML package as it
can only evaluate XPath expressions. Also provided are convenience
functions useful for using CSS selectors on XML nodes. This package is a
port of the Python package 'cssselect'
(<https://cssselect.readthedocs.io/>).

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2020-01-16: cran-scarabee-r33-1.1-3-2 (R port of the Scarabee toolkit)
scaRabee is a port of the Scarabee toolkit originally written as a Matlab-based
application. It provides a framework for simulation and optimization of
pharmacokinetic-pharmacodynamic models at the individual and population level.
It is built on top of the neldermead package, which provides the direct search
algorithm proposed by Nelder and Mead for model optimization.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-r.matlab-r33-3.6.2-1 (Read and write of MAT files)
This package provides methods readMat() and writeMat() to read
and write MAT files. It also makes it possible to communicate
(evaluate code, send and retrieve objects etc.) with MATLAB v6
or higher running locally or on a remote host.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-stable-r36-1.1.4-1 (Functions and Models for Stable Distributions)
Density, distribution, quantile and hazard functions of a stable
variate; generalized regression models for the parameters of a stable
distribution. See the README for how to make equivalent calls to those
of 'stabledist'. See github for Journal article.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rprojroot-r31-1.3-2-1 (Finding Files in Project Subdirectories)
Robust, reliable and flexible paths to files below a project root. 
The 'root' of a project is defined as a directory that matches 
a certain criterion, e.g., it contains a certain regular file.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-roughsets-r35-1.3-0-2 (Rough Set and Fuzzy Rough Set Analysis)
This package provides comprehensive implementations of the rough set
theory (RST) and the fuzzy rough set theory (FRST), and integrates
these two theories into a single package. It provides implementations,
not only for the basic concepts of RST and FRST, but also most common
methods based on them for handling some tasks such as discretization,
feature selection, instance selection, rule induction, and prediction.
RST was introduced by Zdzislaw Pawlak in 1982 as a sophisticated
mathematical tool based on indiscernibility relations to model and
process imprecise or incomplete information. It works on symbolic-
valued datasets for tackling the data analysis problems. By using th
indiscernibility relation for objects/instances, RST does not require
additional parameters to analyze the data. FRST is an extension of RST.
The FRST combines concepts of vagueness and indiscernibility that are
expressed with fuzzy sets (as proposed by Zadeh, in 1965) and RST.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sm-r33-2.2-5.6-2 (Smoothing methods)
This is software linked to the book 'Applied Smoothing Techniques for
Data Analysis - The Kernel Approach with S-Plus Illustrations' Oxford
University Press.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-scrime-r32-1.3.5-1 (Analysis of High-Dimensional Categorical Data)
Tools for the analysis of high-dimensional data developed/implemented 
at the group "Statistical Complexity Reduction In Molecular Epidemiology" 
(SCRIME). Main focus is on SNP data. But most of the functions can also 
be applied to other types of categorical data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    New upstream Bioconductor versions (bioc 3.10)
2020-01-16: cran-timp-r34-1.13.2-1 (Fitting separable nonlinear models)
TIMP is a problem solving environment for fitting separable nonlinear
models to measurements arising in physics and chemistry experiments,
and has been extensively applied to time-resolved spectroscopy and
FLIM-FRET data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-wccsom-r31-1.2.11-1 (SOM networks for patterns with peak shifts)
SOM networks for comparing patterns with peak shifts.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-polca-r36-1.4.1-1 (Polytomous variable Latent Class Analysis)
Latent class analysis and latent class regression models for
polytomous outcome variables. Also known as latent structure
analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-prodlim-r36-2018.04.18-1 (GNU R Tools for estimation of survival)
Fast and user friendly nonparametric estimation in 
censored survival (event history) analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-scales-r32-1.0.0-1 (Scale functions for graphics)
Scales map data to aesthetics, and provide methods for automatically
determining breaks and labels for axes and legends.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rgtk2-r34-2.20.36-1 (R bindings for Gtk 2.8.0 and above)
Facilities in the R language for programming graphical
interfaces using Gtk, the Gimp Tool Kit.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-vegan-r32-2.5-4-1 (Community Ecology Package)
Ordination methods, diversity analysis and other functions
for community and vegetation ecologists.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-spls-r31-2.2-3-1 (Sparse Partial Least Squares Regression)
This package provides functions for fitting a Sparse Partial
Least Squares Regression and Classification

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tibble-r34-2.1.3-1 (Simple Data Frames)
Provides a `tbl_df' class (the `tibble') that provides stricter checking 
and better formatting than the traditional data frame.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-resemble-r33-1.2.2-3 (Similarity/dissimilarity and MBL analysis)
This package implements functions for spectral similarity/dissimilarity
analysis and memory-based learning (MBL) for non-linear modelling in
complex spectral datasets. MBL is also known as local modelling in the
chemometrics literature.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rpart-r31-4.1-15-1 (GNU R Tools for recursive partitioning)
Recursive partitioning and regression trees

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-progress-r33-1.2.2-1 (Statnet project common scripts and utilities)

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-titan-r34-1.0-16-2 (Titration analysis for mass spec data)
GUI to analyze mass spectrometric data on the relative
abundance of two substances from a titration series.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-st-r33-1.2.5-1 (Shrinkage t Statistic and CAT Score)
This package implements the "shrinkage t" statistic introduced in
Opgen-Rhein and Strimmer (2007) and a shrinkage estimate of the
"correlation-adjusted t-score" (CAT score) described in Zuber
and Strimmer (2009). It also offers a convenient interface to
a number of other regularized t-statistics commonly employed in
high-dimensional case-control studies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rprojroot-r35-1.3-2-1 (Finding Files in Project Subdirectories)
Robust, reliable and flexible paths to files below a project root. 
The 'root' of a project is defined as a directory that matches 
a certain criterion, e.g., it contains a certain regular file.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-roughsets-r31-1.3-0-2 (Rough Set and Fuzzy Rough Set Analysis)
This package provides comprehensive implementations of the rough set
theory (RST) and the fuzzy rough set theory (FRST), and integrates
these two theories into a single package. It provides implementations,
not only for the basic concepts of RST and FRST, but also most common
methods based on them for handling some tasks such as discretization,
feature selection, instance selection, rule induction, and prediction.
RST was introduced by Zdzislaw Pawlak in 1982 as a sophisticated
mathematical tool based on indiscernibility relations to model and
process imprecise or incomplete information. It works on symbolic-
valued datasets for tackling the data analysis problems. By using th
indiscernibility relation for objects/instances, RST does not require
additional parameters to analyze the data. FRST is an extension of RST.
The FRST combines concepts of vagueness and indiscernibility that are
expressed with fuzzy sets (as proposed by Zadeh, in 1965) and RST.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-readr-r33-1.3.1-1 (Read Rectangular Text Data)
The goal of 'readr' is to provide a fast and friendly way to read
rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to
flexibly parse many types of data found in the wild, while still
cleanly failing when data unexpectedly changes.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-viridis-r33-0.5.1-2 (Default Color Maps from 'matplotlib')
Port of the new 'matplotlib' color maps ('viridis' - the default -,
'magma', plasma' and 'inferno') to 'R'. 'matplotlib'
http://matplotlib.org/  is a popular plotting library for 'python'.
These color maps are designed in such a way that they will analytically be
perfectly perceptually-uniform, both in regular form and also when
converted to black-and-white. They are also designed to be perceived by
readers with the most common form of color blindness. This is the 'lite'
version of the more complete 'viridis' package that can be found at
<https://cran.r-project.org/package=viridis>.

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2020-01-16: cran-rcppgsl-r33-0.3.4-1 (Rcpp Integration for 'GNU GSL')
'Rcpp' integration for 'GNU GSL' vectors and matrices The 'GNU
Scientific Library' (or 'GSL') is a collection of numerical routines for
scientific computing. It is particularly useful for C and C++ programs
as it provides a standard C interface to a wide range of mathematical
routines. There are over 1000 functions in total with an extensive test
suite. The 'RcppGSL' package provides an easy-to-use interface between
'GSL' data structures and R using concepts from 'Rcpp' which is itself a
package that eases the interfaces between R and C++. This package also
serves as a prime example of how to build a package that uses 'Rcpp' to
connect to another third-party library. The 'autoconf' script, 'inline'
plugin and example package can all be used as a stanza to write a
similar package against another library.

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2020-01-16: cran-robcompositions-r33-2.0.10-1 (Robust Estimation for Compositional Data)
The package includes methods for imputation of compositional data
including robust methods, methods to impute rounded zeros, (robust)
outlier detection for compositional data, (robust) principal component
analysis for compositional data, (robust) factor analysis for
compositional data, (robust) discriminant analysis for compositional
data (Fisher rule), robust regression with compositional predictors and
(robust) Anderson-Darling normality tests for compositional data as well
as popular log-ratio transformations (addLR, cenLR, isomLR, and their
inverse transformations). In addition, visualisation and diagnostic
tools are implemented as well as high and low-level plot functions for
the ternary diagram.

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2020-01-16: cran-xtable-r36-1.8-4-1 (Export tables to LaTeX or HTML)
Coerce data to LaTeX and HTML tables

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-psych-r35-1.8.12-1 (Procedures for Psychological Research)
A number of routines for personality, psychometrics and experimental
psychology. Functions are primarily for scale construction using
factor analysis, cluster analysis and reliability analysis, although
others provide basic descriptive statistics. Item Response Theory is
done using factor analysis of tetrachoric and polychoric correlations.
Functions for simulating particular item and test structures are
included. Several functions serve as a useful front end for structural
equation modeling. Graphical displays of path diagrams, factor analysis
and structural equation models are created using basic graphics. Some
of the functions are written to support a book on psychometrics as well
as publications in personality research. For more information, see the
personality-project.org/r webpage.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-polycor-r36-0.7-10-1 (Polychoric and Polyserial Correlations)
Computes polychoric and polyserial correlations by quick "two-step"
methods or ML, optionally with standard errors; tetrachoric
and biserial correlations are special cases.

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2020-01-16: cran-polyclip-r34-1.10-0-1 (Polygon Clipping)
R port of the Clipper library. Performs polygon clipping operations
(intersection, union, set minus, set difference) for polygonal regions
of arbitrary complexity, including holes. Also computes offset polygons
(spatial buffer zones, morphological dilations, Minkowski dilations)
for polygonal regions and polygonal lines.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-teachingdemos-r33-2.10-2 (Demonstrations for Teaching and Learning)
Demonstration functions that can be used in a classroom to 
demonstrate statistical concepts, or on your own to better 
understand the concepts or the programming.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-xlsxjars-r31-0.6.1-1 (Package required POI jars for xlsx package)
The xlsxjars package collects all the external jars required for the
xlxs package. These external jars are quite large in size (15MB) and
have a slow release cycle. By separating the Java and R development,
the storage footprint on CRAN is reduced. This release corresponds
to POI 3.10.

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2020-01-16: cran-rann-r32-2.6.1-1 (Fast Nearest Neighbour Search)
Finds the k nearest neighbours for every point in a given dataset
in O(N log N) time using Arya and Mount's ANN library (v1.1.3).
There is support for approximate as well as exact searches,
fixed radius searches and bd as well as kd trees.

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2020-01-16: cran-ps-r34-1.3.0-1 (List, Query, Manipulate System Processes)
List, query and manipulate all system processes, on 'Windows', 'Linux'
and 'macOS'.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tsfa-r31-2014.10-1-1 (Time Series Factor Analysis)
Extraction of Factors from Multivariate Time Series.
See ?00tsfa-Intro for more details.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-xts-r36-0.11-2-2 (The eXtensible Time Series)
Provide for uniform handling of R's different time-based data classes
by extending zoo, maximizing native format information preservation
and allowing for user level customization and extension, while
simplifying cross-class interoperability.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-xlsxjars-r34-0.6.1-1 (Package required POI jars for xlsx package)
The xlsxjars package collects all the external jars required for the
xlxs package. These external jars are quite large in size (15MB) and
have a slow release cycle. By separating the Java and R development,
the storage footprint on CRAN is reduced. This release corresponds
to POI 3.10.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-proj4-r33-1.0-9-102 (PROJ.4 cartographic projections library for R)
PROJ.4 cartographic projections library for R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-recipes-r36-0.1.7-1 (Preprocessing Tools to Create Design Matrices)
An extensible framework to create and preprocess design matrices.
Recipes consist of one or more data manipulation and analysis "steps".
Statistical parameters for the steps can be estimated from an initial
data set and then applied to other data sets. The resulting design
matrices can then be used as inputs into statistical or machine learning
models.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-polyclip-r31-1.10-0-1 (Polygon Clipping)
R port of the Clipper library. Performs polygon clipping operations
(intersection, union, set minus, set difference) for polygonal regions
of arbitrary complexity, including holes. Also computes offset polygons
(spatial buffer zones, morphological dilations, Minkowski dilations)
for polygonal regions and polygonal lines.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-vimgui-r31-0.9.0-1 (Visualization & Imputation of Missing Values)
This package introduces new tools for the visualization of missing and/or
imputed values, which can be used for exploring the data and the structure
of the missing and/or imputed values. Depending on this structure of the
missing values, the corresponding methods may help to identify the mechanism
generating the missings and allows to explore the data including missing
values. In addition, the quality of imputation can be visually explored
using various univariate, bivariate, multiple and multivariate plot methods.
A graphical user interface allows an easy handling of the implemented plot
methods.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-statnet.common-r32-3.3.0-1 (Statnet project common scripts and utilities)
Non-statistical utilities used by the software developed 
by the Statnet Project. They may also be of use to others.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rpart.plot-r33-3.0.6-1 (Plot enhanced rpart models)
Plot rpart models. Extends plot.rpart and text.rpart in the rpart package.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-trust-r31-0.1-7-1 (Trust Region Optimization)
local optimization using two derivatives and trust regions

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-timp-r35-1.13.2-1 (Fitting separable nonlinear models)
TIMP is a problem solving environment for fitting separable nonlinear
models to measurements arising in physics and chemistry experiments,
and has been extensively applied to time-resolved spectroscopy and
FLIM-FRET data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-purrr-r33-0.3.2-3 (Functional Programming Tools)
Make your pure functions purr with the 'purrr' package. This package 
completes R's functional programming tools with missing features present 
in other programming languages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-relaimpo-r35-2.2-3-1 (Relative importance of regressors)
relaimpo provides several metrics for assessing relative importance
in linear models. These can be printed, plotted and bootstrapped.
The recommended metric is lmg, which provides a decomposition of
the model explained variance into non-negative contributions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-weightedkmeans-r32-1.2.0-1 (Weighted KMeans Clustering)
Entropy weighted kmeans (ewkm) is a weighted subspace clustering
algorithm that is well suited to very high dimensional data. Weights
are calculated as the importance of a variable with regard to cluster
membership. The feature group weighted kmenas (fgkm) extends this
concept by grouping features and weighting the group in addition
to weihgting individual features.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-urca-r33-1.3-0-2 (Unit Root and Cointegration Tests)
Unit root and cointegration tests encountered in applied econometric
analysis are implemented.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-tibble-r33-2.1.3-1 (Simple Data Frames)
Provides a `tbl_df' class (the `tibble') that provides stricter checking 
and better formatting than the traditional data frame.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-qap-r36-0.1-1-1 (Heuristics for Quadratic Assignment Problem)
Implements heuristics for the Quadratic Assignment Problem (QAP). 
Currently only a simulated annealing heuristic is available.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-zoo-r32-1.8-5-1 (GNU R Tools for ir/regular time series)
zoo: S3 Infrastructure for Regular and 
Irregular Time Series (Z's ordered observations)

An S3 class with methods for totally ordered indexed observations. 
It is particularly aimed at irregular time series of numeric vectors/matrices 
and factors.  zoo's key design goals are independence of a particular 
index/date/time class and consistency with ts and base R by providing 
methods to extend standard generics.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rpart.plot-r36-3.0.8-1 (Plot enhanced rpart models)
Plot rpart models. Extends plot.rpart and text.rpart in the rpart package.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rfast-r36-1.9.5-2 (Efficient and Extremely Fast R Functions)
A collection of fast (utility) functions for data analysis. Column- and
row- wise means, medians, variances, minimums, maximums, many t, F and
G-square tests, many regressions (normal, logistic, Poisson), are some
of the many fast functions. Reference: Tsagris M, Papadakis M. (2018).
Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1
.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-spatial-r36-7.3-11-1 (Kriging and Point Pattern Analysis Functions)
Functions for kriging and point pattern analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rmutil-r32-1.1.3-1 (Repeated Measurements Models Utilities)
A toolkit of functions for nonlinear regression and repeated
measurements not to be used by itself but called by other Lindsey
packages such as 'gnlm', 'stable', 'growth', 'repeated', and 'event'
(available at http://www.commanster.eu/rcode.html).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-reactran-r36-1.4.3.1-2 (Reactive transport modelling in 1D, 2D and 3D)
Routines for developing models that describe reaction and
advective-diffusive transport in one, two or three dimensions.
Includes transport routines in porous media, in estuaries, and
in bodies with variable shape.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-vegan-r35-2.5-4-1 (Community Ecology Package)
Ordination methods, diversity analysis and other functions
for community and vegetation ecologists.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-randomforestsrc-r31-2.8.0-1 (Random Forests for Survival)
A unified treatment of Breiman's random forests for survival, regression
and classification problems based on Ishwaran and Kogalur's random survival
forests (RSF) package. The package runs in both serial and parallel
(OpenMP) modes.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sessioninfo-r31-1.1.1-1 (R Session Information)
Query and print information about the current R session. It is similar
to 'utils::sessionInfo()', but includes more information about packages,
and where they were installed from.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-randomforest-r31-4.6-12-1 (GNU R Tools for random forest class/regress)
Classification and regression based on a forest of trees using random inputs.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-zcompositions-r35-1.3.2-1-1 (Treatment of Zero/Missing Values in Data Sets)
Principled methods for the imputation of zeros, left-censored and
missing data in compositional data sets.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sp-r33-1.3-1-1 (GNU R classes and methods for spatial data)
GNU R classes and methods for spatial data

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-processx-r33-3.4.1-1 (Execute and Control System Processes)
Tools to run system processes in the background. It can check if a
background process is running; wait on a background process to finish;
get the exit status of finished processes; kill background processes. It
can read the standard output and error of the processes, using
non-blocking connections. 'processx' can poll a process for standard
output or error, with a timeout. It can also poll several processes at
once.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-prim-r34-1.0.16-1 (Patient Rule Induction Method)
PRIM for bump hunting in high-dimensional data

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rpubchem-r35-1.5.10-1 (Interface to the PubChem Collection)
Access PubChem data (compounds, substance, assays). Structural information
is provided in the form of SMILES strings. This package only provides
access to a subset of the precalculated data stored by PubChem. Bio-assay
data can be accessed to obtain descriptions as well as the actual data.
It is also possible to search for assay ID's by keyword. Currently the main
limitation is that only 1000 molecules can be downloaded at a time from the
PubChem servers

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rgl-r31-0.95.1441-2 (3D visualization device system)
Provides medium to high level functions for 3D interactive graphics,
including functions modelled on base graphics (plot3d(), etc.) as
well as functions for constructing representations of geometric objects
(cube3d(), etc.). Output may be on screen using OpenGL, or to various
standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
image formats, including PNG, Postscript, SVG, PGF.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-r2html-r32-2.3.2-1 (HTML exportation for R objects)
Includes HTML function and methods to write in an HTML file.
Thus, making HTML reports is easy. Includes a function that
allows redirection on the fly, which appears to be very usefull
for teaching purpose, as the student can keep a copy of the
produced output to keep all that he did during the course.
Package comes with a vignette describing how to write HTML
reports for statistical analysis. Finally, a driver for Sweave
allows to parse HTML flat files containing R code and to
automatically write the corresponding outputs (tables and graphs).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-whisker-r35-0.4-1 ({{mustache}} for R, logicless templating)
logicless templating, reuse templates in many programming
languages including R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rrcov-r36-1.4-7-2 (Scalable Robust Estimators)
Robust Location and Scatter Estimation and Robust Multivariate
Analysis with High Breakdown Point.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-squarem-r32-2017.10-1-1 (Squared Extrapolation Methods For Algorithms)
Algorithms for accelerating the convergence of slow, monotone sequences
from smooth, contraction mapping such as the EM algorithm. It can be
used to accelerate any smooth, linearly convergent acceleration scheme.
A tutorial style introduction to this package is available in a vignette
on the CRAN download page or, when the package is loaded in an R
session, with vignette("SQUAREM").

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-subplex-r35-1.5-4-2 (Subplex optimization algorithm)
The subplex algorithm for unconstrained optimization, developed by Tom Rowan.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-ppls-r36-1.6-1.1-1 (Penalized Partial Least Squares)
This package contains linear and nonlinear regression methods based
on Partial Least Squares and Penalization Techniques. Model parameters
are selected via cross-validation, and confidence intervals ans tests
for the regression coefficients can be conducted via jackknifing.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-robustbase-r35-0.93-5-2 (GNU R Tools for robust methods)
"Essential" Robust Statistics.
The goal is to provide tools allowing to analyze data with robust methods.
This includes regression methodology including model selections and
multivariate statistics where we strive to cover the book
"Robust Statistics, Theory and Methods" by Maronna, Martin and Yohai;
Wiley 2006.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-r6-r35-2.4.0-1 (Classes with reference semantics)
The R6 package allows the creation of classes with reference semantics,
similar to R's built-in reference classes. Compared to reference classes,
R6 classes are simpler and lighter-weight, and they are not built on S4
classes so they do not require the methods package. These classes allow
public and private members, and they support inheritance, even when the
classes are defined in different packages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tseries-r35-0.10-47-2 (Time series analysis and finance)
Package for time series analysis and computational finance

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rattle-r36-5.2.0-1 (Graphical user interface for data mining in R)
Rattle (the R Analytic Tool To Learn Easily) provides a Gnome
(RGtk2) based interface to R functionality for data mining.
The aim is to provide a simple and intuitive interface that
allows a user to quickly load data from a CSV file (or via ODBC),
transform and explore the data, build and evaluate models, and
export models as PMML (predictive modelling markup language) or
as scores. All of this with knowing little about R. All R
commands are logged and commented through the log tab. Thus
they are available to the user as a script file or as an aide
for the user to learn R or to copy-and-paste directly into R
itself. Rattle also exports a number of utility functions and
the graphical user interface, invoked as rattle(), does not
need to be run to deploy these.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tm-r36-0.7-6-1 (Text Mining Package)
A framework for text mining applications within R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-urca-r36-1.3-0-2 (Unit Root and Cointegration Tests)
Unit root and cointegration tests encountered in applied econometric
analysis are implemented.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rjsonio-r31-1.3-1.3-1 (Serialize R objects to JSON)
This is a package that allows conversion to and from data in Javascript
object notation (JSON) format. This allows R objects to be inserted into
Javascript/ECMAScript/ActionScript code and allows R programmers to read
and convert JSON content to R objects. This is an alternative to rjson
package. That version was too slow for converting large R objects to JSON
and is not extensible, but a very useful prototype. It is fast for parsing.
This package uses methods, vectorized operations and C code and callbacks
to R functions for deserializing JSON objects to R. Verison 0.4 of this
package uses a new native parser, implements the transformation code in
C and allocates memory efficiently (rather than concatenating because
of event driven parsing). The result is a significantly faster parsing
of large JSON documents.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-roxygen2-r36-6.1.1-1 (In-source documentation for R)
A Doxygen-like in-source documentation system for Rd, collation,
and NAMESPACE.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-pspline-r34-1.0-18-3 (Penalized Smoothing Splines)
Smoothing splines with penalties on order m derivatives.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-statnet.common-r31-3.3.0-1 (Statnet project common scripts and utilities)
Non-statistical utilities used by the software developed 
by the Statnet Project. They may also be of use to others.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-whisker-r32-0.4-1 ({{mustache}} for R, logicless templating)
logicless templating, reuse templates in many programming
languages including R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-polynomf-r33-2.0-2-1 (Polynomials in R)
Implements univariate polynomial operations in R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-readxl-r32-1.3.1-2 (Read Excel Files)
Import excel files into R. Supports '.xls' via the embedded
'libxls' C library (http://sourceforge.net/projects/libxls/)
and '.xlsx' via the embedded 'RapidXML' C++ library
(http://rapidxml.sourceforge.net). Works on Windows, Mac
 and Linux without external dependencies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-testit-r35-0.10-1 (Simple package for testing R packages)
This package provides two convenience functions assert()
and test_pkg() to facilitate testing R packages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-psych-r32-1.8.12-1 (Procedures for Psychological Research)
A number of routines for personality, psychometrics and experimental
psychology. Functions are primarily for scale construction using
factor analysis, cluster analysis and reliability analysis, although
others provide basic descriptive statistics. Item Response Theory is
done using factor analysis of tetrachoric and polychoric correlations.
Functions for simulating particular item and test structures are
included. Several functions serve as a useful front end for structural
equation modeling. Graphical displays of path diagrams, factor analysis
and structural equation models are created using basic graphics. Some
of the functions are written to support a book on psychometrics as well
as publications in personality research. For more information, see the
personality-project.org/r webpage.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-prim-r35-1.0.16-1 (Patient Rule Induction Method)
PRIM for bump hunting in high-dimensional data

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-weightedkmeans-r31-1.2.0-1 (Weighted KMeans Clustering)
Entropy weighted kmeans (ewkm) is a weighted subspace clustering
algorithm that is well suited to very high dimensional data. Weights
are calculated as the importance of a variable with regard to cluster
membership. The feature group weighted kmenas (fgkm) extends this
concept by grouping features and weighting the group in addition
to weihgting individual features.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tseries-r32-0.10-47-2 (Time series analysis and finance)
Package for time series analysis and computational finance

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-pspline-r31-1.0-18-3 (Penalized Smoothing Splines)
Smoothing splines with penalties on order m derivatives.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-subplex-r32-1.5-4-2 (Subplex optimization algorithm)
The subplex algorithm for unconstrained optimization, developed by Tom Rowan.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-qap-r31-0.1-1-1 (Heuristics for Quadratic Assignment Problem)
Implements heuristics for the Quadratic Assignment Problem (QAP). 
Currently only a simulated annealing heuristic is available.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rjsonio-r34-1.3-1.3-1 (Serialize R objects to JSON)
This is a package that allows conversion to and from data in Javascript
object notation (JSON) format. This allows R objects to be inserted into
Javascript/ECMAScript/ActionScript code and allows R programmers to read
and convert JSON content to R objects. This is an alternative to rjson
package. That version was too slow for converting large R objects to JSON
and is not extensible, but a very useful prototype. It is fast for parsing.
This package uses methods, vectorized operations and C code and callbacks
to R functions for deserializing JSON objects to R. Verison 0.4 of this
package uses a new native parser, implements the transformation code in
C and allocates memory efficiently (rather than concatenating because
of event driven parsing). The result is a significantly faster parsing
of large JSON documents.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-reshape2-r31-1.4.3-1 (Flexibly reshape data)
Reshape lets you flexibly restructure and aggregate data using
just two functions: melt and cast.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-squarem-r35-2017.10-1-1 (Squared Extrapolation Methods For Algorithms)
Algorithms for accelerating the convergence of slow, monotone sequences
from smooth, contraction mapping such as the EM algorithm. It can be
used to accelerate any smooth, linearly convergent acceleration scheme.
A tutorial style introduction to this package is available in a vignette
on the CRAN download page or, when the package is loaded in an R
session, with vignette("SQUAREM").

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-ptak-r32-1.3-34-1 (Principal Tensor Analysis on k modes)
A multiway method to decompose a tensor (array) of any order, as a
generalisation of SVD also supporting non-identity metrics and
penalisations. 2-way SVD with these extensions is also available.
The package includes also some other multiway methods: PCAn
(Tucker-n) and PARAFAC/CANDECOMP with these extensions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rms-r34-5.1-3.1-2 (Regression Modeling Strategies)
Regression modeling, testing, estimation, validation, graphics,
prediction, and typesetting by storing enhanced model design
attributes in the fit. rms is a collection of functions that
assist with and streamline modeling. It also contains functions
for binary and ordinal logistic regression models, ordinal
models for continuous Y with a variety of distribution families,
and the Buckley-James multiple regression model for
right-censored responses, and implements penalized maximum
likelihood estimation for logistic and ordinary linear models.
rms works with almost any regression model, but it was especially
written to work with binary or ordinal regression models,
Cox regression, accelerated failure time models, ordinary
linear models,        the Buckley-James model, generalized least
squares for serially or spatially correlated observations,
generalized linear models, and quantile regression.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-pmmltransformations-r31-1.3.3-1 (Transforms input data from a PMML perspective)
Allows for data to be transformed before using it to construct models.
Builds structures to allow functions in the PMML package to output
transformation details in addition to the model in the resulting PMML file.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-reshape2-r34-1.4.3-1 (Flexibly reshape data)
Reshape lets you flexibly restructure and aggregate data using
just two functions: melt and cast.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rpanel-r31-1.1-4-1 (Simple interactive controls)
rpanel provides a set of functions to build simple GUI controls for
R functions. These are built on the tcltk package. Uses could include
changing a parameter on a graph by animating it with a slider or a
"doublebutton", up to more sophisticated control panels. Some functions
for specific graphical tasks, referred to as 'cartoons', are provided.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-randomforestsrc-r34-2.8.0-1 (Random Forests for Survival)
A unified treatment of Breiman's random forests for survival, regression
and classification problems based on Ishwaran and Kogalur's random survival
forests (RSF) package. The package runs in both serial and parallel
(OpenMP) modes.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcompression-r31-0.93-2-1 (R Package for in-memory compression)
This package is a basic R interface to the zlib and bzip2 facilities for 
compressing and uncompressing data that are in memory rather than in files.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-vcd-r35-1.4-4-1 (Visualizing Categorical Data)
Visualization techniques, data sets, summary and inference procedures
aimed particularly at categorical data. Special emphasis is given to
highly extensible grid graphics. The package was inspired by the book
"Visualizing Categorical Data" by Michael Friendly.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-xlconnectjars-r31-0.2-15-1 (JAR dependencies for the XLConnect)
Provides external JAR dependencies for the XLConnect package.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-v8-r35-2.3-2 (Embedded JavaScript Engine for R)
An R interface to Google's open source JavaScript engine.
V8 is written in C++ and implements ECMAScript as specified in ECMA-262,
5th edition. In addition, this package implements typed arrays as specified
in ECMA 6 used for high-performance computing and libraries compiled
with 'emscripten'.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rgl-r36-0.100.30-1 (3D visualization device system)
Provides medium to high level functions for 3D interactive graphics,
including functions modelled on base graphics (plot3d(), etc.) as
well as functions for constructing representations of geometric objects
(cube3d(), etc.). Output may be on screen using OpenGL, or to various
standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
image formats, including PNG, Postscript, SVG, PGF.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-ppls-r33-1.6-1.1-1 (Penalized Partial Least Squares)
This package contains linear and nonlinear regression methods based
on Partial Least Squares and Penalization Techniques. Model parameters
are selected via cross-validation, and confidence intervals ans tests
for the regression coefficients can be conducted via jackknifing.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-withr-r34-2.1.2-1 (Run Code w/ Temporarily Modified Global State)
A set of functions to run code 'with' safely and temporarily 
modified global state. Many of these functions were originally 
a part of the 'devtools' package, this provides a simple package 
with limited dependencies to provide access to these functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-xlconnect-r35-0.2-15-1 (Excel Connector for R)
Manipulate Excel files from R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-ucminf-r34-1.1-4-2 (Unconstrained non-linear optimization)
An algorithm for general-purpose unconstrained non-linear optimization.
The algorithm is of quasi-Newton type with BFGS updating of the inverse
Hessian and soft line search with a trust region type monitoring of the
input to the line search algorithm. The interface of 'ucminf' is designed
for easy interchange with 'optim'.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-spgrass6-r36-0.8-9-1 (Interface between GRASS 6+ and R)
Interface between GRASS 6+ and R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rglwidget-r33-0.2.1-1 (Rgl in htmlwidgets Framework)
Provides an 'htmlwidgets' framework for the 'rgl' package.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tripack-r32-1.3-8-2 (Triangulation of irregularly spaced data)
A constrained two-dimensional Delaunay triangulation package

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rwekajars-r33-3.9.3-1-1 (R/Weka interface jars)
External jars required for package RWeka.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-prospectr-r36-0.1.3-4 (Processing and sample selection of vis-NIR)
The package provides functions for pretreatment and sample selection
of visible and near infrared diffuse reflectance spectra

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rio-r33-0.5.16-2 (Swiss-Army Knife for Data I/O)
Streamlined data import and export by making assumptions that the user
is probably willing to make: 'import()' and 'export()' determine the
data structure from the file extension, reasonable defaults are used for
data import and export (e.g., 'stringsAsFactors=FALSE'), web-based
import is natively supported (including from SSL/HTTPS), compressed
files can be read directly without explicit decompression, and fast
import packages are used where appropriate. An additional convenience
function, 'convert()', provides a simple method for converting between
file types.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-vctrs-r36-0.2.0-2 (Vector Helpers)
Defines new notions of prototype and size that are used to provide 
tools for consistent and well-founded type-coercion and size-recycling, 
and are in turn connected to ideas of type- and size-stability useful 
for analyzing function interfaces.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-pracma-r34-2.2.5-1 (Practical Numerical Math Functions)
Functions from numerical analysis and linear algebra, numerical optimization,
differential equations, plus some special functions. Uses Matlab function names
where appropriate to simplify porting.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-yaml-r35-2.2.0-1 (Libyaml YAML 1.1 parser and emitter for R)
This package implements the libyaml YAML 1.1 parser and emitter 
(http://pyyaml.org/wiki/LibYAML) for R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-prospectr-r34-0.1.3-4 (Processing and sample selection of vis-NIR)
The package provides functions for pretreatment and sample selection
of visible and near infrared diffuse reflectance spectra

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rcolorbrewer-r34-1.1-2-1 (GNU R Tools for variable-dependent palettes)
The packages provides palettes for drawing nice maps shaded 
according to a variable.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-polynom-r35-1.4-0-1 (Univariate polynomial manipulations in R)
A collection of functions to implement a class for univariate
polynomial manipulations.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-readxl-r35-1.3.1-2 (Read Excel Files)
Import excel files into R. Supports '.xls' via the embedded
'libxls' C library (http://sourceforge.net/projects/libxls/)
and '.xlsx' via the embedded 'RapidXML' C++ library
(http://rapidxml.sourceforge.net). Works on Windows, Mac
 and Linux without external dependencies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rms-r35-5.1-3.1-2 (Regression Modeling Strategies)
Regression modeling, testing, estimation, validation, graphics,
prediction, and typesetting by storing enhanced model design
attributes in the fit. rms is a collection of functions that
assist with and streamline modeling. It also contains functions
for binary and ordinal logistic regression models, ordinal
models for continuous Y with a variety of distribution families,
and the Buckley-James multiple regression model for
right-censored responses, and implements penalized maximum
likelihood estimation for logistic and ordinary linear models.
rms works with almost any regression model, but it was especially
written to work with binary or ordinal regression models,
Cox regression, accelerated failure time models, ordinary
linear models,        the Buckley-James model, generalized least
squares for serially or spatially correlated observations,
generalized linear models, and quantile regression.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-testit-r32-0.10-1 (Simple package for testing R packages)
This package provides two convenience functions assert()
and test_pkg() to facilitate testing R packages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-v8-r34-2.3-2 (Embedded JavaScript Engine for R)
An R interface to Google's open source JavaScript engine.
V8 is written in C++ and implements ECMAScript as specified in ECMA-262,
5th edition. In addition, this package implements typed arrays as specified
in ECMA 6 used for high-performance computing and libraries compiled
with 'emscripten'.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rtsne-r33-0.15-2 (T-distributed Stochastic Neighbor Embedding)
An R wrapper around the fast T-distributed Stochastic 
Neighbor Embedding implementation by Van der Maaten.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-pomp-r35-1.14-1 (Partially observed Markov processes methods)
Inference methods for partially-observed Markov processes

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rmpfr-r32-0.6-1-1 (Multiple Precision Floating-Point Reliable)
Rmpfr provides (S4 classes and methods for) arithmetic including transcendental
("special") functions for arbitrary precision floating point numbers. To this
end, it interfaces to the LGPL'ed MPFR (Multiple Precision Floating-Point
Reliable) Library which itself is based on the GMP (GNU Multiple Precision)
Library.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-vcd-r34-1.4-4-1 (Visualizing Categorical Data)
Visualization techniques, data sets, summary and inference procedures
aimed particularly at categorical data. Special emphasis is given to
highly extensible grid graphics. The package was inspired by the book
"Visualizing Categorical Data" by Michael Friendly.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-xlconnect-r31-0.2-15-1 (Excel Connector for R)
Manipulate Excel files from R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcgmin-r31-2013-2.21-1 (Conjugate Gradient Minimization)
Conjugate gradient minimization of nonlinear functions with box constraints
incorporating the Dai/Yuan update. This implementation should be used in
place of the "CG" algorithm of the optim() function.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rodbc-r35-1.3-16-1 (ODBC Database Access for R)
An ODBC database interface

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcompression-r36-0.93-2-1 (R Package for in-memory compression)
This package is a basic R interface to the zlib and bzip2 facilities for 
compressing and uncompressing data that are in memory rather than in files.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rdpack-r36-0.11-0-1 (Update/Manipulate Rd Documentation Objects)
Functions for manipulation of R documentation objects, including
functions reprompt() and ereprompt() for updating 'Rd' documentation for
functions, methods and classes; 'Rd' macros for citations and import of
references from 'bibtex' files for use in 'Rd' files and 'roxygen2'
comments; 'Rd' macros for evaluating and inserting snippets of 'R' code
and the results of its evaluation or creating graphics on the fly; and
many functions for manipulation of references and Rd files.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tis-r32-1.37.1-1 (Time Indexes and Time Indexed Series)
Functions and S3 classes for time indexes and time indexed
series, which are compatible with FAME frequencies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rmarkdown-r31-1.16-1 (Dynamic Documents for R)
Convert R Markdown documents into a variety of formats.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-reshape-r34-0.8.8-1 (Flexibly reshape data)
Reshape lets you flexibly restructure and aggregate data
using just two functions: melt and cast.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-xopen-r32-1.0.0-1 (Open System Files, 'URLs', Anything)
Cross platform solution to open files, directories or 'URLs' with their
associated programs.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-ptw-r32-1.9-13-1 (Parametric Time Warping)
Parametric Time Warping aligns patterns, i.e. it aims to put corresponding
features at the same locations. The algorithm searches for an optimal
polynomial describing the warping. It is possible to align one sample
to a reference, several samples to the same reference, or several samples
to several references. One can choose between calculating individual
warpings, or one global warping for a set of samples and one reference.
Two optimization criteria are implemented: RMS (Root Mean Square error)
and WCC (Weighted Cross Correlation).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-polynom-r32-1.4-0-1 (Univariate polynomial manipulations in R)
A collection of functions to implement a class for univariate
polynomial manipulations.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rsclient-r36-0.7-3-2 (RSclient: Client for Rserve)
Client for Rserve, allowing to connect to Rserve instances
and issue commands.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-randomforest-r36-4.6-14-2 (GNU R Tools for random forest class/regress)
Classification and regression based on a forest of trees using random inputs.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-pomp-r34-1.14-1 (Partially observed Markov processes methods)
Inference methods for partially-observed Markov processes

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-quadprog-r35-1.5-7-2 (Functionss for Quadratic Programming Problems)
This package contains routines and documentation for solving
quadratic programming problems.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-reshape-r31-0.8.8-1 (Flexibly reshape data)
Reshape lets you flexibly restructure and aggregate data
using just two functions: melt and cast.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r2html-r35-2.3.2-1 (HTML exportation for R objects)
Includes HTML function and methods to write in an HTML file.
Thus, making HTML reports is easy. Includes a function that
allows redirection on the fly, which appears to be very usefull
for teaching purpose, as the student can keep a copy of the
produced output to keep all that he did during the course.
Package comes with a vignette describing how to write HTML
reports for statistical analysis. Finally, a driver for Sweave
allows to parse HTML flat files containing R code and to
automatically write the corresponding outputs (tables and graphs).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcmdrplugin.ezr-r34-1.40-1 (Easy R for medical statistics)
Easy R for medical statistics

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-xml2-r32-1.2.2-2 (Parse XML)
Work with XML files using a simple, consistent interface. Built on top of 
the 'libxml2' C library.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-xlconnectjars-r36-0.2-15-1 (JAR dependencies for the XLConnect)
Provides external JAR dependencies for the XLConnect package.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tripack-r35-1.3-8-2 (Triangulation of irregularly spaced data)
A constrained two-dimensional Delaunay triangulation package

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rmutil-r35-1.1.3-1 (Repeated Measurements Models Utilities)
A toolkit of functions for nonlinear regression and repeated
measurements not to be used by itself but called by other Lindsey
packages such as 'gnlm', 'stable', 'growth', 'repeated', and 'event'
(available at http://www.commanster.eu/rcode.html).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-relimp-r33-1.0-5-1 (Relative Contribution of Effects)
Functions to facilitate inference on the relative importance
of predictors in a linear or generalized linear model, and
a couple of useful Tcl/Tk widgets.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r6-r34-2.4.0-1 (Classes with reference semantics)
The R6 package allows the creation of classes with reference semantics,
similar to R's built-in reference classes. Compared to reference classes,
R6 classes are simpler and lighter-weight, and they are not built on S4
classes so they do not require the methods package. These classes allow
public and private members, and they support inheritance, even when the
classes are defined in different packages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-yaml-r34-2.2.0-1 (Libyaml YAML 1.1 parser and emitter for R)
This package implements the libyaml YAML 1.1 parser and emitter 
(http://pyyaml.org/wiki/LibYAML) for R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-qvcalc-r31-1.0.1-1 (Quasi Variances for Effects in Stat Models)
Functions to compute quasi variances and associated measures of
approximation error.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rmarkdown-r35-1.16-1 (Dynamic Documents for R)
Convert R Markdown documents into a variety of formats.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-zeallot-r36-0.1.0-1 (Multiple/Unpacking/Destructuring Assignment)
Provides a %<-% operator to perform multiple, unpacking, and 
destructuring assignment in R. The operator unpacks the right-hand 
side of an assignment into multiple values and assigns these 
values to variables on the left-hand side of the assignment.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-prettyunits-r34-1.0.2-3 (Human Readable Formatting of Quantities)
Pretty, human readable formatting of quantities.
Time intervals: 1337000 -> 15d 11h 23m 20s.
Vague time intervals: 2674000 -> about a month ago.
Bytes: 1337 -> 1.34 kB.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-qap-r34-0.1-1-1 (Heuristics for Quadratic Assignment Problem)
Implements heuristics for the Quadratic Assignment Problem (QAP). 
Currently only a simulated annealing heuristic is available.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rastervis-r34-0.46-1 (Visualization methods for raster)
The raster package defines classes and methods for spatial raster
data access and manipulation. The rasterVis package complements
raster providing a set of methods for enhanced visualization and
interaction.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-survey-r33-3.36-1 (Analysis of complex survey samples)
Summary statistics, two-sample tests, generalised linear models,
cumulative link models, Cox models, loglinear models, and general
maximum pseudolikelihood estimation for multistage stratified,
cluster-sampled, unequally weighted survey samples. Variances by
Taylor series linearisation or replicate weights. Post-stratification,
calibration, and raking. Two-phase subsampling designs. Graphics.
Predictive margins by direct standardization. PPS sampling without
replacement. Principal components, factor analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-squarem-r36-2017.10-1-1 (Squared Extrapolation Methods For Algorithms)
Algorithms for accelerating the convergence of slow, monotone sequences
from smooth, contraction mapping such as the EM algorithm. It can be
used to accelerate any smooth, linearly convergent acceleration scheme.
A tutorial style introduction to this package is available in a vignette
on the CRAN download page or, when the package is loaded in an R
session, with vignette("SQUAREM").

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-spam-r32-2.3-0-2 (SPArse Matrix)
Set of functions for sparse matrix algebra. Differences with SparseM/Matrix
are: (1) we only support (essentially) one sparse matrix format, (2) based
on transparent and simple structure(s), (3) tailored for MCMC calculations
within GMRF. (4) S3 and S4 like-"compatible" ... and it is fast.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-r.oo-r35-1.22.0-1 (R object-oriented programming)
Methods and classes for object-oriented programming in R
with or without references.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sm-r31-2.2-5.6-2 (Smoothing methods)
This is software linked to the book 'Applied Smoothing Techniques for
Data Analysis - The Kernel Approach with S-Plus Illustrations' Oxford
University Press.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-spgrass6-r33-0.8-9-1 (Interface between GRASS 6+ and R)
Interface between GRASS 6+ and R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rpubchem-r32-1.5.10-1 (Interface to the PubChem Collection)
Access PubChem data (compounds, substance, assays). Structural information
is provided in the form of SMILES strings. This package only provides
access to a subset of the precalculated data stored by PubChem. Bio-assay
data can be accessed to obtain descriptions as well as the actual data.
It is also possible to search for assay ID's by keyword. Currently the main
limitation is that only 1000 molecules can be downloaded at a time from the
PubChem servers

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rastervis-r36-0.46-1 (Visualization methods for raster)
The raster package defines classes and methods for spatial raster
data access and manipulation. The rasterVis package complements
raster providing a set of methods for enhanced visualization and
interaction.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-webshot-r33-0.5.1-1 (Shiny UI Widgets for Small Screens)
Provides UI widget and layout functions for writing Shiny apps that work
well on small screens.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rpanel-r35-1.1-4-1 (Simple interactive controls)
rpanel provides a set of functions to build simple GUI controls for
R functions. These are built on the tcltk package. Uses could include
changing a parameter on a graph by animating it with a slider or a
"doublebutton", up to more sophisticated control panels. Some functions
for specific graphical tasks, referred to as 'cartoons', are provided.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rngtools-r34-1.3.1-1 (Utility for Random Number Generators)
This package contains a set of functions for working with Random 
Number Generators (RNGs). In particular, it defines a generic S4 
framework for getting/setting the current RNG, or RNG data that 
are embedded into objects for reproducibility. Notably, convenient 
default methods greatly facilitate the way current RNG settings 
can be changed.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-vgam-r35-1.1-1-2 (Vector Generalized Linear and Additive Models)
Vector generalized linear and additive models, and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Reduced-Rank VGAMs). This
package fits many models and distribution by maximum likelihood
estimation (MLE) or penalized MLE. Also fits constrained ordination
models in ecology.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rngtools-r31-1.3.1-1 (Utility for Random Number Generators)
This package contains a set of functions for working with Random 
Number Generators (RNGs). In particular, it defines a generic S4 
framework for getting/setting the current RNG, or RNG data that 
are embedded into objects for reproducibility. Notably, convenient 
default methods greatly facilitate the way current RNG settings 
can be changed.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-testit-r31-0.10-1 (Simple package for testing R packages)
This package provides two convenience functions assert()
and test_pkg() to facilitate testing R packages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-usethis-r34-1.5.0-1 (Automate Package and Project Setup)
Automate package and project setup tasks that are otherwise performed
manually. This includes setting up unit testing, test coverage,
continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio'
projects, and more.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sets-r34-1.0-18-1 (Generalized and Customizable Sets)
Data structures and basic operations for ordinary sets, generalizations
such as fuzzy sets, multisets, and fuzzy multisets, customizable sets,
and intervals.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-questionr-r34-0.7.0-1 (Functions to Make Surveys Processing Easier)
Set of functions to make the processing and analysis of surveys easier :
interactive shiny apps and addins for data recoding, contingency tables,
dataset metadata handling, and several convenience functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tinytex-r34-0.16-1 (Functions to Maintain 'TeX Live')
Helper functions to install and maintain the 'LaTeX' distribution named
'TinyTeX' (<https://yihui.name/tinytex/>), a lightweight,
cross-platform, portable, and easy-to-maintain version of 'TeX Live'.
This package also contains helper functions to compile 'LaTeX'
documents, and install missing 'LaTeX' packages automatically.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tinytex-r31-0.16-1 (Functions to Maintain 'TeX Live')
Helper functions to install and maintain the 'LaTeX' distribution named
'TinyTeX' (<https://yihui.name/tinytex/>), a lightweight,
cross-platform, portable, and easy-to-maintain version of 'TeX Live'.
This package also contains helper functions to compile 'LaTeX'
documents, and install missing 'LaTeX' packages automatically.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcppeigen-r32-0.3.3.5.0-2 (Rcpp Eigen templated linear algebra library)
R and Eigen integration using Rcpp. Eigen is a C++ template library
for linear algebra: matrices, vectors, numerical solvers and related
algorithms. It supports dense and sparse matrices on integer,
floating point and complex numbers, decompositions of such matrices,
and solutions of linear systems. Its performance on many algorithms
is comparable with some of the best implementations based on Lapack
and level-3 BLAS. The RcppEigen package includes the header files
from the Eigen C++ template library (currently version 3.2.0).
Thus users do not need to install Eigen itself in order to use
RcppEigen. Since version 3.1.1, Eigen is licensed under the
Mozilla Public License (version 2); earlier version were licensed
under the GNU LGPL version 3 or later. RcppEigen (the Rcpp
bindings/bridge to Eigen) is licensed under the GNU GPL version 2
 or later, as is the rest of Rcpp.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rstudioapi-r33-0.10-1 (Safely access the RStudio API)
This package provides functions to make it easy to access the RStudio
API when available, and provide informative error messages when not.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-usethis-r31-1.5.0-1 (Automate Package and Project Setup)
Automate package and project setup tasks that are otherwise performed
manually. This includes setting up unit testing, test coverage,
continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio'
projects, and more.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sem-r33-3.1-9-2 (Structural Equation Models)
This package contains functions for fitting general linear
structural equation models (with observed and unobserved
variables) using the RAM approach, and for fitting structural
equations in observed-variable models by two-stage least squares.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-st-r31-1.2.5-1 (Shrinkage t Statistic and CAT Score)
This package implements the "shrinkage t" statistic introduced in
Opgen-Rhein and Strimmer (2007) and a shrinkage estimate of the
"correlation-adjusted t-score" (CAT score) described in Zuber
and Strimmer (2009). It also offers a convenient interface to
a number of other regularized t-statistics commonly employed in
high-dimensional case-control studies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-spatial-r32-7.3-11-1 (Kriging and Point Pattern Analysis Functions)
Functions for kriging and point pattern analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-questionr-r36-0.7.0-1 (Functions to Make Surveys Processing Easier)
Set of functions to make the processing and analysis of surveys easier :
interactive shiny apps and addins for data recoding, contingency tables,
dataset metadata handling, and several convenience functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rms-r31-4.5-0-2 (Regression Modeling Strategies)
Regression modeling, testing, estimation, validation, graphics,
prediction, and typesetting by storing enhanced model design
attributes in the fit. rms is a collection of functions that
assist with and streamline modeling. It also contains functions
for binary and ordinal logistic regression models, ordinal
models for continuous Y with a variety of distribution families,
and the Buckley-James multiple regression model for
right-censored responses, and implements penalized maximum
likelihood estimation for logistic and ordinary linear models.
rms works with almost any regression model, but it was especially
written to work with binary or ordinal regression models,
Cox regression, accelerated failure time models, ordinary
linear models,        the Buckley-James model, generalized least
squares for serially or spatially correlated observations,
generalized linear models, and quantile regression.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-robcompositions-r32-2.0.10-1 (Robust Estimation for Compositional Data)
The package includes methods for imputation of compositional data
including robust methods, methods to impute rounded zeros, (robust)
outlier detection for compositional data, (robust) principal component
analysis for compositional data, (robust) factor analysis for
compositional data, (robust) discriminant analysis for compositional
data (Fisher rule), robust regression with compositional predictors and
(robust) Anderson-Darling normality tests for compositional data as well
as popular log-ratio transformations (addLR, cenLR, isomLR, and their
inverse transformations). In addition, visualisation and diagnostic
tools are implemented as well as high and low-level plot functions for
the ternary diagram.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-statmod-r33-1.4.32-2 (Statistical Modeling)
Various statistical modeling functions including growth curve comparisons,
limiting dilution analysis, mixed linear models, heteroscedastic regression,
Tweedie family generalized linear models, the inverse-Gaussian distribution
and Gauss quadrature.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rcgmin-r32-2013-2.21-1 (Conjugate Gradient Minimization)
Conjugate gradient minimization of nonlinear functions with box constraints
incorporating the Dai/Yuan update. This implementation should be used in
place of the "CG" algorithm of the optim() function.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-seriation-r34-1.2-8-2 (Infrastructure for seriation)
Infrastructure for seriation with an implementation of several
seriation/sequencing techniques to reorder matrices, dissimilarity
matrices, and dendrograms. Also contains some visualizations
techniques based on seriation.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rgtk2-r36-2.20.36-1 (R bindings for Gtk 2.8.0 and above)
Facilities in the R language for programming graphical
interfaces using Gtk, the Gimp Tool Kit.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tcltk2-r36-1.2-11-1 (Tcl/Tk Additions)
A series of additional Tcl commands and Tk widgets with style and
various functions (under Windows: DDE exchange, access to the
registry and icon manipulation) to supplement the tcltk package

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-simpleboot-r33-1.1-7-1 (GNU R Tools for simple bootstrap)
Simple bootstrap routines

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-polca-r34-1.4.1-1 (Polytomous variable Latent Class Analysis)
Latent class analysis and latent class regression models for
polytomous outcome variables. Also known as latent structure
analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tables-r33-0.8.8-1 (Formula-driven table generation)
Computes and displays complex tables of summary statistics

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-seriation-r36-1.2-8-2 (Infrastructure for seriation)
Infrastructure for seriation with an implementation of several
seriation/sequencing techniques to reorder matrices, dissimilarity
matrices, and dendrograms. Also contains some visualizations
techniques based on seriation.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rsclient-r33-0.7-3-2 (RSclient: Client for Rserve)
Client for Rserve, allowing to connect to Rserve instances
and issue commands.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sn-r35-1.5-4-1 (Skew-normal and skew-t distributions)
Define and manipulate probability distributions of the skew-normal
family and some related ones (notably the skew-t family) and provide
related statistical methods for data fitting and diagnostics, in the
univariate and in the multivariate case.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-spatial-r35-7.3-11-1 (Kriging and Point Pattern Analysis Functions)
Functions for kriging and point pattern analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sets-r35-1.0-18-1 (Generalized and Customizable Sets)
Data structures and basic operations for ordinary sets, generalizations
such as fuzzy sets, multisets, and fuzzy multisets, customizable sets,
and intervals.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-proto-r32-1.0.0-1 (Prototype object-based programming)
An object oriented system using object-based, also called
prototype-based, rather than class-based object oriented ideas.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-subplex-r36-1.5-4-2 (Subplex optimization algorithm)
The subplex algorithm for unconstrained optimization, developed by Tom Rowan.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rms-r36-5.1-3.1-2 (Regression Modeling Strategies)
Regression modeling, testing, estimation, validation, graphics,
prediction, and typesetting by storing enhanced model design
attributes in the fit. rms is a collection of functions that
assist with and streamline modeling. It also contains functions
for binary and ordinal logistic regression models, ordinal
models for continuous Y with a variety of distribution families,
and the Buckley-James multiple regression model for
right-censored responses, and implements penalized maximum
likelihood estimation for logistic and ordinary linear models.
rms works with almost any regression model, but it was especially
written to work with binary or ordinal regression models,
Cox regression, accelerated failure time models, ordinary
linear models,        the Buckley-James model, generalized least
squares for serially or spatially correlated observations,
generalized linear models, and quantile regression.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-vgam-r34-1.1-1-2 (Vector Generalized Linear and Additive Models)
Vector generalized linear and additive models, and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Reduced-Rank VGAMs). This
package fits many models and distribution by maximum likelihood
estimation (MLE) or penalized MLE. Also fits constrained ordination
models in ecology.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-tseries-r36-0.10-47-2 (Time series analysis and finance)
Package for time series analysis and computational finance

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-sca-r32-0.9-0-1 (Simple Component Analysis)
Simple Component Analysis (SCA) often provides much more interpretable
components than Principal Components (PCA) while still representing
much of the variability in the data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-qvcalc-r32-1.0.1-1 (Quasi Variances for Effects in Stat Models)
Functions to compute quasi variances and associated measures of
approximation error.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-titan-r36-1.0-16-2 (Titration analysis for mass spec data)
GUI to analyze mass spectrometric data on the relative
abundance of two substances from a titration series.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r.oo-r34-1.22.0-1 (R object-oriented programming)
Methods and classes for object-oriented programming in R
with or without references.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-whisker-r36-0.4-1 ({{mustache}} for R, logicless templating)
logicless templating, reuse templates in many programming
languages including R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rgl-r34-0.100.30-1 (3D visualization device system)
Provides medium to high level functions for 3D interactive graphics,
including functions modelled on base graphics (plot3d(), etc.) as
well as functions for constructing representations of geometric objects
(cube3d(), etc.). Output may be on screen using OpenGL, or to various
standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
image formats, including PNG, Postscript, SVG, PGF.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rjava-r32-0.9-8-2 (Low-level R to Java interface)
Low-level interface to Java VM very much like .C/.Call and friends.
Allows creation of objects, calling methods and accessing fields.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-qvcalc-r35-1.0.1-1 (Quasi Variances for Effects in Stat Models)
Functions to compute quasi variances and associated measures of
approximation error.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-reactran-r33-1.4.3.1-2 (Reactive transport modelling in 1D, 2D and 3D)
Routines for developing models that describe reaction and
advective-diffusive transport in one, two or three dimensions.
Includes transport routines in porous media, in estuaries, and
in bodies with variable shape.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-sn-r34-1.5-4-1 (Skew-normal and skew-t distributions)
Define and manipulate probability distributions of the skew-normal
family and some related ones (notably the skew-t family) and provide
related statistical methods for data fitting and diagnostics, in the
univariate and in the multivariate case.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rmutil-r31-1.1.3-1 (Repeated Measurements Models Utilities)
A toolkit of functions for nonlinear regression and repeated
measurements not to be used by itself but called by other Lindsey
packages such as 'gnlm', 'stable', 'growth', 'repeated', and 'event'
(available at http://www.commanster.eu/rcode.html).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-timp-r36-1.13.2-1 (Fitting separable nonlinear models)
TIMP is a problem solving environment for fitting separable nonlinear
models to measurements arising in physics and chemistry experiments,
and has been extensively applied to time-resolved spectroscopy and
FLIM-FRET data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sourcetools-r32-0.1.7-1 (Reading, Tokenizing and Parsing R Code)
Tools for the reading and tokenization of R code. The 'sourcetools'
package provides both an R and C++ interface for the tokenization of 
R code, and helpers for interacting with the tokenized representation
of R code.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcmdr-r33-2.4-2-1 (R Commander)
A platform-independent basic-statistics GUI (graphical user
interface) for R, based on the tcltk package.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r2html-r31-2.3.2-1 (HTML exportation for R objects)
Includes HTML function and methods to write in an HTML file.
Thus, making HTML reports is easy. Includes a function that
allows redirection on the fly, which appears to be very usefull
for teaching purpose, as the student can keep a copy of the
produced output to keep all that he did during the course.
Package comes with a vignette describing how to write HTML
reports for statistical analysis. Finally, a driver for Sweave
allows to parse HTML flat files containing R code and to
automatically write the corresponding outputs (tables and graphs).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-zeallot-r35-0.1.0-1 (Multiple/Unpacking/Destructuring Assignment)
Provides a %<-% operator to perform multiple, unpacking, and 
destructuring assignment in R. The operator unpacks the right-hand 
side of an assignment into multiple values and assigns these 
values to variables on the left-hand side of the assignment.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-shiny-r35-1.3.2-1 (Web Application Framework for R)
Makes it incredibly easy to build interactive web applications with R. 
Automatic "reactive" binding between inputs and outputs and extensive 
pre-built widgets make it possible to build beautiful, responsive, 
and powerful applications with minimal effort.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcmdrplugin.ezr-r35-1.40-1 (Easy R for medical statistics)
Easy R for medical statistics

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcmdrplugin.doby-r34-0.1-3-1 (Rcmdr doBy Plug-In)
This package provides an Rcmdr "plug-in" for the core doBy functions
in the doBy package, which helps with computing groupwise summary statistics.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tripack-r36-1.3-8-2 (Triangulation of irregularly spaced data)
A constrained two-dimensional Delaunay triangulation package

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rmpi-r31-0.6-9-1 (R Interface Wrapper to MPI)
Rmpi provides an interface (wrapper) to MPI APIs. It also provides
an interactive R slave environment.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-vcd-r36-1.4-4-1 (Visualizing Categorical Data)
Visualization techniques, data sets, summary and inference procedures
aimed particularly at categorical data. Special emphasis is given to
highly extensible grid graphics. The package was inspired by the book
"Visualizing Categorical Data" by Michael Friendly.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-processx-r36-3.4.1-1 (Execute and Control System Processes)
Tools to run system processes in the background. It can check if a
background process is running; wait on a background process to finish;
get the exit status of finished processes; kill background processes. It
can read the standard output and error of the processes, using
non-blocking connections. 'processx' can poll a process for standard
output or error, with a timeout. It can also poll several processes at
once.

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2020-01-16: cran-rgl-r35-0.100.30-1 (3D visualization device system)
Provides medium to high level functions for 3D interactive graphics,
including functions modelled on base graphics (plot3d(), etc.) as
well as functions for constructing representations of geometric objects
(cube3d(), etc.). Output may be on screen using OpenGL, or to various
standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
image formats, including PNG, Postscript, SVG, PGF.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcmdcheck-r32-1.3.3-1 (Run 'R CMD check' from 'R')
Run 'R CMD check' from 'R' programmatically, and capture the results of
the individual checks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-r.methodss3-r35-1.7.1-1 (Utility function for defining S3 methods)
Methods that simplify the setup of S3 generic functions and S3 methods.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rtsne-r31-0.15-2 (T-distributed Stochastic Neighbor Embedding)
An R wrapper around the fast T-distributed Stochastic 
Neighbor Embedding implementation by Van der Maaten.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-zeallot-r32-0.1.0-1 (Multiple/Unpacking/Destructuring Assignment)
Provides a %<-% operator to perform multiple, unpacking, and 
destructuring assignment in R. The operator unpacks the right-hand 
side of an assignment into multiple values and assigns these 
values to variables on the left-hand side of the assignment.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-qap-r35-0.1-1-1 (Heuristics for Quadratic Assignment Problem)
Implements heuristics for the Quadratic Assignment Problem (QAP). 
Currently only a simulated annealing heuristic is available.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rweka-r34-0.4-40-1 (R/Weka interface)
An R interface to Weka (Version 3.7.11). Weka is a collection of machine
learning algorithms for data mining tasks written in Java, containing
tools for data pre-processing, classification, regression, clustering,
association rules, and visualization. Package RWeka contains the interface
code, the Weka jar is in a separate package RWekajars. For more information
on Weka see http://www.cs.waikato.ac.nz/~ml/weka/.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-truncnorm-r32-1.0-7-1 (Truncated Normal Distribution)
Density, probability, quantile and random number generation functions
for the truncated normal distribution.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rhpcblasctl-r32-0.18-205-1 (Control the Number of Threads on 'BLAS')
Control the number of threads on 'BLAS' (Aka 'GotoBLAS', 'OpenBLAS',
'ACML', 'BLIS' and 'MKL'). And possible to control the number of threads
in 'OpenMP'. Get a number of logical cores and physical cores if
feasible.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tidyr-r32-1.0.0-2 (Easily Tidy Data)
An evolution of 'reshape2'. It's designed specifically for data 
tidying (not general reshaping or aggregating) and works well 
with 'dplyr' data pipelines.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-polynomf-r36-2.0-2-1 (Polynomials in R)
Implements univariate polynomial operations in R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcgmin-r35-2013-2.21-1 (Conjugate Gradient Minimization)
Conjugate gradient minimization of nonlinear functions with box constraints
incorporating the Dai/Yuan update. This implementation should be used in
place of the "CG" algorithm of the optim() function.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-robcompositions-r35-2.0.10-1 (Robust Estimation for Compositional Data)
The package includes methods for imputation of compositional data
including robust methods, methods to impute rounded zeros, (robust)
outlier detection for compositional data, (robust) principal component
analysis for compositional data, (robust) factor analysis for
compositional data, (robust) discriminant analysis for compositional
data (Fisher rule), robust regression with compositional predictors and
(robust) Anderson-Darling normality tests for compositional data as well
as popular log-ratio transformations (addLR, cenLR, isomLR, and their
inverse transformations). In addition, visualisation and diagnostic
tools are implemented as well as high and low-level plot functions for
the ternary diagram.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-readxl-r31-1.3.1-2 (Read Excel Files)
Import excel files into R. Supports '.xls' via the embedded
'libxls' C library (http://sourceforge.net/projects/libxls/)
and '.xlsx' via the embedded 'RapidXML' C++ library
(http://rapidxml.sourceforge.net). Works on Windows, Mac
 and Linux without external dependencies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rcurl-r36-1.95-4.12-1 (Network client (HTTP/FTP/...) R interface)
The package allows one to compose general HTTP requests and provides
convenient functions to fetch URIs, get & post forms, etc. and process
the results returned by the Web server. This provides a great deal of
control over the HTTP/FTP/... connection and the form of the request 
while providing a higher-level interface than is available just using
R socket connections. Additionally, the underlying implementation is
robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads),
SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects,
authentication, etc.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-timp-r33-1.13.2-1 (Fitting separable nonlinear models)
TIMP is a problem solving environment for fitting separable nonlinear
models to measurements arising in physics and chemistry experiments,
and has been extensively applied to time-resolved spectroscopy and
FLIM-FRET data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-roxygen2-r33-6.1.1-1 (In-source documentation for R)
A Doxygen-like in-source documentation system for Rd, collation,
and NAMESPACE.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-readstata13-r35-0.9.2-2 (Import 'Stata' Data Files)
Function to read and write the 'Stata' file format.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-quadprog-r32-1.5-7-2 (Functionss for Quadratic Programming Problems)
This package contains routines and documentation for solving
quadratic programming problems.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-vcd-r31-1.4-4-1 (Visualizing Categorical Data)
Visualization techniques, data sets, summary and inference procedures
aimed particularly at categorical data. Special emphasis is given to
highly extensible grid graphics. The package was inspired by the book
"Visualizing Categorical Data" by Michael Friendly.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rpanel-r32-1.1-4-1 (Simple interactive controls)
rpanel provides a set of functions to build simple GUI controls for
R functions. These are built on the tcltk package. Uses could include
changing a parameter on a graph by animating it with a slider or a
"doublebutton", up to more sophisticated control panels. Some functions
for specific graphical tasks, referred to as 'cartoons', are provided.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-polynom-r36-1.4-0-1 (Univariate polynomial manipulations in R)
A collection of functions to implement a class for univariate
polynomial manipulations.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rsvgdevice-r33-0.6.4.4-2 (R SVG graphics device)
A graphics device for R that uses the w3.org xml standard
for Scalable Vector Graphics.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rsvgdevice-r36-0.6.4.4-2 (R SVG graphics device)
A graphics device for R that uses the w3.org xml standard
for Scalable Vector Graphics.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rhpcblasctl-r33-0.18-205-1 (Control the Number of Threads on 'BLAS')
Control the number of threads on 'BLAS' (Aka 'GotoBLAS', 'OpenBLAS',
'ACML', 'BLIS' and 'MKL'). And possible to control the number of threads
in 'OpenMP'. Get a number of logical cores and physical cores if
feasible.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-scrime-r31-1.3.5-1 (Analysis of High-Dimensional Categorical Data)
Tools for the analysis of high-dimensional data developed/implemented 
at the group "Statistical Complexity Reduction In Molecular Epidemiology" 
(SCRIME). Main focus is on SNP data. But most of the functions can also 
be applied to other types of categorical data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    New upstream Bioconductor versions (bioc 3.10)
2020-01-16: cran-survival-r35-2.44-1.1-1 (GNU R Tools for survival analysis)
survival analysis: descriptive statistics, two-sample tests,
parametric accelerated failure models, Cox model.
Delayed entry (truncation) allowed for all models;
interval censoring for parametric models. Case-cohort designs.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-stepplr-r32-0.93-2 (L2 penalized logistic regression)
L2 penalized logistic regression for both continuous and discrete
predictors, with forward stagewise/forward stepwise variable
selection procedure.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-scales-r31-1.0.0-1 (Scale functions for graphics)
Scales map data to aesthetics, and provide methods for automatically
determining breaks and labels for axes and legends.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sourcetools-r36-0.1.7-1 (Reading, Tokenizing and Parsing R Code)
Tools for the reading and tokenization of R code. The 'sourcetools'
package provides both an R and C++ interface for the tokenization of 
R code, and helpers for interacting with the tokenized representation
of R code.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-wccsom-r32-1.2.11-1 (SOM networks for patterns with peak shifts)
SOM networks for comparing patterns with peak shifts.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tframe-r36-2015.12-1.1-1 (Time Frame coding kernel)
The tframe package provides a kernel of functions for programming
time series methods in a way that is relatively independently of
the representation of time. It also provides plotting, time
windowing, and some other utility functions which are specifically
intended for time series. See the Guide distributed as a vignette,
or ?tframe.Intro for more details. (User utilities other than the
programming kernel have been moved into package tfplot.)

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r.matlab-r36-3.6.2-1 (Read and write of MAT files)
This package provides methods readMat() and writeMat() to read
and write MAT files. It also makes it possible to communicate
(evaluate code, send and retrieve objects etc.) with MATLAB v6
or higher running locally or on a remote host.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-scarabee-r36-1.1-3-2 (R port of the Scarabee toolkit)
scaRabee is a port of the Scarabee toolkit originally written as a Matlab-based
application. It provides a framework for simulation and optimization of
pharmacokinetic-pharmacodynamic models at the individual and population level.
It is built on top of the neldermead package, which provides the direct search
algorithm proposed by Nelder and Mead for model optimization.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-ppls-r34-1.6-1.1-1 (Penalized Partial Least Squares)
This package contains linear and nonlinear regression methods based
on Partial Least Squares and Penalization Techniques. Model parameters
are selected via cross-validation, and confidence intervals ans tests
for the regression coefficients can be conducted via jackknifing.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-xts-r35-0.11-2-2 (The eXtensible Time Series)
Provide for uniform handling of R's different time-based data classes
by extending zoo, maximizing native format information preservation
and allowing for user level customization and extension, while
simplifying cross-class interoperability.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-pryr-r31-0.1.4-1 (Tools for Computing on the Language)
Useful tools to pry back the covers of R and understand the language at
a deeper level.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-trimcluster-r34-0.1-2.1-1 (Cluster analysis with trimming)
Trimmed k-means clustering.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-urca-r35-1.3-0-2 (Unit Root and Cointegration Tests)
Unit root and cointegration tests encountered in applied econometric
analysis are implemented.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rvest-r31-0.3.2-1 (Easily harvest web pages)
Wrappers around the 'xml2' and 'httr' packages to make it easy to
download, then manipulate, HTML and XML.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-progress-r36-1.2.2-1 (Statnet project common scripts and utilities)

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-resemble-r36-1.2.2-3 (Similarity/dissimilarity and MBL analysis)
This package implements functions for spectral similarity/dissimilarity
analysis and memory-based learning (MBL) for non-linear modelling in
complex spectral datasets. MBL is also known as local modelling in the
chemometrics literature.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-shiny-r32-1.3.2-1 (Web Application Framework for R)
Makes it incredibly easy to build interactive web applications with R. 
Automatic "reactive" binding between inputs and outputs and extensive 
pre-built widgets make it possible to build beautiful, responsive, 
and powerful applications with minimal effort.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-robustbase-r31-0.93-5-2 (GNU R Tools for robust methods)
"Essential" Robust Statistics.
The goal is to provide tools allowing to analyze data with robust methods.
This includes regression methodology including model selections and
multivariate statistics where we strive to cover the book
"Robust Statistics, Theory and Methods" by Maronna, Martin and Yohai;
Wiley 2006.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-vrmlgen-r35-1.4.9-1 (Generate 3D visualizations)
vrmlgen creates 3D scatter and bar plots, visualizations of 3D meshes,
parametric functions and height maps in web-formats like the Virtual
Reality Markup Language (VRML, filetype .wrl) and the LiveGraphics3D format.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-prim-r36-1.0.16-1 (Patient Rule Induction Method)
PRIM for bump hunting in high-dimensional data

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sparsem-r31-1.77-2 (Sparse Linear Algebra)
Basic linear algebra for sparse matrices

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rhpcblasctl-r36-0.18-205-1 (Control the Number of Threads on 'BLAS')
Control the number of threads on 'BLAS' (Aka 'GotoBLAS', 'OpenBLAS',
'ACML', 'BLIS' and 'MKL'). And possible to control the number of threads
in 'OpenMP'. Get a number of logical cores and physical cores if
feasible.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-raster-r35-3.0-7-1 (Geographic data analysis and modeling)
Reading, writing, manipulating, analyzing and modeling of gridded spatial
data. The package implements basic and high-level functions. Processing of
very large files is supported.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcpproll-r31-0.3.0-1 (Efficient Rolling / Windowed Operations)
Provides fast and efficient routines for common rolling / windowed
operations. Routines for the efficient computation of windowed mean,
median, sum, product, minimum, maximum, standard deviation and variance
are provided.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sandwich-r35-2.5-1-1 (GNU R std err estimators for time-series data)
sandwich: Robust Covariance Matrix Estimators
Model-robust standard error estimators for cross-sectional, 
time series, and longitudinal data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-varselrf-r31-0.7-8-1 (Variable selection using random forests)
Variable selection from random forests using both backwards variable
elimination (for the selection of small sets of non-redundant variables)
and selection based on the importance spectrum (somewhat similar to
scree plots; for the selection of large, potentially highly-correlated
variables). Main applications in high-dimensional data (e.g., microarray
data, and other genomics and proteomics applications). You can use rpvm
instead of Rmpi if you want but I've only tested with Rmpi.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tidyr-r35-1.0.0-2 (Easily Tidy Data)
An evolution of 'reshape2'. It's designed specifically for data 
tidying (not general reshaping or aggregating) and works well 
with 'dplyr' data pipelines.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-vctrs-r34-0.2.0-2 (Vector Helpers)
Defines new notions of prototype and size that are used to provide 
tools for consistent and well-founded type-coercion and size-recycling, 
and are in turn connected to ideas of type- and size-stability useful 
for analyzing function interfaces.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-sgeostat-r31-1.0-27-3 (Framework for Geostatistical Modeling in S+)
An Object-oriented Framework for Geostatistical Modeling in S+

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rcmdrplugin.survival-r36-1.2-0-1 (R Commander Plug-in for the survival Package)
This package provides an R Commander plug-in for the survival package,
with dialogs for Cox models, parametric survival regression models,
estimation of survival curves, and testing for differences in survival
curves, along with data-management facilities and a variety of tests,
and graphs.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sourcetools-r33-0.1.7-1 (Reading, Tokenizing and Parsing R Code)
Tools for the reading and tokenization of R code. The 'sourcetools'
package provides both an R and C++ interface for the tokenization of 
R code, and helpers for interacting with the tokenized representation
of R code.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rwave-r31-2.4-8-1 (Time-Frequency analysis of 1-D signals)
Rwave is a library of R functions which provide an environment for
the Time-Frequency analysis of 1-D signals (and especially for the
wavelet and Gabor transforms of noisy signals). It was originally
written for Splus by Rene Carmona, Bruno Torresani, and Wen L. 
wang, first at the University of California at Irvine and then
at Princeton University. Credit should also be given to Andrea
Wang whose functions on the dyadic wavelet transform are included.
Rwave is based on the book: "Practical Time-Frequency Analysis:
Gabor and Wavelet Transforms with an Implementation in S", by Rene
Carmona, Wen L. Hwang and Bruno Torresani, Academic Press, 1998.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-zoo-r33-1.8-5-1 (GNU R Tools for ir/regular time series)
zoo: S3 Infrastructure for Regular and 
Irregular Time Series (Z's ordered observations)

An S3 class with methods for totally ordered indexed observations. 
It is particularly aimed at irregular time series of numeric vectors/matrices 
and factors.  zoo's key design goals are independence of a particular 
index/date/time class and consistency with ts and base R by providing 
methods to extend standard generics.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-ppls-r35-1.6-1.1-1 (Penalized Partial Least Squares)
This package contains linear and nonlinear regression methods based
on Partial Least Squares and Penalization Techniques. Model parameters
are selected via cross-validation, and confidence intervals ans tests
for the regression coefficients can be conducted via jackknifing.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-vrmlgen-r32-1.4.9-1 (Generate 3D visualizations)
vrmlgen creates 3D scatter and bar plots, visualizations of 3D meshes,
parametric functions and height maps in web-formats like the Virtual
Reality Markup Language (VRML, filetype .wrl) and the LiveGraphics3D format.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-urca-r34-1.3-0-2 (Unit Root and Cointegration Tests)
Unit root and cointegration tests encountered in applied econometric
analysis are implemented.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-withr-r36-2.1.2-1 (Run Code w/ Temporarily Modified Global State)
A set of functions to run code 'with' safely and temporarily 
modified global state. Many of these functions were originally 
a part of the 'devtools' package, this provides a simple package 
with limited dependencies to provide access to these functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-shape-r31-1.4.4-1 (Plotting graphical shapes, colors)
Functions for plotting graphical shapes such as ellipses,
circles, cylinders, arrows, ...

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sparsem-r34-1.77-2 (Sparse Linear Algebra)
Basic linear algebra for sparse matrices

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-tester-r36-0.1.7-1 (Tests and checks characteristics of R objects)
tester allows you to test characteristics of common R objects.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-stepplr-r35-0.93-2 (L2 penalized logistic regression)
L2 penalized logistic regression for both continuous and discrete
predictors, with forward stagewise/forward stepwise variable
selection procedure.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-vimgui-r32-0.9.0-1 (Visualization & Imputation of Missing Values)
This package introduces new tools for the visualization of missing and/or
imputed values, which can be used for exploring the data and the structure
of the missing and/or imputed values. Depending on this structure of the
missing values, the corresponding methods may help to identify the mechanism
generating the missings and allows to explore the data including missing
values. In addition, the quality of imputation can be visually explored
using various univariate, bivariate, multiple and multivariate plot methods.
A graphical user interface allows an easy handling of the implemented plot
methods.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sgeostat-r34-1.0-27-3 (Framework for Geostatistical Modeling in S+)
An Object-oriented Framework for Geostatistical Modeling in S+

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rcppziggurat-r32-0.1.5-1 (Integration of Ziggurat RNG Implementations)
The Ziggurat generator for normally distributed random numbers,
originally proposed by Marsaglia and Tsang (2000,
) has been improved upon a few times starting
with Leong et al (2005, ). This package
provides an aggregation in order to compare different implementations in
order to provide an 'faster but good enough' alternative for use with R
and C++ code.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-varselrf-r34-0.7-8-1 (Variable selection using random forests)
Variable selection from random forests using both backwards variable
elimination (for the selection of small sets of non-redundant variables)
and selection based on the importance spectrum (somewhat similar to
scree plots; for the selection of large, potentially highly-correlated
variables). Main applications in high-dimensional data (e.g., microarray
data, and other genomics and proteomics applications). You can use rpvm
instead of Rmpi if you want but I've only tested with Rmpi.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcpproll-r34-0.3.0-1 (Efficient Rolling / Windowed Operations)
Provides fast and efficient routines for common rolling / windowed
operations. Routines for the efficient computation of windowed mean,
median, sum, product, minimum, maximum, standard deviation and variance
are provided.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-prim-r33-1.0.16-1 (Patient Rule Induction Method)
PRIM for bump hunting in high-dimensional data

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-randomforest-r33-4.6-12-1 (GNU R Tools for random forest class/regress)
Classification and regression based on a forest of trees using random inputs.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-proj4-r31-1.0-9-102 (PROJ.4 cartographic projections library for R)
PROJ.4 cartographic projections library for R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-polycor-r35-0.7-10-1 (Polychoric and Polyserial Correlations)
Computes polychoric and polyserial correlations by quick "two-step"
methods or ML, optionally with standard errors; tetrachoric
and biserial correlations are special cases.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-teachingdemos-r32-2.10-2 (Demonstrations for Teaching and Learning)
Demonstration functions that can be used in a classroom to 
demonstrate statistical concepts, or on your own to better 
understand the concepts or the programming.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-ranger-r36-0.11.2-1 (Manage Life Cycle of Package)
This package can be used to solve Linear Programming / Linear 
Optimization problems by using the simplex algorithm.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r2stats-r33-0.68-39-1 (GTK GUI for fitting and comparing GLM and GLM)
R2STATS is a gWidgetsRGtk2 GUI for fitting and comparing GLM or GLMM (based
on Douglas Bates' lme4 package) in R. It is designed to make comparisons
between numerous models easy, both numerically and graphically, which may
be useful for teaching. Relevant plots are automatically produced for each
model family. R2STATS is *not* a generic graphical interface for R, but a
GUI for statistical modelling in a model comparison approach.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcmdrmisc-r35-1.0-9-1 (R Commander Miscellaneous Functions)
Various statistical, graphics, and data-management functions
used by the Rcmdr package in the R Commander GUI for R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-trust-r33-0.1-7-1 (Trust Region Optimization)
local optimization using two derivatives and trust regions

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tis-r33-1.37.1-1 (Time Indexes and Time Indexed Series)
Functions and S3 classes for time indexes and time indexed
series, which are compatible with FAME frequencies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-purrr-r31-0.3.2-3 (Functional Programming Tools)
Make your pure functions purr with the 'purrr' package. This package 
completes R's functional programming tools with missing features present 
in other programming languages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-vimgui-r35-0.10.0-1 (Visualization & Imputation of Missing Values)
This package introduces new tools for the visualization of missing and/or
imputed values, which can be used for exploring the data and the structure
of the missing and/or imputed values. Depending on this structure of the
missing values, the corresponding methods may help to identify the mechanism
generating the missings and allows to explore the data including missing
values. In addition, the quality of imputation can be visually explored
using various univariate, bivariate, multiple and multivariate plot methods.
A graphical user interface allows an easy handling of the implemented plot
methods.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-visnetwork-r34-2.0.8-1 (Network Visualization)
Provides an R interface to the 'vis.js' JavaScript charting library. It
allows an interactive visualization of networks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-ptw-r33-1.9-13-1 (Parametric Time Warping)
Parametric Time Warping aligns patterns, i.e. it aims to put corresponding
features at the same locations. The algorithm searches for an optimal
polynomial describing the warping. It is possible to align one sample
to a reference, several samples to the same reference, or several samples
to several references. One can choose between calculating individual
warpings, or one global warping for a set of samples and one reference.
Two optimization criteria are implemented: RMS (Root Mean Square error)
and WCC (Weighted Cross Correlation).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-survey-r34-3.36-1 (Analysis of complex survey samples)
Summary statistics, two-sample tests, generalised linear models,
cumulative link models, Cox models, loglinear models, and general
maximum pseudolikelihood estimation for multistage stratified,
cluster-sampled, unequally weighted survey samples. Variances by
Taylor series linearisation or replicate weights. Post-stratification,
calibration, and raking. Two-phase subsampling designs. Graphics.
Predictive margins by direct standardization. PPS sampling without
replacement. Principal components, factor analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sp-r31-1.3-1-1 (GNU R classes and methods for spatial data)
GNU R classes and methods for spatial data

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rwekajars-r34-3.9.3-1-1 (R/Weka interface jars)
External jars required for package RWeka.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-prodlim-r32-2018.04.18-1 (GNU R Tools for estimation of survival)
Fast and user friendly nonparametric estimation in 
censored survival (event history) analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rglwidget-r34-0.2.1-1 (Rgl in htmlwidgets Framework)
Provides an 'htmlwidgets' framework for the 'rgl' package.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-recipes-r35-0.1.7-1 (Preprocessing Tools to Create Design Matrices)
An extensible framework to create and preprocess design matrices.
Recipes consist of one or more data manipulation and analysis "steps".
Statistical parameters for the steps can be estimated from an initial
data set and then applied to other data sets. The resulting design
matrices can then be used as inputs into statistical or machine learning
models.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-randomfields-r34-3.3.6-2 (Simulation and Analysis of Random Fields)
Simulation of Gaussian and extreme value random fields; conditional
simulation; kriging; maximum likelihood estimation

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-simpleboot-r36-1.1-7-1 (GNU R Tools for simple bootstrap)
Simple bootstrap routines

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcpparmadillo-r35-0.9.800.1.0-2 (Rcpp integration for Armadillo)
R and Armadillo integration using Rcpp Armadillo is a templated
C++ linear algebra library (by Conrad Sanderson) that aims towards
a good balance between speed and ease of use. Integer, floating
point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions
are provided through optional integration with LAPACK and ATLAS
libraries. A delayed evaluation approach is employed (during compile
time) to combine several operations into one, and to reduce (or
eliminate) the need for temporaries. This is accomplished through
recursive templates and template meta-programming. This library is
useful if C++ has been decided as the language of choice (due
to speed and/or integration capabilities), rather than another
language. The RcppArmadillo package includes the header files
from the templated Armadillo library. Thus users do not need to
install Armadillo itself in order to use RcppArmadillo. This
Armadillo integration provides a nice illustration of the
capabilities of the Rcpp package for seamless R and C++
integration. Armadillo is licensed under the MPL 2.0, while
RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is
licensed under the GNU GPL version 2 or later, as is the
rest of Rcpp.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-raster-r32-3.0-7-1 (Geographic data analysis and modeling)
Reading, writing, manipulating, analyzing and modeling of gridded spatial
data. The package implements basic and high-level functions. Processing of
very large files is supported.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-yaml-r33-2.2.0-1 (Libyaml YAML 1.1 parser and emitter for R)
This package implements the libyaml YAML 1.1 parser and emitter 
(http://pyyaml.org/wiki/LibYAML) for R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rwekajars-r36-3.9.3-1-1 (R/Weka interface jars)
External jars required for package RWeka.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-prospectr-r33-0.1.3-4 (Processing and sample selection of vis-NIR)
The package provides functions for pretreatment and sample selection
of visible and near infrared diffuse reflectance spectra

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rglwidget-r36-0.2.1-1 (Rgl in htmlwidgets Framework)
Provides an 'htmlwidgets' framework for the 'rgl' package.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcmdrmisc-r31-1.0-9-1 (R Commander Miscellaneous Functions)
Various statistical, graphics, and data-management functions
used by the Rcmdr package in the R Commander GUI for R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r2winbugs-r32-2.1-21-1 (Running WinBUGS and OpenBUGS from R / S-PLUS)
Using this package, it is possible to call a BUGS model, summarize
inferences and convergence in a table and graph, and save the
simulations in arrays for easy access in R / S-PLUS. In S-PLUS,
the openbugs functionality and the windows emulation functionality
is not yet available.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rgenoud-r34-5.8-3.0-1 (GENetic Optimization Using Derivatives)
A genetic algorithm plus derivative optimizer

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rio-r32-0.5.16-2 (Swiss-Army Knife for Data I/O)
Streamlined data import and export by making assumptions that the user
is probably willing to make: 'import()' and 'export()' determine the
data structure from the file extension, reasonable defaults are used for
data import and export (e.g., 'stringsAsFactors=FALSE'), web-based
import is natively supported (including from SSL/HTTPS), compressed
files can be read directly without explicit decompression, and fast
import packages are used where appropriate. An additional convenience
function, 'convert()', provides a simple method for converting between
file types.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcdklibs-r31-2.0-1 (CDK libraries packaged for R)
This package provides the CDK libraries for use in the R environment.
Given the size of the library itself, this package is not expected to
change very frequently. To make use of the CDK within R, it is suggested
that you use the rcdk package. Note that it is possible to directly
interact with the CDK using rJava. However rcdk exposes functionality
in a more idiomatic way

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-prodlim-r35-2018.04.18-1 (GNU R Tools for estimation of survival)
Fast and user friendly nonparametric estimation in 
censored survival (event history) analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-pomp-r36-2.3-2 (Partially observed Markov processes methods)
Inference methods for partially-observed Markov processes

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rstudioapi-r36-0.10-1 (Safely access the RStudio API)
This package provides functions to make it easy to access the RStudio
API when available, and provide informative error messages when not.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rpart-r33-4.1-15-1 (GNU R Tools for recursive partitioning)
Recursive partitioning and regression trees

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-relaimpo-r32-2.2-3-1 (Relative importance of regressors)
relaimpo provides several metrics for assessing relative importance
in linear models. These can be printed, plotted and bootstrapped.
The recommended metric is lmg, which provides a decomposition of
the model explained variance into non-negative contributions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-readr-r31-1.3.1-1 (Read Rectangular Text Data)
The goal of 'readr' is to provide a fast and friendly way to read
rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to
flexibly parse many types of data found in the wild, while still
cleanly failing when data unexpectedly changes.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-pscl-r31-1.5.2-1 (Political Science Computational Laboratory)
Bayesian analysis of item-response theory (IRT) models, roll call analysis;
computing highest density regions; maximum likelihood estimation of zero-
inflated and hurdle models for count data; goodness-of-fit measures for
GLMs; data sets used in writing and teaching at the Political Science
Computational Laboratory; seats-votes curves.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-recipes-r32-0.1.7-1 (Preprocessing Tools to Create Design Matrices)
An extensible framework to create and preprocess design matrices.
Recipes consist of one or more data manipulation and analysis "steps".
Statistical parameters for the steps can be estimated from an initial
data set and then applied to other data sets. The resulting design
matrices can then be used as inputs into statistical or machine learning
models.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rgenoud-r31-5.8-3.0-1 (GENetic Optimization Using Derivatives)
A genetic algorithm plus derivative optimizer

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-praise-r36-1.0.0-1 (Praise Users)
Build friendly R packages that praise their users if they have 
done something good, or they just need it to feel better.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcmdrplugin.ezr-r33-1.40-1 (Easy R for medical statistics)
Easy R for medical statistics

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-proto-r35-1.0.0-1 (Prototype object-based programming)
An object oriented system using object-based, also called
prototype-based, rather than class-based object oriented ideas.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-xts-r34-0.11-2-2 (The eXtensible Time Series)
Provide for uniform handling of R's different time-based data classes
by extending zoo, maximizing native format information preservation
and allowing for user level customization and extension, while
simplifying cross-class interoperability.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-tkrplot-r33-0.0-24-1 (TK Rplot)
simple mechanism for placing R graphics in a Tk widget

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-polycor-r32-0.7-8-2 (Polychoric and Polyserial Correlations)
Computes polychoric and polyserial correlations by quick "two-step"
methods or ML, optionally with standard errors; tetrachoric
and biserial correlations are special cases.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-prabclus-r33-2.3-1-1 (Functions for Clustering)
Distance-based parametric bootstrap tests for clustering with spatial
neighborhood information. Some distance measures, Clustering of
presence-absence, abundance and multilocus genetical data for
species delimitation, nearest neighbor based noise detection.
Try package?prabclus for on overview.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcompression-r33-0.93-2-1 (R Package for in-memory compression)
This package is a basic R interface to the zlib and bzip2 facilities for 
compressing and uncompressing data that are in memory rather than in files.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-yaml-r36-2.2.0-1 (Libyaml YAML 1.1 parser and emitter for R)
This package implements the libyaml YAML 1.1 parser and emitter 
(http://pyyaml.org/wiki/LibYAML) for R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rrcov-r34-1.4-7-2 (Scalable Robust Estimators)
Robust Location and Scatter Estimation and Robust Multivariate
Analysis with High Breakdown Point.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rcmdrplugin.ma-r36-0.0-2-1 (GUI for Conducting Meta-Analyses in R)
This is an R-Commander plug-in for meta-analysis. This package enables
the user to conduct a meta-analysis in a menu-driven, graphical user
interface environment (e.g., SPSS). It uses recommended procedures as
described in The Handbook of Research Synthesis and Meta-Analysis
(Cooper, Hedges, & Valentine, 2009).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcdklibs-r34-2.0-1 (CDK libraries packaged for R)
This package provides the CDK libraries for use in the R environment.
Given the size of the library itself, this package is not expected to
change very frequently. To make use of the CDK within R, it is suggested
that you use the rcdk package. Note that it is possible to directly
interact with the CDK using rJava. However rcdk exposes functionality
in a more idiomatic way

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rjava-r35-0.9-8-2 (Low-level R to Java interface)
Low-level interface to Java VM very much like .C/.Call and friends.
Allows creation of objects, calling methods and accessing fields.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tables-r34-0.8.8-1 (Formula-driven table generation)
Computes and displays complex tables of summary statistics

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rocr-r33-1.0-7-1 (Visualizing scoring classifier performance)
ROC graphs, sensitivity/specificity curves, lift charts, and
precision/recall plots are popular examples of trade-off
visualizations for specific pairs of performance measures. ROCR
is a flexible tool for creating cutoff-parameterized 2D
performance curves by freely combining two from over 25
performance measures (new performance measures can be added
using a standard interface). Curves from different cross-
alidation or bootstrapping runs can be averaged by different
methods, and standard deviations, standard errors or box plots
can be used to visualize the variability across the runs. The
parameterization can be visualized by printing cutoff values
at the corresponding curve positions, or by coloring the curve
according to cutoff. All components of a performance plot can
be quickly adjusted using a flexible parameter dispatching
mechanism. Despite its flexibility, ROCR is easy to use, with
only three commands and reasonable default values for all
optional parameters.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcppeigen-r33-0.3.3.5.0-2 (Rcpp Eigen templated linear algebra library)
R and Eigen integration using Rcpp. Eigen is a C++ template library
for linear algebra: matrices, vectors, numerical solvers and related
algorithms. It supports dense and sparse matrices on integer,
floating point and complex numbers, decompositions of such matrices,
and solutions of linear systems. Its performance on many algorithms
is comparable with some of the best implementations based on Lapack
and level-3 BLAS. The RcppEigen package includes the header files
from the Eigen C++ template library (currently version 3.2.0).
Thus users do not need to install Eigen itself in order to use
RcppEigen. Since version 3.1.1, Eigen is licensed under the
Mozilla Public License (version 2); earlier version were licensed
under the GNU LGPL version 3 or later. RcppEigen (the Rcpp
bindings/bridge to Eigen) is licensed under the GNU GPL version 2
 or later, as is the rest of Rcpp.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-statmod-r35-1.4.32-2 (Statistical Modeling)
Various statistical modeling functions including growth curve comparisons,
limiting dilution analysis, mixed linear models, heteroscedastic regression,
Tweedie family generalized linear models, the inverse-Gaussian distribution
and Gauss quadrature.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rcppziggurat-r31-0.1.5-1 (Integration of Ziggurat RNG Implementations)
The Ziggurat generator for normally distributed random numbers,
originally proposed by Marsaglia and Tsang (2000,
) has been improved upon a few times starting
with Leong et al (2005, ). This package
provides an aggregation in order to compare different implementations in
order to provide an 'faster but good enough' alternative for use with R
and C++ code.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-polynomf-r35-2.0-2-1 (Polynomials in R)
Implements univariate polynomial operations in R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tester-r31-0.1.7-1 (Tests and checks characteristics of R objects)
tester allows you to test characteristics of common R objects.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-shiny-r31-1.3.2-1 (Web Application Framework for R)
Makes it incredibly easy to build interactive web applications with R. 
Automatic "reactive" binding between inputs and outputs and extensive 
pre-built widgets make it possible to build beautiful, responsive, 
and powerful applications with minimal effort.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-webshot-r35-0.5.1-1 (Shiny UI Widgets for Small Screens)
Provides UI widget and layout functions for writing Shiny apps that work
well on small screens.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcpp-r32-1.0.2-2 (Seamless R and C++ Integration)
The Rcpp package provides R functions as well as a C++ library which
facilitate the integration of R and C++.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rsclient-r32-0.7-3-2 (RSclient: Client for Rserve)
Client for Rserve, allowing to connect to Rserve instances
and issue commands.

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2020-01-16: cran-scatterplot3d-r31-0.3-41-1 (3D Scatter Plot)
Plots a three dimensional (3D) point cloud.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-xtable-r32-1.8-4-1 (Export tables to LaTeX or HTML)
Coerce data to LaTeX and HTML tables

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sys-r35-3.3-1 (Tools for Running System Commands in R)
Drop-in replacements for the base system2() function with fine control
and consistent behavior across platforms. Supports clean interruption,
timeout, background tasks, and streaming STDIN / STDOUT / STDERR over
binary or text connections. Arguments on Windows automatically get
encoded and quoted to work on different locales.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rvest-r32-0.3.4-1 (Easily harvest web pages)
Wrappers around the 'xml2' and 'httr' packages to make it easy to
download, then manipulate, HTML and XML.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-qtl-r34-1.44-9-1 (Quantitative trait loci)
Analysis of experimental crosses to identify genes 
(called quantitative trait loci, QTLs) contributing 
to variation in quantitative traits.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-testthat-r31-2.2.1-1 (Testthat code)
A testing package specifically tailored for R that's fun,
flexible and easy to set up.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-pmmltransformations-r32-1.3.3-1 (Transforms input data from a PMML perspective)
Allows for data to be transformed before using it to construct models.
Builds structures to allow functions in the PMML package to output
transformation details in addition to the model in the resulting PMML file.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rwave-r32-2.4-8-1 (Time-Frequency analysis of 1-D signals)
Rwave is a library of R functions which provide an environment for
the Time-Frequency analysis of 1-D signals (and especially for the
wavelet and Gabor transforms of noisy signals). It was originally
written for Splus by Rene Carmona, Bruno Torresani, and Wen L. 
wang, first at the University of California at Irvine and then
at Princeton University. Credit should also be given to Andrea
Wang whose functions on the dyadic wavelet transform are included.
Rwave is based on the book: "Practical Time-Frequency Analysis:
Gabor and Wavelet Transforms with an Implementation in S", by Rene
Carmona, Wen L. Hwang and Bruno Torresani, Academic Press, 1998.

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2020-01-16: cran-rocr-r36-1.0-7-1 (Visualizing scoring classifier performance)
ROC graphs, sensitivity/specificity curves, lift charts, and
precision/recall plots are popular examples of trade-off
visualizations for specific pairs of performance measures. ROCR
is a flexible tool for creating cutoff-parameterized 2D
performance curves by freely combining two from over 25
performance measures (new performance measures can be added
using a standard interface). Curves from different cross-
alidation or bootstrapping runs can be averaged by different
methods, and standard deviations, standard errors or box plots
can be used to visualize the variability across the runs. The
parameterization can be visualized by printing cutoff values
at the corresponding curve positions, or by coloring the curve
according to cutoff. All components of a performance plot can
be quickly adjusted using a flexible parameter dispatching
mechanism. Despite its flexibility, ROCR is easy to use, with
only three commands and reasonable default values for all
optional parameters.

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2020-01-16: cran-rgdal-r36-1.4-6-1 (GNU R Bindings for GDAL)
GNU R Bindings for GDAL

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-shape-r32-1.4.4-1 (Plotting graphical shapes, colors)
Functions for plotting graphical shapes such as ellipses,
circles, cylinders, arrows, ...

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rodbc-r33-1.3-16-1 (ODBC Database Access for R)
An ODBC database interface

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-r.oo-r31-1.22.0-1 (R object-oriented programming)
Methods and classes for object-oriented programming in R
with or without references.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-webshot-r32-0.5.1-1 (Shiny UI Widgets for Small Screens)
Provides UI widget and layout functions for writing Shiny apps that work
well on small screens.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rtsne-r35-0.15-2 (T-distributed Stochastic Neighbor Embedding)
An R wrapper around the fast T-distributed Stochastic 
Neighbor Embedding implementation by Van der Maaten.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-sda-r34-1.3.7-1 (Shrinkage Discriminant Analysis)
This package provides an efficient framework for high-dimensional
linear and diagonal discriminant analysis with variable selection.
The classifier is trained using James-Stein-type shrinkage estimators
and predictor variables are ranked using correlation-adjusted t-scores
(CAT scores). Variable selection error is controlled using false
non-discovery rates or higher criticism.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rsvgdevice-r31-0.6.4.4-2 (R SVG graphics device)
A graphics device for R that uses the w3.org xml standard
for Scalable Vector Graphics.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tree-r32-1.0-39-1 (GNU R Tools for classification trees)
Classification and Regression Trees.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rpart.plot-r35-3.0.6-1 (Plot enhanced rpart models)
Plot rpart models. Extends plot.rpart and text.rpart in the rpart package.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-vgam-r31-1.0-3-1 (Vector Generalized Linear and Additive Models)
Vector generalized linear and additive models, and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Reduced-Rank VGAMs). This
package fits many models and distribution by maximum likelihood
estimation (MLE) or penalized MLE. Also fits constrained ordination
models in ecology.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-statmod-r32-1.4.32-2 (Statistical Modeling)
Various statistical modeling functions including growth curve comparisons,
limiting dilution analysis, mixed linear models, heteroscedastic regression,
Tweedie family generalized linear models, the inverse-Gaussian distribution
and Gauss quadrature.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-signal-r33-0.7-6-2 (Signal processing)
A set of signal processing R functions originally written for Matlab/Octave.
Includes filter generation utilities, filtering functions, resampling
routines, and visualization of filter models. It also includes interpolation
functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rematch-r34-1.0.1-1 (Match Regular Expressions with a Nicer API)
A small wrapper on 'regexpr' to extract the matches
and captured groups from the match of a regular expression
to a character vector.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tfplot-r33-2015.12-1-1 (Time Frame User Utilities)
Utilities in this package are for simple manipulation and quick
plotting of time series data. These utilities use the tframe
package which provides a programming kernel for time series.
Extensions to tframe provided in tframePlus can also be used.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-runit-r34-0.4.32-1 (R Unit test framework)
R functions implementing a standard Unit Testing framework,
with additional code inspection and report generation tools

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-scales-r36-1.0.0-1 (Scale functions for graphics)
Scales map data to aesthetics, and provide methods for automatically
determining breaks and labels for axes and legends.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-robustbase-r36-0.93-5-2 (GNU R Tools for robust methods)
"Essential" Robust Statistics.
The goal is to provide tools allowing to analyze data with robust methods.
This includes regression methodology including model selections and
multivariate statistics where we strive to cover the book
"Robust Statistics, Theory and Methods" by Maronna, Martin and Yohai;
Wiley 2006.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-tframe-r31-2015.12-1.1-1 (Time Frame coding kernel)
The tframe package provides a kernel of functions for programming
time series methods in a way that is relatively independently of
the representation of time. It also provides plotting, time
windowing, and some other utility functions which are specifically
intended for time series. See the Guide distributed as a vignette,
or ?tframe.Intro for more details. (User utilities other than the
programming kernel have been moved into package tfplot.)

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-processx-r35-3.4.1-1 (Execute and Control System Processes)
Tools to run system processes in the background. It can check if a
background process is running; wait on a background process to finish;
get the exit status of finished processes; kill background processes. It
can read the standard output and error of the processes, using
non-blocking connections. 'processx' can poll a process for standard
output or error, with a timeout. It can also poll several processes at
once.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-spgrass6-r32-0.8-9-1 (Interface between GRASS 6+ and R)
Interface between GRASS 6+ and R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rpubchem-r33-1.5.10-1 (Interface to the PubChem Collection)
Access PubChem data (compounds, substance, assays). Structural information
is provided in the form of SMILES strings. This package only provides
access to a subset of the precalculated data stored by PubChem. Bio-assay
data can be accessed to obtain descriptions as well as the actual data.
It is also possible to search for assay ID's by keyword. Currently the main
limitation is that only 1000 molecules can be downloaded at a time from the
PubChem servers

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-spatial-r33-7.3-11-1 (Kriging and Point Pattern Analysis Functions)
Functions for kriging and point pattern analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-scrime-r36-1.3.5-1 (Analysis of High-Dimensional Categorical Data)
Tools for the analysis of high-dimensional data developed/implemented 
at the group "Statistical Complexity Reduction In Molecular Epidemiology" 
(SCRIME). Main focus is on SNP data. But most of the functions can also 
be applied to other types of categorical data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    New upstream Bioconductor versions (bioc 3.10)
2020-01-16: cran-trimcluster-r35-0.1-2.1-1 (Cluster analysis with trimming)
Trimmed k-means clustering.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sn-r33-1.5-4-1 (Skew-normal and skew-t distributions)
Define and manipulate probability distributions of the skew-normal
family and some related ones (notably the skew-t family) and provide
related statistical methods for data fitting and diagnostics, in the
univariate and in the multivariate case.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rematch-r31-1.0.1-1 (Match Regular Expressions with a Nicer API)
A small wrapper on 'regexpr' to extract the matches
and captured groups from the match of a regular expression
to a character vector.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-stable-r32-1.1.4-1 (Functions and Models for Stable Distributions)
Density, distribution, quantile and hazard functions of a stable
variate; generalized regression models for the parameters of a stable
distribution. See the README for how to make equivalent calls to those
of 'stabledist'. See github for Journal article.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-testthat-r34-2.2.1-1 (Testthat code)
A testing package specifically tailored for R that's fun,
flexible and easy to set up.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rmpi-r34-0.6-9-1 (R Interface Wrapper to MPI)
Rmpi provides an interface (wrapper) to MPI APIs. It also provides
an interactive R slave environment.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rex-r31-1.1.2-1 (Friendly Regular Expressions)
A friendly interface for the construction of regular expressions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-scatterplot3d-r36-0.3-41-1 (3D Scatter Plot)
Plots a three dimensional (3D) point cloud.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcmdcheck-r33-1.3.3-1 (Run 'R CMD check' from 'R')
Run 'R CMD check' from 'R' programmatically, and capture the results of
the individual checks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-purrr-r32-0.3.2-3 (Functional Programming Tools)
Make your pure functions purr with the 'purrr' package. This package 
completes R's functional programming tools with missing features present 
in other programming languages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-spls-r36-2.2-3-1 (Sparse Partial Least Squares Regression)
This package provides functions for fitting a Sparse Partial
Least Squares Regression and Classification

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-stable-r35-1.1.4-1 (Functions and Models for Stable Distributions)
Density, distribution, quantile and hazard functions of a stable
variate; generalized regression models for the parameters of a stable
distribution. See the README for how to make equivalent calls to those
of 'stabledist'. See github for Journal article.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tsfa-r33-2014.10-1-1 (Time Series Factor Analysis)
Extraction of Factors from Multivariate Time Series.
See ?00tsfa-Intro for more details.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-proj4-r32-1.0-9-102 (PROJ.4 cartographic projections library for R)
PROJ.4 cartographic projections library for R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sda-r35-1.3.7-1 (Shrinkage Discriminant Analysis)
This package provides an efficient framework for high-dimensional
linear and diagonal discriminant analysis with variable selection.
The classifier is trained using James-Stein-type shrinkage estimators
and predictor variables are ranked using correlation-adjusted t-scores
(CAT scores). Variable selection error is controlled using false
non-discovery rates or higher criticism.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rstudioapi-r31-0.10-1 (Safely access the RStudio API)
This package provides functions to make it easy to access the RStudio
API when available, and provide informative error messages when not.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-praise-r31-1.0.0-1 (Praise Users)
Build friendly R packages that praise their users if they have 
done something good, or they just need it to feel better.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-zeallot-r33-0.1.0-1 (Multiple/Unpacking/Destructuring Assignment)
Provides a %<-% operator to perform multiple, unpacking, and 
destructuring assignment in R. The operator unpacks the right-hand 
side of an assignment into multiple values and assigns these 
values to variables on the left-hand side of the assignment.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-quantreg-r31-5.51-2 (Quantile Regression)
Quantile regression and related methods.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-quadprog-r33-1.5-7-2 (Functionss for Quadratic Programming Problems)
This package contains routines and documentation for solving
quadratic programming problems.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-quantreg-r34-5.51-2 (Quantile Regression)
Quantile regression and related methods.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-psy-r33-1.1-1 (Various procedures used in psychometry)
Kappa, ICC, Cronbach alpha, screeplot, mtmm

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rhpcblasctl-r31-0.18-205-1 (Control the Number of Threads on 'BLAS')
Control the number of threads on 'BLAS' (Aka 'GotoBLAS', 'OpenBLAS',
'ACML', 'BLIS' and 'MKL'). And possible to control the number of threads
in 'OpenMP'. Get a number of logical cores and physical cores if
feasible.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-roxygen2-r32-6.1.1-1 (In-source documentation for R)
A Doxygen-like in-source documentation system for Rd, collation,
and NAMESPACE.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-speaq-r34-2.0.0-1 (NMR Spectrum Alignment Tools)
We introduce a novel suite of informatics tools for the quantitative analysis
of NMR metabolomic profile data. The core of the processing cascade is a novel
peak alignment algorithm, called hierarchical Cluster-based Peak Alignment
(CluPA). The algorithm aligns a target spectrum to the reference spectrum in
a top-down fashion by building a hierarchical cluster tree from peak lists of
reference and target spectra and then dividing the spectra into smaller
segments based on the most distant clusters of the tree. To reduce the
computational time to estimate the spectral misalignment, the method makes
use of Fast Fourier Transformation (FFT) cross-correlation. Since the method
returns a high-quality alignment, we can propose a simple methodology to study
the variability of the NMR spectra. For each aligned NMR data point the ratio
of the between-group and within-group sum of squares (BW-ratio) is calculated
to quantify the difference in variability between and within predefined groups
of NMR spectra. This differential analysis is related to the calculation of
the F-statistic or a one-way ANOVA, but without distributional assumptions.
Statistical inference based on the BW-ratio is achieved by bootstrapping the
null distribution from the experimental data. Related publication is
available at http://www.biomedcentral.com/1471-2105/12/405/.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-ps-r31-1.3.0-1 (List, Query, Manipulate System Processes)
List, query and manipulate all system processes, on 'Windows', 'Linux'
and 'macOS'.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-statnet.common-r33-3.3.0-1 (Statnet project common scripts and utilities)
Non-statistical utilities used by the software developed 
by the Statnet Project. They may also be of use to others.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-weightedkmeans-r33-1.2.0-1 (Weighted KMeans Clustering)
Entropy weighted kmeans (ewkm) is a weighted subspace clustering
algorithm that is well suited to very high dimensional data. Weights
are calculated as the importance of a variable with regard to cluster
membership. The feature group weighted kmenas (fgkm) extends this
concept by grouping features and weighting the group in addition
to weihgting individual features.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-readr-r32-1.3.1-1 (Read Rectangular Text Data)
The goal of 'readr' is to provide a fast and friendly way to read
rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to
flexibly parse many types of data found in the wild, while still
cleanly failing when data unexpectedly changes.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-zip-r33-2.0.4-1 (Cross-Platform 'zip' Compression)
Cross-Platform 'zip' Compression Library. A replacement for the 'zip'
function, that does not require any additional external tools on any
platform.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-spls-r33-2.2-3-1 (Sparse Partial Least Squares Regression)
This package provides functions for fitting a Sparse Partial
Least Squares Regression and Classification

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-usingr-r33-2.0-6-1 (GNU R data sets for "Using R for Intro Stats")
A collection of datasets to accompany the textbook
"Using R for Introductory Statistics."

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tsfa-r36-2014.10-1-1 (Time Series Factor Analysis)
Extraction of Factors from Multivariate Time Series.
See ?00tsfa-Intro for more details.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rvmmin-r34-2018-4.17-1 (Variable Metric Nonlinear Mininization)
Variable metric nonlinear function minimization with bounds constraints.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-proxy-r36-0.4-23-1 (Distance and Similarity Measures)
Provides an extensible framework for the efficient calculation of
auto- and cross-proximities, along with implementations of the
most popular ones.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-vim-r32-4.8.0-1 (Missing Values Visualization and Imputation)
This package introduces new tools for the visualization of missing and/or
imputed values, which can be used for exploring the data and the structure
of the missing and/or imputed values. Depending on this structure of the
missing values, the corresponding methods may help to identify the
mechanism generating the missing values and allows to explore the data
including missing values. In addition, the quality of imputation can be
visually explored using various univariate, bivariate, multiple and
multivariate plot methods. A graphical user interface available in the
separate package VIMGUI allows an easy handling of the implemented plot
methods.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-png-r32-0.1-7-2 (Read and write PNG images)
This package provides an easy and simple way to read, write and
display bitmap images stored in the PNG format. It can read and
write both files and in-memory raw vectors.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcppziggurat-r36-0.1.5-1 (Integration of Ziggurat RNG Implementations)
The Ziggurat generator for normally distributed random numbers,
originally proposed by Marsaglia and Tsang (2000,
) has been improved upon a few times starting
with Leong et al (2005, ). This package
provides an aggregation in order to compare different implementations in
order to provide an 'faster but good enough' alternative for use with R
and C++ code.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcmdrplugin.ma-r35-0.0-2-1 (GUI for Conducting Meta-Analyses in R)
This is an R-Commander plug-in for meta-analysis. This package enables
the user to conduct a meta-analysis in a menu-driven, graphical user
interface environment (e.g., SPSS). It uses recommended procedures as
described in The Handbook of Research Synthesis and Meta-Analysis
(Cooper, Hedges, & Valentine, 2009).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rex-r36-1.1.2-1 (Friendly Regular Expressions)
A friendly interface for the construction of regular expressions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-xtable-r35-1.8-4-1 (Export tables to LaTeX or HTML)
Coerce data to LaTeX and HTML tables

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-simpleboot-r31-1.1-7-1 (GNU R Tools for simple bootstrap)
Simple bootstrap routines

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tm-r32-0.7-6-1 (Text Mining Package)
A framework for text mining applications within R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-teachingdemos-r35-2.10-2 (Demonstrations for Teaching and Learning)
Demonstration functions that can be used in a classroom to 
demonstrate statistical concepts, or on your own to better 
understand the concepts or the programming.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-vegan-r33-2.5-4-1 (Community Ecology Package)
Ordination methods, diversity analysis and other functions
for community and vegetation ecologists.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sys-r34-3.3-1 (Tools for Running System Commands in R)
Drop-in replacements for the base system2() function with fine control
and consistent behavior across platforms. Supports clean interruption,
timeout, background tasks, and streaming STDIN / STDOUT / STDERR over
binary or text connections. Arguments on Windows automatically get
encoded and quoted to work on different locales.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-reactran-r32-1.4.3.1-2 (Reactive transport modelling in 1D, 2D and 3D)
Routines for developing models that describe reaction and
advective-diffusive transport in one, two or three dimensions.
Includes transport routines in porous media, in estuaries, and
in bodies with variable shape.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-sourcetools-r31-0.1.7-1 (Reading, Tokenizing and Parsing R Code)
Tools for the reading and tokenization of R code. The 'sourcetools'
package provides both an R and C++ interface for the tokenization of 
R code, and helpers for interacting with the tokenized representation
of R code.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rserve-r33-1.7-3.1-1 (Binary R server)
Rserve acts as a socket server (TCP/IP or local sockets) which allows binary
requests to be sent to R. Every connection has a separate workspace and
working directory. Client-side implementations are available for popular
languages such as C/C++ and Java, allowing any application to use facilities
of R without the need of linking to R code. Rserve supports remote connection,
user authentication and file transfer. A simple R client is included in this
package as well.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rmpi-r35-0.6-9-1 (R Interface Wrapper to MPI)
Rmpi provides an interface (wrapper) to MPI APIs. It also provides
an interactive R slave environment.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-qtl-r35-1.44-9-1 (Quantitative trait loci)
Analysis of experimental crosses to identify genes 
(called quantitative trait loci, QTLs) contributing 
to variation in quantitative traits.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-truncnorm-r33-1.0-7-1 (Truncated Normal Distribution)
Density, probability, quantile and random number generation functions
for the truncated normal distribution.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-remotes-r36-2.1.0-1 (R Pkg Installation from Remote Repositories)
Run 'R CMD check' from 'R' programmatically, and capture the results of
the individual checks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-som-r35-0.3-5.1-1 (Self-Organizing Map)
Self-Organizing Map (with application in gene clustering)

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sensominer-r34-1.23-1 (Sensory data analysis with R)
an R package for analysing sensory data

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-purrr-r35-0.3.2-3 (Functional Programming Tools)
Make your pure functions purr with the 'purrr' package. This package 
completes R's functional programming tools with missing features present 
in other programming languages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-r.utils-r36-2.9.0-1 (Various programming utilities)
This package provides utility methods useful when programming
and developing R packages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-vrmlgen-r33-1.4.9-1 (Generate 3D visualizations)
vrmlgen creates 3D scatter and bar plots, visualizations of 3D meshes,
parametric functions and height maps in web-formats like the Virtual
Reality Markup Language (VRML, filetype .wrl) and the LiveGraphics3D format.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-zcompositions-r33-1.3.2-1-1 (Treatment of Zero/Missing Values in Data Sets)
Principled methods for the imputation of zeros, left-censored and
missing data in compositional data sets.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-proj4-r35-1.0-9-102 (PROJ.4 cartographic projections library for R)
PROJ.4 cartographic projections library for R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-ppls-r31-1.6-1.1-1 (Penalized Partial Least Squares)
This package contains linear and nonlinear regression methods based
on Partial Least Squares and Penalization Techniques. Model parameters
are selected via cross-validation, and confidence intervals ans tests
for the regression coefficients can be conducted via jackknifing.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-randomfields-r35-3.3.6-2 (Simulation and Analysis of Random Fields)
Simulation of Gaussian and extreme value random fields; conditional
simulation; kriging; maximum likelihood estimation

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-tsp-r32-1.1-7-1 (Traveling Salesperson Problem)
Basic infrastructure and some algorithms for the traveling salesperson
problem (also traveling salesman problem; TSP). The package provides
some simple algorithms and an interface to Concorde, the currently
fastest TSP solver. Concorde itself is not included in the package
and has to be obtained separately.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rsnns-r34-0.4-12-1 (Stuttgart Neural Network Simulator in R)
The Stuttgart Neural Network Simulator (SNNS) is a library containing many
standard implementations of neural networks. This package wraps the SNNS
functionality to make it available from within R. Using the RSNNS low-level
interface, all of the algorithmic functionality and flexibility of SNNS can
be accessed. Furthermore, the package contains a convenient high-level
interface, so that the most common neural network topologies and learning
algorithms integrate seamlessly into R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-pryr-r34-0.1.4-1 (Tools for Computing on the Language)
Useful tools to pry back the covers of R and understand the language at
a deeper level.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-selectr-r36-0.4-1-1 (Translate CSS Selectors to XPath Expressions)
Translates a CSS3 selector into an equivalent XPath expression. This
allows us to use CSS selectors when working with the XML package as it
can only evaluate XPath expressions. Also provided are convenience
functions useful for using CSS selectors on XML nodes. This package is a
port of the Python package 'cssselect'
(<https://cssselect.readthedocs.io/>).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-snow-r32-0.4-3-1 (Simple Network of Workstations)
Support for simple parallel computing in R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tsa-r33-1.2-1 (Time Series Analysis)
Contains R functions and datasets detailed in the book "Time
Series Analysis with Applications in R (second edition)" by
Jonathan Cryer and Kung-Sik Chan

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-psych-r33-1.8.12-1 (Procedures for Psychological Research)
A number of routines for personality, psychometrics and experimental
psychology. Functions are primarily for scale construction using
factor analysis, cluster analysis and reliability analysis, although
others provide basic descriptive statistics. Item Response Theory is
done using factor analysis of tetrachoric and polychoric correlations.
Functions for simulating particular item and test structures are
included. Several functions serve as a useful front end for structural
equation modeling. Graphical displays of path diagrams, factor analysis
and structural equation models are created using basic graphics. Some
of the functions are written to support a book on psychometrics as well
as publications in personality research. For more information, see the
personality-project.org/r webpage.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-stringi-r34-1.4.3-1 (Character String Processing Facilities)
Allows for fast, correct, consistent, portable, as well as 
convenient character string/text processing in every locale 
and any native encoding. Owing to the use of the ICU library, 
the package provides R users with platform-independent 
functions known to Java, Perl, Python, PHP, and Ruby 
programmers. Among available features there are: pattern 
searching (e.g., with ICU Java-like regular expressions 
or the Unicode Collation Algorithm), random string generation, 
case mapping, string transliteration, concatenation, Unicode 
normalization, date-time formatting and parsing, etc.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rattle-r35-5.2.0-1 (Graphical user interface for data mining in R)
Rattle (the R Analytic Tool To Learn Easily) provides a Gnome
(RGtk2) based interface to R functionality for data mining.
The aim is to provide a simple and intuitive interface that
allows a user to quickly load data from a CSV file (or via ODBC),
transform and explore the data, build and evaluate models, and
export models as PMML (predictive modelling markup language) or
as scores. All of this with knowing little about R. All R
commands are logged and commented through the log tab. Thus
they are available to the user as a script file or as an aide
for the user to learn R or to copy-and-paste directly into R
itself. Rattle also exports a number of utility functions and
the graphical user interface, invoked as rattle(), does not
need to be run to deploy these.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-stringi-r31-1.4.3-1 (Character String Processing Facilities)
Allows for fast, correct, consistent, portable, as well as 
convenient character string/text processing in every locale 
and any native encoding. Owing to the use of the ICU library, 
the package provides R users with platform-independent 
functions known to Java, Perl, Python, PHP, and Ruby 
programmers. Among available features there are: pattern 
searching (e.g., with ICU Java-like regular expressions 
or the Unicode Collation Algorithm), random string generation, 
case mapping, string transliteration, concatenation, Unicode 
normalization, date-time formatting and parsing, etc.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tcltk2-r31-1.2-11-1 (Tcl/Tk Additions)
A series of additional Tcl commands and Tk widgets with style and
various functions (under Windows: DDE exchange, access to the
registry and icon manipulation) to supplement the tcltk package

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rdpack-r32-0.8-0-1 (Update/Manipulate Rd Documentation Objects)
Functions for manipulation of R documentation objects, including
functions reprompt() and ereprompt() for updating 'Rd' documentation for
functions, methods and classes; 'Rd' macros for citations and import of
references from 'bibtex' files for use in 'Rd' files and 'roxygen2'
comments; 'Rd' macros for evaluating and inserting snippets of 'R' code
and the results of its evaluation or creating graphics on the fly; and
many functions for manipulation of references and Rd files.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-readr-r35-1.3.1-1 (Read Rectangular Text Data)
The goal of 'readr' is to provide a fast and friendly way to read
rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to
flexibly parse many types of data found in the wild, while still
cleanly failing when data unexpectedly changes.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-waveslim-r34-1.7.5.1-2 (Basic wavelet routines)
Basic wavelet routines for time series (1D), image (2D) and
array (3D) analysis.The code provided here is based on wavelet
methodology developed in Percival and Walden (2000); Gencay,
Selcuk and Whitcher (2001); the dual-tree complex wavelet 
transform (DTCWT) from Kingsbury (1999, 2001) as implemented
by Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-simcomp-r36-3.3-1 (Simultaneous Comparisons for Mult. Endpoints)
Simultaneous tests and confidence intervals for one-way experimental
designs with one or many normally distributed, primary response
variables (endpoints). The procedure of Hasler and Hothorn (2011,2012)
is applied for differences or ratios of means. Various contrasts can
be chosen, unbalanced sample sizes are allowed as well as heterogeneous
variances or covariance matrices.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-stepplr-r33-0.93-2 (L2 penalized logistic regression)
L2 penalized logistic regression for both continuous and discrete
predictors, with forward stagewise/forward stepwise variable
selection procedure.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rserve-r34-1.7-3.1-1 (Binary R server)
Rserve acts as a socket server (TCP/IP or local sockets) which allows binary
requests to be sent to R. Every connection has a separate workspace and
working directory. Client-side implementations are available for popular
languages such as C/C++ and Java, allowing any application to use facilities
of R without the need of linking to R code. Rserve supports remote connection,
user authentication and file transfer. A simple R client is included in this
package as well.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-testit-r36-0.10-1 (Simple package for testing R packages)
This package provides two convenience functions assert()
and test_pkg() to facilitate testing R packages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rlang-r36-0.4.0-2 (Functions for Base Types and Core R)
A toolbox for working with base types, core R features like 
the condition system, and core `Tidyverse' features like tidy evaluation.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-usingr-r34-2.0-6-1 (GNU R data sets for "Using R for Intro Stats")
A collection of datasets to accompany the textbook
"Using R for Introductory Statistics."

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-pryr-r35-0.1.4-1 (Tools for Computing on the Language)
Useful tools to pry back the covers of R and understand the language at
a deeper level.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tidyselect-r34-0.2.5-1 (Select from a Set of Strings)
A backend for the selecting functions of the 'tidyverse'. It makes it
easy to implement select-like functions in your own packages in a way
that is consistent with other 'tidyverse' interfaces for selection.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rjava-r31-0.9-8-2 (Low-level R to Java interface)
Low-level interface to Java VM very much like .C/.Call and friends.
Allows creation of objects, calling methods and accessing fields.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-urca-r31-1.3-0-2 (Unit Root and Cointegration Tests)
Unit root and cointegration tests encountered in applied econometric
analysis are implemented.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-proto-r31-1.0.0-1 (Prototype object-based programming)
An object oriented system using object-based, also called
prototype-based, rather than class-based object oriented ideas.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rpart.plot-r32-3.0.6-1 (Plot enhanced rpart models)
Plot rpart models. Extends plot.rpart and text.rpart in the rpart package.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-waveslim-r31-1.7.5.1-2 (Basic wavelet routines)
Basic wavelet routines for time series (1D), image (2D) and
array (3D) analysis.The code provided here is based on wavelet
methodology developed in Percival and Walden (2000); Gencay,
Selcuk and Whitcher (2001); the dual-tree complex wavelet 
transform (DTCWT) from Kingsbury (1999, 2001) as implemented
by Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rvmmin-r33-2018-4.17-1 (Variable Metric Nonlinear Mininization)
Variable metric nonlinear function minimization with bounds constraints.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-prospectr-r32-0.1.3-4 (Processing and sample selection of vis-NIR)
The package provides functions for pretreatment and sample selection
of visible and near infrared diffuse reflectance spectra

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-timedate-r31-3043.102-1 (Rmetrics - Chronological and Calendar Objects)
Environment for teaching "Financial Engineering and Computational Finance"

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-recipes-r33-0.1.7-1 (Preprocessing Tools to Create Design Matrices)
An extensible framework to create and preprocess design matrices.
Recipes consist of one or more data manipulation and analysis "steps".
Statistical parameters for the steps can be estimated from an initial
data set and then applied to other data sets. The resulting design
matrices can then be used as inputs into statistical or machine learning
models.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-ttr-r36-0.23-5-1 (Technical Trading Rules)
Technical analysis and other functions to construct technical trading 
rules with R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-readstata13-r34-0.9.2-2 (Import 'Stata' Data Files)
Function to read and write the 'Stata' file format.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-sna-r36-2.4-1 (Tools for Social Network Analysis)
A range of tools for social network analysis, including node and graph-level
indices, structural distance and covariance methods, structural equivalence
detection, network regression, random graph generation, and 2D/3D network
visualization.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcmdrplugin.survival-r34-1.2-0-1 (R Commander Plug-in for the survival Package)
This package provides an R Commander plug-in for the survival package,
with dialogs for Cox models, parametric survival regression models,
estimation of survival curves, and testing for differences in survival
curves, along with data-management facilities and a variety of tests,
and graphs.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sandwich-r36-2.5-1-1 (GNU R std err estimators for time-series data)
sandwich: Robust Covariance Matrix Estimators
Model-robust standard error estimators for cross-sectional, 
time series, and longitudinal data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-robustbase-r33-0.93-5-2 (GNU R Tools for robust methods)
"Essential" Robust Statistics.
The goal is to provide tools allowing to analyze data with robust methods.
This includes regression methodology including model selections and
multivariate statistics where we strive to cover the book
"Robust Statistics, Theory and Methods" by Maronna, Martin and Yohai;
Wiley 2006.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-prabclus-r32-2.3-1-1 (Functions for Clustering)
Distance-based parametric bootstrap tests for clustering with spatial
neighborhood information. Some distance measures, Clustering of
presence-absence, abundance and multilocus genetical data for
species delimitation, nearest neighbor based noise detection.
Try package?prabclus for on overview.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-pscl-r35-1.5.2-1 (Political Science Computational Laboratory)
Bayesian analysis of item-response theory (IRT) models, roll call analysis;
computing highest density regions; maximum likelihood estimation of zero-
inflated and hurdle models for count data; goodness-of-fit measures for
GLMs; data sets used in writing and teaching at the Political Science
Computational Laboratory; seats-votes curves.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-xml-r32-3.98-1.20-1 (Tools for parsing and generating XML within R)
Tools for parsing and generating XML within R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r.methodss3-r34-1.7.1-1 (Utility function for defining S3 methods)
Methods that simplify the setup of S3 generic functions and S3 methods.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-smatr-r36-3.4-8-1 (Major Axis Estimation and Testing Routines)
s package provides methods of fitting bivariate lines in allometry using
the major axis (MA) or standardised major axis (SMA), and for making
inferences about such lines. The available methods of inference include
confidence intervals and one-sample tests for slope and elevation, testing
for a common slope or elevation amongst several allometric lines,
constructing a confidence interval for a common slope or elevation, and
testing for no shift along a common axis, amongst several samples.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-r6-r31-2.4.0-1 (Classes with reference semantics)
The R6 package allows the creation of classes with reference semantics,
similar to R's built-in reference classes. Compared to reference classes,
R6 classes are simpler and lighter-weight, and they are not built on S4
classes so they do not require the methods package. These classes allow
public and private members, and they support inheritance, even when the
classes are defined in different packages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-readxl-r36-1.3.1-2 (Read Excel Files)
Import excel files into R. Supports '.xls' via the embedded
'libxls' C library (http://sourceforge.net/projects/libxls/)
and '.xlsx' via the embedded 'RapidXML' C++ library
(http://rapidxml.sourceforge.net). Works on Windows, Mac
 and Linux without external dependencies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-tkrplot-r32-0.0-24-1 (TK Rplot)
simple mechanism for placing R graphics in a Tk widget

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-polycor-r33-0.7-8-2 (Polychoric and Polyserial Correlations)
Computes polychoric and polyserial correlations by quick "two-step"
methods or ML, optionally with standard errors; tetrachoric
and biserial correlations are special cases.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-relaimpo-r33-2.2-3-1 (Relative importance of regressors)
relaimpo provides several metrics for assessing relative importance
in linear models. These can be printed, plotted and bootstrapped.
The recommended metric is lmg, which provides a decomposition of
the model explained variance into non-negative contributions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rdpack-r35-0.11-0-1 (Update/Manipulate Rd Documentation Objects)
Functions for manipulation of R documentation objects, including
functions reprompt() and ereprompt() for updating 'Rd' documentation for
functions, methods and classes; 'Rd' macros for citations and import of
references from 'bibtex' files for use in 'Rd' files and 'roxygen2'
comments; 'Rd' macros for evaluating and inserting snippets of 'R' code
and the results of its evaluation or creating graphics on the fly; and
many functions for manipulation of references and Rd files.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r2stats-r35-0.68-39-1 (GTK GUI for fitting and comparing GLM and GLM)
R2STATS is a gWidgetsRGtk2 GUI for fitting and comparing GLM or GLMM (based
on Douglas Bates' lme4 package) in R. It is designed to make comparisons
between numerous models easy, both numerically and graphically, which may
be useful for teaching. Relevant plots are automatically produced for each
model family. R2STATS is *not* a generic graphical interface for R, but a
GUI for statistical modelling in a model comparison approach.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-zcompositions-r34-1.3.2-1-1 (Treatment of Zero/Missing Values in Data Sets)
Principled methods for the imputation of zeros, left-censored and
missing data in compositional data sets.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rda-r36-1.0.2-2.1-1 (Shrunken Centroids RDA)
Shrunken Centroids Regularized Discriminant Analysis
for the classification purpose in high dimensional data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-xopen-r33-1.0.0-1 (Open System Files, 'URLs', Anything)
Cross platform solution to open files, directories or 'URLs' with their
associated programs.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rvest-r35-0.3.4-1 (Easily harvest web pages)
Wrappers around the 'xml2' and 'httr' packages to make it easy to
download, then manipulate, HTML and XML.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-timedate-r34-3043.102-1 (Rmetrics - Chronological and Calendar Objects)
Environment for teaching "Financial Engineering and Computational Finance"

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sde-r32-2.0.15-1 (Stochastic Differential Equations)
Companion package to the book Simulation and Inference for Stochastic
Differential Equations With R Examples, ISBN 978-0-387-75838-1, Springer, NY.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rwave-r35-2.4-8-1 (Time-Frequency analysis of 1-D signals)
Rwave is a library of R functions which provide an environment for
the Time-Frequency analysis of 1-D signals (and especially for the
wavelet and Gabor transforms of noisy signals). It was originally
written for Splus by Rene Carmona, Bruno Torresani, and Wen L. 
wang, first at the University of California at Irvine and then
at Princeton University. Credit should also be given to Andrea
Wang whose functions on the dyadic wavelet transform are included.
Rwave is based on the book: "Practical Time-Frequency Analysis:
Gabor and Wavelet Transforms with an Implementation in S", by Rene
Carmona, Wen L. Hwang and Bruno Torresani, Academic Press, 1998.

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2020-01-16: cran-rattle-r32-5.2.0-1 (Graphical user interface for data mining in R)
Rattle (the R Analytic Tool To Learn Easily) provides a Gnome
(RGtk2) based interface to R functionality for data mining.
The aim is to provide a simple and intuitive interface that
allows a user to quickly load data from a CSV file (or via ODBC),
transform and explore the data, build and evaluate models, and
export models as PMML (predictive modelling markup language) or
as scores. All of this with knowing little about R. All R
commands are logged and commented through the log tab. Thus
they are available to the user as a script file or as an aide
for the user to learn R or to copy-and-paste directly into R
itself. Rattle also exports a number of utility functions and
the graphical user interface, invoked as rattle(), does not
need to be run to deploy these.

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2020-01-16: cran-som-r34-0.3-5.1-1 (Self-Organizing Map)
Self-Organizing Map (with application in gene clustering)

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-psm-r32-0.8-12-2 (Non-Linear Mixed-Effects modelling)
This package provides functions for estimation of linear and non-linear
mixed-effects models using stochastic differential equations. Moreover
it provides functions for finding smoothed estimates of model states
and for simulation. The package allows for any multivariate non-linear
time-variant model to be specified, and it also handles multidimensional
input, co-variates, missing observations and specification of dosage regimen.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-tfplot-r34-2015.12-1-1 (Time Frame User Utilities)
Utilities in this package are for simple manipulation and quick
plotting of time series data. These utilities use the tframe
package which provides a programming kernel for time series.
Extensions to tframe provided in tframePlus can also be used.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-robustrankaggreg-r33-1.1-2 (Methods for robust rank aggregation)
Methods for aggregating ranked lists, especially lists of genes. It 
implements the Robust Rank Aggregation (Kolde et. al in preparation) 
and some other simple algorithms for the task. RRA method uses a 
probabilistic model for aggregation that is robust to noise and also 
facilitates the calculation of significance probabilities for all the 
elements in the final ranking.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-shape-r35-1.4.4-1 (Plotting graphical shapes, colors)
Functions for plotting graphical shapes such as ellipses,
circles, cylinders, arrows, ...

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-signal-r34-0.7-6-2 (Signal processing)
A set of signal processing R functions originally written for Matlab/Octave.
Includes filter generation utilities, filtering functions, resampling
routines, and visualization of filter models. It also includes interpolation
functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-scarabee-r35-1.1-3-2 (R port of the Scarabee toolkit)
scaRabee is a port of the Scarabee toolkit originally written as a Matlab-based
application. It provides a framework for simulation and optimization of
pharmacokinetic-pharmacodynamic models at the individual and population level.
It is built on top of the neldermead package, which provides the direct search
algorithm proposed by Nelder and Mead for model optimization.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-r.matlab-r35-3.6.2-1 (Read and write of MAT files)
This package provides methods readMat() and writeMat() to read
and write MAT files. It also makes it possible to communicate
(evaluate code, send and retrieve objects etc.) with MATLAB v6
or higher running locally or on a remote host.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sna-r31-2.4-1 (Tools for Social Network Analysis)
A range of tools for social network analysis, including node and graph-level
indices, structural distance and covariance methods, structural equivalence
detection, network regression, random graph generation, and 2D/3D network
visualization.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rtsne-r32-0.15-2 (T-distributed Stochastic Neighbor Embedding)
An R wrapper around the fast T-distributed Stochastic 
Neighbor Embedding implementation by Van der Maaten.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-r2stats-r32-0.68-39-1 (GTK GUI for fitting and comparing GLM and GLM)
R2STATS is a gWidgetsRGtk2 GUI for fitting and comparing GLM or GLMM (based
on Douglas Bates' lme4 package) in R. It is designed to make comparisons
between numerous models easy, both numerically and graphically, which may
be useful for teaching. Relevant plots are automatically produced for each
model family. R2STATS is *not* a generic graphical interface for R, but a
GUI for statistical modelling in a model comparison approach.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-v8-r31-2.3-2 (Embedded JavaScript Engine for R)
An R interface to Google's open source JavaScript engine.
V8 is written in C++ and implements ECMAScript as specified in ECMA-262,
5th edition. In addition, this package implements typed arrays as specified
in ECMA 6 used for high-performance computing and libraries compiled
with 'emscripten'.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-r2html-r36-2.3.2-1 (HTML exportation for R objects)
Includes HTML function and methods to write in an HTML file.
Thus, making HTML reports is easy. Includes a function that
allows redirection on the fly, which appears to be very usefull
for teaching purpose, as the student can keep a copy of the
produced output to keep all that he did during the course.
Package comes with a vignette describing how to write HTML
reports for statistical analysis. Finally, a driver for Sweave
allows to parse HTML flat files containing R code and to
automatically write the corresponding outputs (tables and graphs).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-proc-r32-1.15.3-1 (Display and analyze ROC curves)
Display and analyze ROC curves

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-ttr-r31-0.23-5-1 (Technical Trading Rules)
Technical analysis and other functions to construct technical trading 
rules with R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tidyr-r31-1.0.0-2 (Easily Tidy Data)
An evolution of 'reshape2'. It's designed specifically for data 
tidying (not general reshaping or aggregating) and works well 
with 'dplyr' data pipelines.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-survival-r36-2.44-1.1-1 (GNU R Tools for survival analysis)
survival analysis: descriptive statistics, two-sample tests,
parametric accelerated failure models, Cox model.
Delayed entry (truncation) allowed for all models;
interval censoring for parametric models. Case-cohort designs.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tkrplot-r35-0.0-24-1 (TK Rplot)
simple mechanism for placing R graphics in a Tk widget

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-viridis-r36-0.5.1-2 (Default Color Maps from 'matplotlib')
Port of the new 'matplotlib' color maps ('viridis' - the default -,
'magma', plasma' and 'inferno') to 'R'. 'matplotlib'
http://matplotlib.org/  is a popular plotting library for 'python'.
These color maps are designed in such a way that they will analytically be
perfectly perceptually-uniform, both in regular form and also when
converted to black-and-white. They are also designed to be perceived by
readers with the most common form of color blindness. This is the 'lite'
version of the more complete 'viridis' package that can be found at
<https://cran.r-project.org/package=viridis>.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rmpfr-r33-0.6-1-1 (Multiple Precision Floating-Point Reliable)
Rmpfr provides (S4 classes and methods for) arithmetic including transcendental
("special") functions for arbitrary precision floating point numbers. To this
end, it interfaces to the LGPL'ed MPFR (Multiple Precision Floating-Point
Reliable) Library which itself is based on the GMP (GNU Multiple Precision)
Library.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcppgsl-r36-0.3.4-1 (Rcpp Integration for 'GNU GSL')
'Rcpp' integration for 'GNU GSL' vectors and matrices The 'GNU
Scientific Library' (or 'GSL') is a collection of numerical routines for
scientific computing. It is particularly useful for C and C++ programs
as it provides a standard C interface to a wide range of mathematical
routines. There are over 1000 functions in total with an extensive test
suite. The 'RcppGSL' package provides an easy-to-use interface between
'GSL' data structures and R using concepts from 'Rcpp' which is itself a
package that eases the interfaces between R and C++. This package also
serves as a prime example of how to build a package that uses 'Rcpp' to
connect to another third-party library. The 'autoconf' script, 'inline'
plugin and example package can all be used as a stanza to write a
similar package against another library.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-pscl-r34-1.5.2-1 (Political Science Computational Laboratory)
Bayesian analysis of item-response theory (IRT) models, roll call analysis;
computing highest density regions; maximum likelihood estimation of zero-
inflated and hurdle models for count data; goodness-of-fit measures for
GLMs; data sets used in writing and teaching at the Political Science
Computational Laboratory; seats-votes curves.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rda-r31-1.0.2-2.1-1 (Shrunken Centroids RDA)
Shrunken Centroids Regularized Discriminant Analysis
for the classification purpose in high dimensional data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-progress-r35-1.2.2-1 (Statnet project common scripts and utilities)

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-resemble-r35-1.2.2-3 (Similarity/dissimilarity and MBL analysis)
This package implements functions for spectral similarity/dissimilarity
analysis and memory-based learning (MBL) for non-linear modelling in
complex spectral datasets. MBL is also known as local modelling in the
chemometrics literature.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rmutil-r36-1.1.3-1 (Repeated Measurements Models Utilities)
A toolkit of functions for nonlinear regression and repeated
measurements not to be used by itself but called by other Lindsey
packages such as 'gnlm', 'stable', 'growth', 'repeated', and 'event'
(available at http://www.commanster.eu/rcode.html).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-prodlim-r33-2018.04.18-1 (GNU R Tools for estimation of survival)
Fast and user friendly nonparametric estimation in 
censored survival (event history) analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r2winbugs-r33-2.1-21-1 (Running WinBUGS and OpenBUGS from R / S-PLUS)
Using this package, it is possible to call a BUGS model, summarize
inferences and convergence in a table and graph, and save the
simulations in arrays for easy access in R / S-PLUS. In S-PLUS,
the openbugs functionality and the windows emulation functionality
is not yet available.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-polca-r31-1.4.1-1 (Polytomous variable Latent Class Analysis)
Latent class analysis and latent class regression models for
polytomous outcome variables. Also known as latent structure
analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-quantmod-r32-0.4-15-2 (Quantitative Financial Modelling Framework)
Specify, build, trade, and analyse quantitative financial trading strategies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-teachingdemos-r36-2.10-2 (Demonstrations for Teaching and Learning)
Demonstration functions that can be used in a classroom to 
demonstrate statistical concepts, or on your own to better 
understand the concepts or the programming.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-readstata13-r32-0.9.2-2 (Import 'Stata' Data Files)
Function to read and write the 'Stata' file format.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-webshot-r31-0.5.1-1 (Shiny UI Widgets for Small Screens)
Provides UI widget and layout functions for writing Shiny apps that work
well on small screens.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-ps-r36-1.3.0-1 (List, Query, Manipulate System Processes)
List, query and manipulate all system processes, on 'Windows', 'Linux'
and 'macOS'.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rngtools-r36-1.4-1 (Utility for Random Number Generators)
This package contains a set of functions for working with Random 
Number Generators (RNGs). In particular, it defines a generic S4 
framework for getting/setting the current RNG, or RNG data that 
are embedded into objects for reproducibility. Notably, convenient 
default methods greatly facilitate the way current RNG settings 
can be changed.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rann-r31-2.6.1-1 (Fast Nearest Neighbour Search)
Finds the k nearest neighbours for every point in a given dataset
in O(N log N) time using Arya and Mount's ANN library (v1.1.3).
There is support for approximate as well as exact searches,
fixed radius searches and bd as well as kd trees.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-stabledist-r32-0.7-1-1 (Stable Distribution Functions)
Density, Probability and Quantile functions, and random number
generation for (skew) stable distributions, using the
parametrizations of Nolan.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rhpcblasctl-r35-0.18-205-1 (Control the Number of Threads on 'BLAS')
Control the number of threads on 'BLAS' (Aka 'GotoBLAS', 'OpenBLAS',
'ACML', 'BLIS' and 'MKL'). And possible to control the number of threads
in 'OpenMP'. Get a number of logical cores and physical cores if
feasible.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-webshot-r34-0.5.1-1 (Shiny UI Widgets for Small Screens)
Provides UI widget and layout functions for writing Shiny apps that work
well on small screens.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r.methodss3-r32-1.7.1-1 (Utility function for defining S3 methods)
Methods that simplify the setup of S3 generic functions and S3 methods.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tinytex-r33-0.16-1 (Functions to Maintain 'TeX Live')
Helper functions to install and maintain the 'LaTeX' distribution named
'TinyTeX' (<https://yihui.name/tinytex/>), a lightweight,
cross-platform, portable, and easy-to-maintain version of 'TeX Live'.
This package also contains helper functions to compile 'LaTeX'
documents, and install missing 'LaTeX' packages automatically.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-timeseries-r32-3042.102-1 (Rmetrics - Financial Time Series Objects)
Environment for teaching "Financial Engineering and Computational Finance"

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-usethis-r33-1.5.0-1 (Automate Package and Project Setup)
Automate package and project setup tasks that are otherwise performed
manually. This includes setting up unit testing, test coverage,
continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio'
projects, and more.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-statmod-r31-1.4.32-2 (Statistical Modeling)
Various statistical modeling functions including growth curve comparisons,
limiting dilution analysis, mixed linear models, heteroscedastic regression,
Tweedie family generalized linear models, the inverse-Gaussian distribution
and Gauss quadrature.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-stringr-r36-1.4.0-1 (GNU R Tools for string function wrappers)
stringr is a set of simple wrappers that make R's string functions more 
consistent, simpler and easier to use. It does this by ensuring that: 
function and argument names (and positions) are consistent, all functions 
deal with NA's and zero length character appropriately, and the output 
data structures from each function matches the input data structures of 
other functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tsfa-r32-2014.10-1-1 (Time Series Factor Analysis)
Extraction of Factors from Multivariate Time Series.
See ?00tsfa-Intro for more details.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rematch-r32-1.0.1-1 (Match Regular Expressions with a Nicer API)
A small wrapper on 'regexpr' to extract the matches
and captured groups from the match of a regular expression
to a character vector.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-statmod-r34-1.4.32-2 (Statistical Modeling)
Various statistical modeling functions including growth curve comparisons,
limiting dilution analysis, mixed linear models, heteroscedastic regression,
Tweedie family generalized linear models, the inverse-Gaussian distribution
and Gauss quadrature.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-xts-r33-0.11-2-2 (The eXtensible Time Series)
Provide for uniform handling of R's different time-based data classes
by extending zoo, maximizing native format information preservation
and allowing for user level customization and extension, while
simplifying cross-class interoperability.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-profilemodel-r36-0.6.0-1 (Inference functions profiling tools)
profileModel provides tools that can be used to calculate, evaluate, plot
and use for inference the profiles of *arbitrary* inference functions for
for *arbitrary* 'glm'-like fitted models with linear predictors.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rpart-r36-4.1-15-1 (GNU R Tools for recursive partitioning)
Recursive partitioning and regression trees

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-vcd-r32-1.4-4-1 (Visualizing Categorical Data)
Visualization techniques, data sets, summary and inference procedures
aimed particularly at categorical data. Special emphasis is given to
highly extensible grid graphics. The package was inspired by the book
"Visualizing Categorical Data" by Michael Friendly.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-ptw-r34-1.9-13-1 (Parametric Time Warping)
Parametric Time Warping aligns patterns, i.e. it aims to put corresponding
features at the same locations. The algorithm searches for an optimal
polynomial describing the warping. It is possible to align one sample
to a reference, several samples to the same reference, or several samples
to several references. One can choose between calculating individual
warpings, or one global warping for a set of samples and one reference.
Two optimization criteria are implemented: RMS (Root Mean Square error)
and WCC (Weighted Cross Correlation).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sourcetools-r35-0.1.7-1 (Reading, Tokenizing and Parsing R Code)
Tools for the reading and tokenization of R code. The 'sourcetools'
package provides both an R and C++ interface for the tokenization of 
R code, and helpers for interacting with the tokenized representation
of R code.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rsnns-r32-0.4-12-1 (Stuttgart Neural Network Simulator in R)
The Stuttgart Neural Network Simulator (SNNS) is a library containing many
standard implementations of neural networks. This package wraps the SNNS
functionality to make it available from within R. Using the RSNNS low-level
interface, all of the algorithmic functionality and flexibility of SNNS can
be accessed. Furthermore, the package contains a convenient high-level
interface, so that the most common neural network topologies and learning
algorithms integrate seamlessly into R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-pracma-r32-2.2.5-1 (Practical Numerical Math Functions)
Functions from numerical analysis and linear algebra, numerical optimization,
differential equations, plus some special functions. Uses Matlab function names
where appropriate to simplify porting.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-zoo-r35-1.8-5-1 (GNU R Tools for ir/regular time series)
zoo: S3 Infrastructure for Regular and 
Irregular Time Series (Z's ordered observations)

An S3 class with methods for totally ordered indexed observations. 
It is particularly aimed at irregular time series of numeric vectors/matrices 
and factors.  zoo's key design goals are independence of a particular 
index/date/time class and consistency with ts and base R by providing 
methods to extend standard generics.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tis-r34-1.37.1-1 (Time Indexes and Time Indexed Series)
Functions and S3 classes for time indexes and time indexed
series, which are compatible with FAME frequencies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-usingr-r36-2.0-6-1 (GNU R data sets for "Using R for Intro Stats")
A collection of datasets to accompany the textbook
"Using R for Introductory Statistics."

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-ucminf-r32-1.1-4-2 (Unconstrained non-linear optimization)
An algorithm for general-purpose unconstrained non-linear optimization.
The algorithm is of quasi-Newton type with BFGS updating of the inverse
Hessian and soft line search with a trust region type monitoring of the
input to the line search algorithm. The interface of 'ucminf' is designed
for easy interchange with 'optim'.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rematch-r35-1.0.1-1 (Match Regular Expressions with a Nicer API)
A small wrapper on 'regexpr' to extract the matches
and captured groups from the match of a regular expression
to a character vector.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-trust-r36-0.1-7-1 (Trust Region Optimization)
local optimization using two derivatives and trust regions

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-quantreg-r35-5.51-2 (Quantile Regression)
Quantile regression and related methods.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rsvgdevice-r34-0.6.4.4-2 (R SVG graphics device)
A graphics device for R that uses the w3.org xml standard
for Scalable Vector Graphics.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-scatterplot3d-r35-0.3-41-1 (3D Scatter Plot)
Plots a three dimensional (3D) point cloud.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-spls-r32-2.2-3-1 (Sparse Partial Least Squares Regression)
This package provides functions for fitting a Sparse Partial
Least Squares Regression and Classification

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-reshapegui-r32-0.1.0-1 (GUI for the reshape2 and plyr packages)
A tool for learning how to use the functions, melt, acast/dcast, and ddply.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-testit-r34-0.10-1 (Simple package for testing R packages)
This package provides two convenience functions assert()
and test_pkg() to facilitate testing R packages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-speaq-r35-2.6.0-1 (NMR Spectrum Alignment Tools)
We introduce a novel suite of informatics tools for the quantitative analysis
of NMR metabolomic profile data. The core of the processing cascade is a novel
peak alignment algorithm, called hierarchical Cluster-based Peak Alignment
(CluPA). The algorithm aligns a target spectrum to the reference spectrum in
a top-down fashion by building a hierarchical cluster tree from peak lists of
reference and target spectra and then dividing the spectra into smaller
segments based on the most distant clusters of the tree. To reduce the
computational time to estimate the spectral misalignment, the method makes
use of Fast Fourier Transformation (FFT) cross-correlation. Since the method
returns a high-quality alignment, we can propose a simple methodology to study
the variability of the NMR spectra. For each aligned NMR data point the ratio
of the between-group and within-group sum of squares (BW-ratio) is calculated
to quantify the difference in variability between and within predefined groups
of NMR spectra. This differential analysis is related to the calculation of
the F-statistic or a one-way ANOVA, but without distributional assumptions.
Statistical inference based on the BW-ratio is achieved by bootstrapping the
null distribution from the experimental data. Related publication is
available at http://www.biomedcentral.com/1471-2105/12/405/.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-readjdx-r36-0.3.250-1 (Import Data in the JCAMP-DX Format)
Import data written in the JCAMP-DX format. This is an
instrument-independent format used in the field of spectroscopy.
Examples include IR, NMR, and Raman spectroscopy. See the vignette for
background and supported formats. The official JCAMP-DX site is
http://www.jcamp-dx.org/.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rserve-r36-1.7-3.1-1 (Binary R server)
Rserve acts as a socket server (TCP/IP or local sockets) which allows binary
requests to be sent to R. Every connection has a separate workspace and
working directory. Client-side implementations are available for popular
languages such as C/C++ and Java, allowing any application to use facilities
of R without the need of linking to R code. Rserve supports remote connection,
user authentication and file transfer. A simple R client is included in this
package as well.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-statnet.common-r34-3.3.0-1 (Statnet project common scripts and utilities)
Non-statistical utilities used by the software developed 
by the Statnet Project. They may also be of use to others.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-ptw-r35-1.9-13-1 (Parametric Time Warping)
Parametric Time Warping aligns patterns, i.e. it aims to put corresponding
features at the same locations. The algorithm searches for an optimal
polynomial describing the warping. It is possible to align one sample
to a reference, several samples to the same reference, or several samples
to several references. One can choose between calculating individual
warpings, or one global warping for a set of samples and one reference.
Two optimization criteria are implemented: RMS (Root Mean Square error)
and WCC (Weighted Cross Correlation).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-readxl-r34-1.3.1-2 (Read Excel Files)
Import excel files into R. Supports '.xls' via the embedded
'libxls' C library (http://sourceforge.net/projects/libxls/)
and '.xlsx' via the embedded 'RapidXML' C++ library
(http://rapidxml.sourceforge.net). Works on Windows, Mac
 and Linux without external dependencies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rcpp-r33-1.0.2-2 (Seamless R and C++ Integration)
The Rcpp package provides R functions as well as a C++ library which
facilitate the integration of R and C++.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rweka-r31-0.4-40-1 (R/Weka interface)
An R interface to Weka (Version 3.7.11). Weka is a collection of machine
learning algorithms for data mining tasks written in Java, containing
tools for data pre-processing, classification, regression, clustering,
association rules, and visualization. Package RWeka contains the interface
code, the Weka jar is in a separate package RWekajars. For more information
on Weka see http://www.cs.waikato.ac.nz/~ml/weka/.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-zoo-r34-1.8-5-1 (GNU R Tools for ir/regular time series)
zoo: S3 Infrastructure for Regular and 
Irregular Time Series (Z's ordered observations)

An S3 class with methods for totally ordered indexed observations. 
It is particularly aimed at irregular time series of numeric vectors/matrices 
and factors.  zoo's key design goals are independence of a particular 
index/date/time class and consistency with ts and base R by providing 
methods to extend standard generics.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tis-r35-1.37.1-1 (Time Indexes and Time Indexed Series)
Functions and S3 classes for time indexes and time indexed
series, which are compatible with FAME frequencies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rtsne-r34-0.15-2 (T-distributed Stochastic Neighbor Embedding)
An R wrapper around the fast T-distributed Stochastic 
Neighbor Embedding implementation by Van der Maaten.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-processx-r31-3.4.1-1 (Execute and Control System Processes)
Tools to run system processes in the background. It can check if a
background process is running; wait on a background process to finish;
get the exit status of finished processes; kill background processes. It
can read the standard output and error of the processes, using
non-blocking connections. 'processx' can poll a process for standard
output or error, with a timeout. It can also poll several processes at
once.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcdk-r35-3.4.7.1-1 (Interface to the CDK Libraries)
This package allows the user to access functionality in the CDK,
a Java framework for cheminformatics. This allows the user to load
molecules, evaluate fingerprints, calculate molecular descriptors
and so on. In addition the CDK API allows the user to view structures
in 2D.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rocr-r32-1.0-7-1 (Visualizing scoring classifier performance)
ROC graphs, sensitivity/specificity curves, lift charts, and
precision/recall plots are popular examples of trade-off
visualizations for specific pairs of performance measures. ROCR
is a flexible tool for creating cutoff-parameterized 2D
performance curves by freely combining two from over 25
performance measures (new performance measures can be added
using a standard interface). Curves from different cross-
alidation or bootstrapping runs can be averaged by different
methods, and standard deviations, standard errors or box plots
can be used to visualize the variability across the runs. The
parameterization can be visualized by printing cutoff values
at the corresponding curve positions, or by coloring the curve
according to cutoff. All components of a performance plot can
be quickly adjusted using a flexible parameter dispatching
mechanism. Despite its flexibility, ROCR is easy to use, with
only three commands and reasonable default values for all
optional parameters.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-subselect-r34-0.14-2 (Selecting variable subsets)
A collection of functions which (i) assess the quality of variable
subsets as surrogates for a full data set, in either an exploratory
data analysis or in the context of a multivariate linear model, and
(ii) search for subsets which are optimal under various criteria.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-sroc-r31-0.1-2-3 (Nonparametric Smooth ROC Curves)
This package contains a collection of functions to perform
 nonparametric estimation of receiver operating 
 characteristic (ROC) curves for continuous data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sca-r31-0.9-0-1 (Simple Component Analysis)
Simple Component Analysis (SCA) often provides much more interpretable
components than Principal Components (PCA) while still representing
much of the variability in the data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rstudioapi-r34-0.10-1 (Safely access the RStudio API)
This package provides functions to make it easy to access the RStudio
API when available, and provide informative error messages when not.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-processx-r34-3.4.1-1 (Execute and Control System Processes)
Tools to run system processes in the background. It can check if a
background process is running; wait on a background process to finish;
get the exit status of finished processes; kill background processes. It
can read the standard output and error of the processes, using
non-blocking connections. 'processx' can poll a process for standard
output or error, with a timeout. It can also poll several processes at
once.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-xfun-r31-0.10-1 (Misc. functions by Yihui Xie)
Miscellaneous functions commonly used in other packages maintained
by 'Yihui Xie'.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-teachingdemos-r31-2.10-2 (Demonstrations for Teaching and Learning)
Demonstration functions that can be used in a classroom to 
demonstrate statistical concepts, or on your own to better 
understand the concepts or the programming.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-ucminf-r35-1.1-4-2 (Unconstrained non-linear optimization)
An algorithm for general-purpose unconstrained non-linear optimization.
The algorithm is of quasi-Newton type with BFGS updating of the inverse
Hessian and soft line search with a trust region type monitoring of the
input to the line search algorithm. The interface of 'ucminf' is designed
for easy interchange with 'optim'.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-withr-r33-2.1.2-1 (Run Code w/ Temporarily Modified Global State)
A set of functions to run code 'with' safely and temporarily 
modified global state. Many of these functions were originally 
a part of the 'devtools' package, this provides a simple package 
with limited dependencies to provide access to these functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcmdrmisc-r32-1.0-9-1 (R Commander Miscellaneous Functions)
Various statistical, graphics, and data-management functions
used by the Rcmdr package in the R Commander GUI for R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-pracma-r35-2.2.5-1 (Practical Numerical Math Functions)
Functions from numerical analysis and linear algebra, numerical optimization,
differential equations, plus some special functions. Uses Matlab function names
where appropriate to simplify porting.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tree-r36-1.0-40-1 (GNU R Tools for classification trees)
Classification and Regression Trees.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-subselect-r36-0.14-2 (Selecting variable subsets)
A collection of functions which (i) assess the quality of variable
subsets as surrogates for a full data set, in either an exploratory
data analysis or in the context of a multivariate linear model, and
(ii) search for subsets which are optimal under various criteria.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-testthat-r35-2.2.1-1 (Testthat code)
A testing package specifically tailored for R that's fun,
flexible and easy to set up.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-runit-r35-0.4.32-1 (R Unit test framework)
R functions implementing a standard Unit Testing framework,
with additional code inspection and report generation tools

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-wilcoxcv-r32-1.0-2-1 (Wilcoxon-based variable selection in cv)
This package provides functions to perform fast variable selection
based on the Wilcoxon rank sum test in the cross-validation or
Monte-Carlo cross-validation settings, for use in microarray-based
binary classification.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-trimcluster-r31-0.1-2.1-1 (Cluster analysis with trimming)
Trimmed k-means clustering.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rmutil-r34-1.1.3-1 (Repeated Measurements Models Utilities)
A toolkit of functions for nonlinear regression and repeated
measurements not to be used by itself but called by other Lindsey
packages such as 'gnlm', 'stable', 'growth', 'repeated', and 'event'
(available at http://www.commanster.eu/rcode.html).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcpp-r36-1.0.2-2 (Seamless R and C++ Integration)
The Rcpp package provides R functions as well as a C++ library which
facilitate the integration of R and C++.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-r2winbugs-r31-2.1-21-1 (Running WinBUGS and OpenBUGS from R / S-PLUS)
Using this package, it is possible to call a BUGS model, summarize
inferences and convergence in a table and graph, and save the
simulations in arrays for easy access in R / S-PLUS. In S-PLUS,
the openbugs functionality and the windows emulation functionality
is not yet available.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-simpleboot-r34-1.1-7-1 (GNU R Tools for simple bootstrap)
Simple bootstrap routines

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-slam-r31-0.1-34-2 (Sparse Lightweight Arrays and Matrices)
Data structures and algorithms for sparse arrays and matrices,
based on index arrays and simple triplet representations, respectively.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-polynomf-r34-2.0-2-1 (Polynomials in R)
Implements univariate polynomial operations in R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcolorbrewer-r32-1.1-2-1 (GNU R Tools for variable-dependent palettes)
The packages provides palettes for drawing nice maps shaded 
according to a variable.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-promises-r32-1.1.0-1 (Promise-Based Asynchronous Programming)
Provides fundamental abstractions for doing asynchronous programming in
R using promises. Asynchronous programming is useful for allowing a
single R process to orchestrate multiple tasks in the background while
also attending to something else. Semantics are similar to 'JavaScript'
promises, but with a syntax that is idiomatic R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-signal-r36-0.7-6-2 (Signal processing)
A set of signal processing R functions originally written for Matlab/Octave.
Includes filter generation utilities, filtering functions, resampling
routines, and visualization of filter models. It also includes interpolation
functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-polynomf-r31-2.0-2-1 (Polynomials in R)
Implements univariate polynomial operations in R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tfplot-r36-2015.12-1-1 (Time Frame User Utilities)
Utilities in this package are for simple manipulation and quick
plotting of time series data. These utilities use the tframe
package which provides a programming kernel for time series.
Extensions to tframe provided in tframePlus can also be used.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcdk-r34-3.4.7.1-1 (Interface to the CDK Libraries)
This package allows the user to access functionality in the CDK,
a Java framework for cheminformatics. This allows the user to load
molecules, evaluate fingerprints, calculate molecular descriptors
and so on. In addition the CDK API allows the user to view structures
in 2D.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-reshape2-r33-1.4.3-1 (Flexibly reshape data)
Reshape lets you flexibly restructure and aggregate data using
just two functions: melt and cast.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-scales-r33-1.0.0-1 (Scale functions for graphics)
Scales map data to aesthetics, and provide methods for automatically
determining breaks and labels for axes and legends.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rms-r32-4.5-0-2 (Regression Modeling Strategies)
Regression modeling, testing, estimation, validation, graphics,
prediction, and typesetting by storing enhanced model design
attributes in the fit. rms is a collection of functions that
assist with and streamline modeling. It also contains functions
for binary and ordinal logistic regression models, ordinal
models for continuous Y with a variety of distribution families,
and the Buckley-James multiple regression model for
right-censored responses, and implements penalized maximum
likelihood estimation for logistic and ordinary linear models.
rms works with almost any regression model, but it was especially
written to work with binary or ordinal regression models,
Cox regression, accelerated failure time models, ordinary
linear models,        the Buckley-James model, generalized least
squares for serially or spatially correlated observations,
generalized linear models, and quantile regression.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-scrime-r33-1.3.5-1 (Analysis of High-Dimensional Categorical Data)
Tools for the analysis of high-dimensional data developed/implemented 
at the group "Statistical Complexity Reduction In Molecular Epidemiology" 
(SCRIME). Main focus is on SNP data. But most of the functions can also 
be applied to other types of categorical data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    New upstream Bioconductor versions (bioc 3.10)
2020-01-16: cran-profilemodel-r31-0.6.0-1 (Inference functions profiling tools)
profileModel provides tools that can be used to calculate, evaluate, plot
and use for inference the profiles of *arbitrary* inference functions for
for *arbitrary* 'glm'-like fitted models with linear predictors.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tree-r33-1.0-39-1 (GNU R Tools for classification trees)
Classification and Regression Trees.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-robcompositions-r31-2.0.10-1 (Robust Estimation for Compositional Data)
The package includes methods for imputation of compositional data
including robust methods, methods to impute rounded zeros, (robust)
outlier detection for compositional data, (robust) principal component
analysis for compositional data, (robust) factor analysis for
compositional data, (robust) discriminant analysis for compositional
data (Fisher rule), robust regression with compositional predictors and
(robust) Anderson-Darling normality tests for compositional data as well
as popular log-ratio transformations (addLR, cenLR, isomLR, and their
inverse transformations). In addition, visualisation and diagnostic
tools are implemented as well as high and low-level plot functions for
the ternary diagram.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r2html-r34-2.3.2-1 (HTML exportation for R objects)
Includes HTML function and methods to write in an HTML file.
Thus, making HTML reports is easy. Includes a function that
allows redirection on the fly, which appears to be very usefull
for teaching purpose, as the student can keep a copy of the
produced output to keep all that he did during the course.
Package comes with a vignette describing how to write HTML
reports for statistical analysis. Finally, a driver for Sweave
allows to parse HTML flat files containing R code and to
automatically write the corresponding outputs (tables and graphs).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r2winbugs-r35-2.1-21-1 (Running WinBUGS and OpenBUGS from R / S-PLUS)
Using this package, it is possible to call a BUGS model, summarize
inferences and convergence in a table and graph, and save the
simulations in arrays for easy access in R / S-PLUS. In S-PLUS,
the openbugs functionality and the windows emulation functionality
is not yet available.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-visnetwork-r36-2.0.8-1 (Network Visualization)
Provides an R interface to the 'vis.js' JavaScript charting library. It
allows an interactive visualization of networks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rsqlite-r36-2.1.2-1 (SQLite interface for R)
Database Interface R driver for SQLite. This package embeds the SQLite
database engine in R and provides an interface compliant with the DBI
package. The source for the SQLite engine (version 3.7.17) is included.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-xlconnectjars-r33-0.2-15-1 (JAR dependencies for the XLConnect)
Provides external JAR dependencies for the XLConnect package.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-timeseries-r35-3042.102-1 (Rmetrics - Financial Time Series Objects)
Environment for teaching "Financial Engineering and Computational Finance"

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-visnetwork-r33-2.0.8-1 (Network Visualization)
Provides an R interface to the 'vis.js' JavaScript charting library. It
allows an interactive visualization of networks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-spatialnp-r34-1.1-3-1 (Spatial Multivariate nonparametric methods)
This package contains test and estimates of location, tests of independence,
tests of sphericity and several estimates of shape all based on spatial signs,
symmetrized signs, ranks and signed ranks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r.matlab-r34-3.6.2-1 (Read and write of MAT files)
This package provides methods readMat() and writeMat() to read
and write MAT files. It also makes it possible to communicate
(evaluate code, send and retrieve objects etc.) with MATLAB v6
or higher running locally or on a remote host.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-scarabee-r34-1.1-3-2 (R port of the Scarabee toolkit)
scaRabee is a port of the Scarabee toolkit originally written as a Matlab-based
application. It provides a framework for simulation and optimization of
pharmacokinetic-pharmacodynamic models at the individual and population level.
It is built on top of the neldermead package, which provides the direct search
algorithm proposed by Nelder and Mead for model optimization.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcppeigen-r35-0.3.3.5.0-2 (Rcpp Eigen templated linear algebra library)
R and Eigen integration using Rcpp. Eigen is a C++ template library
for linear algebra: matrices, vectors, numerical solvers and related
algorithms. It supports dense and sparse matrices on integer,
floating point and complex numbers, decompositions of such matrices,
and solutions of linear systems. Its performance on many algorithms
is comparable with some of the best implementations based on Lapack
and level-3 BLAS. The RcppEigen package includes the header files
from the Eigen C++ template library (currently version 3.2.0).
Thus users do not need to install Eigen itself in order to use
RcppEigen. Since version 3.1.1, Eigen is licensed under the
Mozilla Public License (version 2); earlier version were licensed
under the GNU LGPL version 3 or later. RcppEigen (the Rcpp
bindings/bridge to Eigen) is licensed under the GNU GPL version 2
 or later, as is the rest of Rcpp.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-shape-r34-1.4.4-1 (Plotting graphical shapes, colors)
Functions for plotting graphical shapes such as ellipses,
circles, cylinders, arrows, ...

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rio-r31-0.5.16-2 (Swiss-Army Knife for Data I/O)
Streamlined data import and export by making assumptions that the user
is probably willing to make: 'import()' and 'export()' determine the
data structure from the file extension, reasonable defaults are used for
data import and export (e.g., 'stringsAsFactors=FALSE'), web-based
import is natively supported (including from SSL/HTTPS), compressed
files can be read directly without explicit decompression, and fast
import packages are used where appropriate. An additional convenience
function, 'convert()', provides a simple method for converting between
file types.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-xml2-r31-1.2.2-2 (Parse XML)
Work with XML files using a simple, consistent interface. Built on top of 
the 'libxml2' C library.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-stringi-r35-1.4.3-1 (Character String Processing Facilities)
Allows for fast, correct, consistent, portable, as well as 
convenient character string/text processing in every locale 
and any native encoding. Owing to the use of the ICU library, 
the package provides R users with platform-independent 
functions known to Java, Perl, Python, PHP, and Ruby 
programmers. Among available features there are: pattern 
searching (e.g., with ICU Java-like regular expressions 
or the Unicode Collation Algorithm), random string generation, 
case mapping, string transliteration, concatenation, Unicode 
normalization, date-time formatting and parsing, etc.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-spatialnp-r36-1.1-3-1 (Spatial Multivariate nonparametric methods)
This package contains test and estimates of location, tests of independence,
tests of sphericity and several estimates of shape all based on spatial signs,
symmetrized signs, ranks and signed ranks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rwave-r34-2.4-8-1 (Time-Frequency analysis of 1-D signals)
Rwave is a library of R functions which provide an environment for
the Time-Frequency analysis of 1-D signals (and especially for the
wavelet and Gabor transforms of noisy signals). It was originally
written for Splus by Rene Carmona, Bruno Torresani, and Wen L. 
wang, first at the University of California at Irvine and then
at Princeton University. Credit should also be given to Andrea
Wang whose functions on the dyadic wavelet transform are included.
Rwave is based on the book: "Practical Time-Frequency Analysis:
Gabor and Wavelet Transforms with an Implementation in S", by Rene
Carmona, Wen L. Hwang and Bruno Torresani, Academic Press, 1998.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-progress-r31-1.2.2-1 (Statnet project common scripts and utilities)

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rootsolve-r36-1.7-2 (Analysis of ordinary differential equations)
Routines to find the root of nonlinear functions, and to perform
steady-state and equilibrium analysis of ordinary differential
equations (ODE). Includes routines that: (1) generate gradient
and Jacobian matrices (full and banded), (2) find roots of
non-linear equations by the Newton-Raphson method, (3) estimate
steady-state conditions of a system of (differential) equations
in full, banded or sparse form, using the Newton-Raphson method,
or by dynamically running, (4) solve the steady-state conditions
for uni-and multicomponent 1-D, 2-D, and 3-D partial differential
equations, that have been converted to ODEs by numerical differencing
(using the method-of-lines approach). Includes fortran code.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-progress-r34-1.2.2-1 (Statnet project common scripts and utilities)

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-resemble-r34-1.2.2-3 (Similarity/dissimilarity and MBL analysis)
This package implements functions for spectral similarity/dissimilarity
analysis and memory-based learning (MBL) for non-linear modelling in
complex spectral datasets. MBL is also known as local modelling in the
chemometrics literature.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rcurl-r33-1.95-4.12-1 (Network client (HTTP/FTP/...) R interface)
The package allows one to compose general HTTP requests and provides
convenient functions to fetch URIs, get & post forms, etc. and process
the results returned by the Web server. This provides a great deal of
control over the HTTP/FTP/... connection and the form of the request 
while providing a higher-level interface than is available just using
R socket connections. Additionally, the underlying implementation is
robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads),
SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects,
authentication, etc.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sem-r35-3.1-9-2 (Structural Equation Models)
This package contains functions for fitting general linear
structural equation models (with observed and unobserved
variables) using the RAM approach, and for fitting structural
equations in observed-variable models by two-stage least squares.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-readxl-r33-1.3.1-2 (Read Excel Files)
Import excel files into R. Supports '.xls' via the embedded
'libxls' C library (http://sourceforge.net/projects/libxls/)
and '.xlsx' via the embedded 'RapidXML' C++ library
(http://rapidxml.sourceforge.net). Works on Windows, Mac
 and Linux without external dependencies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rcmdrplugin.doby-r31-0.1-3-1 (Rcmdr doBy Plug-In)
This package provides an Rcmdr "plug-in" for the core doBy functions
in the doBy package, which helps with computing groupwise summary statistics.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-stabledist-r35-0.7-1-1 (Stable Distribution Functions)
Density, Probability and Quantile functions, and random number
generation for (skew) stable distributions, using the
parametrizations of Nolan.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rootsolve-r34-1.7-2 (Analysis of ordinary differential equations)
Routines to find the root of nonlinear functions, and to perform
steady-state and equilibrium analysis of ordinary differential
equations (ODE). Includes routines that: (1) generate gradient
and Jacobian matrices (full and banded), (2) find roots of
non-linear equations by the Newton-Raphson method, (3) estimate
steady-state conditions of a system of (differential) equations
in full, banded or sparse form, using the Newton-Raphson method,
or by dynamically running, (4) solve the steady-state conditions
for uni-and multicomponent 1-D, 2-D, and 3-D partial differential
equations, that have been converted to ODEs by numerical differencing
(using the method-of-lines approach). Includes fortran code.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-scarabee-r31-1.1-3-2 (R port of the Scarabee toolkit)
scaRabee is a port of the Scarabee toolkit originally written as a Matlab-based
application. It provides a framework for simulation and optimization of
pharmacokinetic-pharmacodynamic models at the individual and population level.
It is built on top of the neldermead package, which provides the direct search
algorithm proposed by Nelder and Mead for model optimization.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r.matlab-r31-3.6.2-1 (Read and write of MAT files)
This package provides methods readMat() and writeMat() to read
and write MAT files. It also makes it possible to communicate
(evaluate code, send and retrieve objects etc.) with MATLAB v6
or higher running locally or on a remote host.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-runit-r32-0.4.32-1 (R Unit test framework)
R functions implementing a standard Unit Testing framework,
with additional code inspection and report generation tools

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sensominer-r31-1.23-1 (Sensory data analysis with R)
an R package for analysing sensory data

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-proc-r36-1.15.3-1 (Display and analyze ROC curves)
Display and analyze ROC curves

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r6-r36-2.4.0-1 (Classes with reference semantics)
The R6 package allows the creation of classes with reference semantics,
similar to R's built-in reference classes. Compared to reference classes,
R6 classes are simpler and lighter-weight, and they are not built on S4
classes so they do not require the methods package. These classes allow
public and private members, and they support inheritance, even when the
classes are defined in different packages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tm-r35-0.7-6-1 (Text Mining Package)
A framework for text mining applications within R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcppeigen-r31-0.3.3.5.0-2 (Rcpp Eigen templated linear algebra library)
R and Eigen integration using Rcpp. Eigen is a C++ template library
for linear algebra: matrices, vectors, numerical solvers and related
algorithms. It supports dense and sparse matrices on integer,
floating point and complex numbers, decompositions of such matrices,
and solutions of linear systems. Its performance on many algorithms
is comparable with some of the best implementations based on Lapack
and level-3 BLAS. The RcppEigen package includes the header files
from the Eigen C++ template library (currently version 3.2.0).
Thus users do not need to install Eigen itself in order to use
RcppEigen. Since version 3.1.1, Eigen is licensed under the
Mozilla Public License (version 2); earlier version were licensed
under the GNU LGPL version 3 or later. RcppEigen (the Rcpp
bindings/bridge to Eigen) is licensed under the GNU GPL version 2
 or later, as is the rest of Rcpp.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-simecol-r36-0.8-13-1 (Simulation of ecological dynamic systems)
simecol is an object oriented framework to simulate ecological (and other)
dynamic systems. It can be used for differential equations, individual-based
(or agent-based) and other models as well. The package helps to organize
scenarios (avoids copy and paste) and improves readability and usability of
code.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-scales-r34-1.0.0-1 (Scale functions for graphics)
Scales map data to aesthetics, and provide methods for automatically
determining breaks and labels for axes and legends.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rio-r36-0.5.16-2 (Swiss-Army Knife for Data I/O)
Streamlined data import and export by making assumptions that the user
is probably willing to make: 'import()' and 'export()' determine the
data structure from the file extension, reasonable defaults are used for
data import and export (e.g., 'stringsAsFactors=FALSE'), web-based
import is natively supported (including from SSL/HTTPS), compressed
files can be read directly without explicit decompression, and fast
import packages are used where appropriate. An additional convenience
function, 'convert()', provides a simple method for converting between
file types.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-reshapegui-r35-0.1.0-1 (GUI for the reshape2 and plyr packages)
A tool for learning how to use the functions, melt, acast/dcast, and ddply.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-polspline-r36-1.1.16-2 (Polynomial spline routines)
Routines for the polynomial spline fitting routines hazard regression,
hazard estimation with flexible tails, logspline, lspec, polyclass,
and polymars, by C. Kooperberg and co-authors

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-sparsem-r33-1.77-2 (Sparse Linear Algebra)
Basic linear algebra for sparse matrices

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rcmdr-r36-2.6-0-1 (R Commander)
A platform-independent basic-statistics GUI (graphical user
interface) for R, based on the tcltk package.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r2html-r33-2.3.2-1 (HTML exportation for R objects)
Includes HTML function and methods to write in an HTML file.
Thus, making HTML reports is easy. Includes a function that
allows redirection on the fly, which appears to be very usefull
for teaching purpose, as the student can keep a copy of the
produced output to keep all that he did during the course.
Package comes with a vignette describing how to write HTML
reports for statistical analysis. Finally, a driver for Sweave
allows to parse HTML flat files containing R code and to
automatically write the corresponding outputs (tables and graphs).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sfsmisc-r36-1.1-4-1 (Utilities from Statistik ETH Zurich seminar)
Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich,
quite a few related to graphics; many ported from S-plus times.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tidyselect-r31-0.2.5-1 (Select from a Set of Strings)
A backend for the selecting functions of the 'tidyverse'. It makes it
easy to implement select-like functions in your own packages in a way
that is consistent with other 'tidyverse' interfaces for selection.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-polspline-r34-1.1.16-2 (Polynomial spline routines)
Routines for the polynomial spline fitting routines hazard regression,
hazard estimation with flexible tails, logspline, lspec, polyclass,
and polymars, by C. Kooperberg and co-authors

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-polyclip-r33-1.10-0-1 (Polygon Clipping)
R port of the Clipper library. Performs polygon clipping operations
(intersection, union, set minus, set difference) for polygonal regions
of arbitrary complexity, including holes. Also computes offset polygons
(spatial buffer zones, morphological dilations, Minkowski dilations)
for polygonal regions and polygonal lines.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-scrime-r34-1.3.5-1 (Analysis of High-Dimensional Categorical Data)
Tools for the analysis of high-dimensional data developed/implemented 
at the group "Statistical Complexity Reduction In Molecular Epidemiology" 
(SCRIME). Main focus is on SNP data. But most of the functions can also 
be applied to other types of categorical data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    New upstream Bioconductor versions (bioc 3.10)
2020-01-16: cran-relimp-r35-1.0-5-1 (Relative Contribution of Effects)
Functions to facilitate inference on the relative importance
of predictors in a linear or generalized linear model, and
a couple of useful Tcl/Tk widgets.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rvest-r34-0.3.4-1 (Easily harvest web pages)
Wrappers around the 'xml2' and 'httr' packages to make it easy to
download, then manipulate, HTML and XML.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-varselrf-r36-0.7-8-1 (Variable selection using random forests)
Variable selection from random forests using both backwards variable
elimination (for the selection of small sets of non-redundant variables)
and selection based on the importance spectrum (somewhat similar to
scree plots; for the selection of large, potentially highly-correlated
variables). Main applications in high-dimensional data (e.g., microarray
data, and other genomics and proteomics applications). You can use rpvm
instead of Rmpi if you want but I've only tested with Rmpi.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcpproll-r36-0.3.0-1 (Efficient Rolling / Windowed Operations)
Provides fast and efficient routines for common rolling / windowed
operations. Routines for the efficient computation of windowed mean,
median, sum, product, minimum, maximum, standard deviation and variance
are provided.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-robustrankaggreg-r35-1.1-2 (Methods for robust rank aggregation)
Methods for aggregating ranked lists, especially lists of genes. It 
implements the Robust Rank Aggregation (Kolde et. al in preparation) 
and some other simple algorithms for the task. RRA method uses a 
probabilistic model for aggregation that is robust to noise and also 
facilitates the calculation of significance probabilities for all the 
elements in the final ranking.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-xlsxjars-r33-0.6.1-1 (Package required POI jars for xlsx package)
The xlsxjars package collects all the external jars required for the
xlxs package. These external jars are quite large in size (15MB) and
have a slow release cycle. By separating the Java and R development,
the storage footprint on CRAN is reduced. This release corresponds
to POI 3.10.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rmutil-r33-1.1.3-1 (Repeated Measurements Models Utilities)
A toolkit of functions for nonlinear regression and repeated
measurements not to be used by itself but called by other Lindsey
packages such as 'gnlm', 'stable', 'growth', 'repeated', and 'event'
(available at http://www.commanster.eu/rcode.html).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-v8-r36-2.3-2 (Embedded JavaScript Engine for R)
An R interface to Google's open source JavaScript engine.
V8 is written in C++ and implements ECMAScript as specified in ECMA-262,
5th edition. In addition, this package implements typed arrays as specified
in ECMA 6 used for high-performance computing and libraries compiled
with 'emscripten'.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rcppprogress-r32-0.4.1-1 (Interruptible Progress Bar)
Allows to display a progress bar in the R console for long running
computations taking place in c++ code, and support for interrupting
those computations even in multithreaded code, typically using OpenMP.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-stringi-r32-1.4.3-1 (Character String Processing Facilities)
Allows for fast, correct, consistent, portable, as well as 
convenient character string/text processing in every locale 
and any native encoding. Owing to the use of the ICU library, 
the package provides R users with platform-independent 
functions known to Java, Perl, Python, PHP, and Ruby 
programmers. Among available features there are: pattern 
searching (e.g., with ICU Java-like regular expressions 
or the Unicode Collation Algorithm), random string generation, 
case mapping, string transliteration, concatenation, Unicode 
normalization, date-time formatting and parsing, etc.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tibble-r32-2.1.3-1 (Simple Data Frames)
Provides a `tbl_df' class (the `tibble') that provides stricter checking 
and better formatting than the traditional data frame.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-proc-r33-1.15.3-1 (Display and analyze ROC curves)
Display and analyze ROC curves

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-timedate-r35-3043.102-1 (Rmetrics - Chronological and Calendar Objects)
Environment for teaching "Financial Engineering and Computational Finance"

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sgeostat-r36-1.0-27-3 (Framework for Geostatistical Modeling in S+)
An Object-oriented Framework for Geostatistical Modeling in S+

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-snow-r33-0.4-3-1 (Simple Network of Workstations)
Support for simple parallel computing in R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcmdcheck-r35-1.3.3-1 (Run 'R CMD check' from 'R')
Run 'R CMD check' from 'R' programmatically, and capture the results of
the individual checks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-waveslim-r35-1.7.5.1-2 (Basic wavelet routines)
Basic wavelet routines for time series (1D), image (2D) and
array (3D) analysis.The code provided here is based on wavelet
methodology developed in Percival and Walden (2000); Gencay,
Selcuk and Whitcher (2001); the dual-tree complex wavelet 
transform (DTCWT) from Kingsbury (1999, 2001) as implemented
by Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-r2stats-r34-0.68-39-1 (GTK GUI for fitting and comparing GLM and GLM)
R2STATS is a gWidgetsRGtk2 GUI for fitting and comparing GLM or GLMM (based
on Douglas Bates' lme4 package) in R. It is designed to make comparisons
between numerous models easy, both numerically and graphically, which may
be useful for teaching. Relevant plots are automatically produced for each
model family. R2STATS is *not* a generic graphical interface for R, but a
GUI for statistical modelling in a model comparison approach.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-titan-r33-1.0-16-2 (Titration analysis for mass spec data)
GUI to analyze mass spectrometric data on the relative
abundance of two substances from a titration series.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-registry-r32-0.5-1-1 (Infrastructure for R Package Registries)
Provides a generic infrastructure for creating and using registries.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tibble-r35-2.1.3-1 (Simple Data Frames)
Provides a `tbl_df' class (the `tibble') that provides stricter checking 
and better formatting than the traditional data frame.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-readstata13-r36-0.9.2-2 (Import 'Stata' Data Files)
Function to read and write the 'Stata' file format.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-randomfieldsutils-r36-0.5.3-2 (Utilities for Random Fields)
Various utilities are provided that might be used in 
spatial statistics and elsewhere. It delivers a method 
for solving linear equations that checks the sparsity 
of the matrix before any algorithm is used. Furthermore, 
it includes the Struve functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-relimp-r32-1.0-5-1 (Relative Contribution of Effects)
Functions to facilitate inference on the relative importance
of predictors in a linear or generalized linear model, and
a couple of useful Tcl/Tk widgets.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-ptak-r31-1.3-34-1 (Principal Tensor Analysis on k modes)
A multiway method to decompose a tensor (array) of any order, as a
generalisation of SVD also supporting non-identity metrics and
penalisations. 2-way SVD with these extensions is also available.
The package includes also some other multiway methods: PCAn
(Tucker-n) and PARAFAC/CANDECOMP with these extensions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-r.methodss3-r36-1.7.1-1 (Utility function for defining S3 methods)
Methods that simplify the setup of S3 generic functions and S3 methods.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-xlsx-r35-0.6.1-1 (Excel 2007 and Excel 97/2000/XP/2003 support)
Provide R functions to read/write/format Excel 2007 and
Excel 97/2000/XP/2003 file formats.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-r2stats-r31-0.68-39-1 (GTK GUI for fitting and comparing GLM and GLM)
R2STATS is a gWidgetsRGtk2 GUI for fitting and comparing GLM or GLMM (based
on Douglas Bates' lme4 package) in R. It is designed to make comparisons
between numerous models easy, both numerically and graphically, which may
be useful for teaching. Relevant plots are automatically produced for each
model family. R2STATS is *not* a generic graphical interface for R, but a
GUI for statistical modelling in a model comparison approach.

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2020-01-16: cran-readr-r34-1.3.1-1 (Read Rectangular Text Data)
The goal of 'readr' is to provide a fast and friendly way to read
rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to
flexibly parse many types of data found in the wild, while still
cleanly failing when data unexpectedly changes.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-randomforest-r35-4.6-12-1 (GNU R Tools for random forest class/regress)
Classification and regression based on a forest of trees using random inputs.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rgl-r33-0.100.30-1 (3D visualization device system)
Provides medium to high level functions for 3D interactive graphics,
including functions modelled on base graphics (plot3d(), etc.) as
well as functions for constructing representations of geometric objects
(cube3d(), etc.). Output may be on screen using OpenGL, or to various
standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
image formats, including PNG, Postscript, SVG, PGF.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-utf8-r34-1.1.4-1 (Unicode Text Processing)
Process and print 'UTF-8' encoded international text (Unicode). Input,
validate, normalize, encode, format, and display.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tables-r31-0.8.8-1 (Formula-driven table generation)
Computes and displays complex tables of summary statistics

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-xlconnectjars-r34-0.2-15-1 (JAR dependencies for the XLConnect)
Provides external JAR dependencies for the XLConnect package.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rgtk2-r33-2.20.31-2 (R bindings for Gtk 2.8.0 and above)
Facilities in the R language for programming graphical
interfaces using Gtk, the Gimp Tool Kit.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcmdcheck-r31-1.3.3-1 (Run 'R CMD check' from 'R')
Run 'R CMD check' from 'R' programmatically, and capture the results of
the individual checks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rrcov-r31-1.4-7-2 (Scalable Robust Estimators)
Robust Location and Scatter Estimation and Robust Multivariate
Analysis with High Breakdown Point.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-snow-r36-0.4-3-1 (Simple Network of Workstations)
Support for simple parallel computing in R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rsnns-r35-0.4-12-1 (Stuttgart Neural Network Simulator in R)
The Stuttgart Neural Network Simulator (SNNS) is a library containing many
standard implementations of neural networks. This package wraps the SNNS
functionality to make it available from within R. Using the RSNNS low-level
interface, all of the algorithmic functionality and flexibility of SNNS can
be accessed. Furthermore, the package contains a convenient high-level
interface, so that the most common neural network topologies and learning
algorithms integrate seamlessly into R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-vgamdata-r32-1.0-3-1 (Data supporting the VGAM package)
Data sets to accompany the VGAM package. These are used to illustrate
vector generalized linear and additive models, and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column Interaction Models,
and constrained ordination models in ecology.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-readstata13-r33-0.9.2-2 (Import 'Stata' Data Files)
Function to read and write the 'Stata' file format.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-truncnorm-r31-1.0-7-1 (Truncated Normal Distribution)
Density, probability, quantile and random number generation functions
for the truncated normal distribution.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rgenoud-r33-5.8-3.0-1 (GENetic Optimization Using Derivatives)
A genetic algorithm plus derivative optimizer

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-proj4-r34-1.0-9-102 (PROJ.4 cartographic projections library for R)
PROJ.4 cartographic projections library for R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-utf8-r35-1.1.4-1 (Unicode Text Processing)
Process and print 'UTF-8' encoded international text (Unicode). Input,
validate, normalize, encode, format, and display.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-r.methodss3-r33-1.7.1-1 (Utility function for defining S3 methods)
Methods that simplify the setup of S3 generic functions and S3 methods.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-purrr-r34-0.3.2-3 (Functional Programming Tools)
Make your pure functions purr with the 'purrr' package. This package 
completes R's functional programming tools with missing features present 
in other programming languages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-qap-r33-0.1-1-1 (Heuristics for Quadratic Assignment Problem)
Implements heuristics for the Quadratic Assignment Problem (QAP). 
Currently only a simulated annealing heuristic is available.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-testit-r33-0.10-1 (Simple package for testing R packages)
This package provides two convenience functions assert()
and test_pkg() to facilitate testing R packages.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tkrplot-r34-0.0-24-1 (TK Rplot)
simple mechanism for placing R graphics in a Tk widget

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sem-r34-3.1-9-2 (Structural Equation Models)
This package contains functions for fitting general linear
structural equation models (with observed and unobserved
variables) using the RAM approach, and for fitting structural
equations in observed-variable models by two-stage least squares.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-tm-r34-0.7-6-1 (Text Mining Package)
A framework for text mining applications within R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-xlsx-r34-0.6.1-1 (Excel 2007 and Excel 97/2000/XP/2003 support)
Provide R functions to read/write/format Excel 2007 and
Excel 97/2000/XP/2003 file formats.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcdklibs-r36-2.0-1 (CDK libraries packaged for R)
This package provides the CDK libraries for use in the R environment.
Given the size of the library itself, this package is not expected to
change very frequently. To make use of the CDK within R, it is suggested
that you use the rcdk package. Note that it is possible to directly
interact with the CDK using rJava. However rcdk exposes functionality
in a more idiomatic way

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-speaq-r32-2.0.0-1 (NMR Spectrum Alignment Tools)
We introduce a novel suite of informatics tools for the quantitative analysis
of NMR metabolomic profile data. The core of the processing cascade is a novel
peak alignment algorithm, called hierarchical Cluster-based Peak Alignment
(CluPA). The algorithm aligns a target spectrum to the reference spectrum in
a top-down fashion by building a hierarchical cluster tree from peak lists of
reference and target spectra and then dividing the spectra into smaller
segments based on the most distant clusters of the tree. To reduce the
computational time to estimate the spectral misalignment, the method makes
use of Fast Fourier Transformation (FFT) cross-correlation. Since the method
returns a high-quality alignment, we can propose a simple methodology to study
the variability of the NMR spectra. For each aligned NMR data point the ratio
of the between-group and within-group sum of squares (BW-ratio) is calculated
to quantify the difference in variability between and within predefined groups
of NMR spectra. This differential analysis is related to the calculation of
the F-statistic or a one-way ANOVA, but without distributional assumptions.
Statistical inference based on the BW-ratio is achieved by bootstrapping the
null distribution from the experimental data. Related publication is
available at http://www.biomedcentral.com/1471-2105/12/405/.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-survey-r31-3.36-1 (Analysis of complex survey samples)
Summary statistics, two-sample tests, generalised linear models,
cumulative link models, Cox models, loglinear models, and general
maximum pseudolikelihood estimation for multistage stratified,
cluster-sampled, unequally weighted survey samples. Variances by
Taylor series linearisation or replicate weights. Post-stratification,
calibration, and raking. Two-phase subsampling designs. Graphics.
Predictive margins by direct standardization. PPS sampling without
replacement. Principal components, factor analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcompression-r35-0.93-2-1 (R Package for in-memory compression)
This package is a basic R interface to the zlib and bzip2 facilities for 
compressing and uncompressing data that are in memory rather than in files.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tkrplot-r31-0.0-24-1 (TK Rplot)
simple mechanism for placing R graphics in a Tk widget

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-truncnorm-r35-1.0-8-1 (Truncated Normal Distribution)
Density, probability, quantile and random number generation functions
for the truncated normal distribution.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rvmmin-r36-2018-4.17-1 (Variable Metric Nonlinear Mininization)
Variable metric nonlinear function minimization with bounds constraints.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-png-r31-0.1-7-2 (Read and write PNG images)
This package provides an easy and simple way to read, write and
display bitmap images stored in the PNG format. It can read and
write both files and in-memory raw vectors.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-vim-r31-4.8.0-1 (Missing Values Visualization and Imputation)
This package introduces new tools for the visualization of missing and/or
imputed values, which can be used for exploring the data and the structure
of the missing and/or imputed values. Depending on this structure of the
missing values, the corresponding methods may help to identify the
mechanism generating the missing values and allows to explore the data
including missing values. In addition, the quality of imputation can be
visually explored using various univariate, bivariate, multiple and
multivariate plot methods. A graphical user interface available in the
separate package VIMGUI allows an easy handling of the implemented plot
methods.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tidyselect-r36-0.2.5-1 (Select from a Set of Strings)
A backend for the selecting functions of the 'tidyverse'. It makes it
easy to implement select-like functions in your own packages in a way
that is consistent with other 'tidyverse' interfaces for selection.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-vctrs-r32-0.2.0-2 (Vector Helpers)
Defines new notions of prototype and size that are used to provide 
tools for consistent and well-founded type-coercion and size-recycling, 
and are in turn connected to ideas of type- and size-stability useful 
for analyzing function interfaces.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-usethis-r35-1.5.0-1 (Automate Package and Project Setup)
Automate package and project setup tasks that are otherwise performed
manually. This includes setting up unit testing, test coverage,
continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio'
projects, and more.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tinytex-r35-0.16-1 (Functions to Maintain 'TeX Live')
Helper functions to install and maintain the 'LaTeX' distribution named
'TinyTeX' (<https://yihui.name/tinytex/>), a lightweight,
cross-platform, portable, and easy-to-maintain version of 'TeX Live'.
This package also contains helper functions to compile 'LaTeX'
documents, and install missing 'LaTeX' packages automatically.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rweka-r35-0.4-40-1 (R/Weka interface)
An R interface to Weka (Version 3.7.11). Weka is a collection of machine
learning algorithms for data mining tasks written in Java, containing
tools for data pre-processing, classification, regression, clustering,
association rules, and visualization. Package RWeka contains the interface
code, the Weka jar is in a separate package RWekajars. For more information
on Weka see http://www.cs.waikato.ac.nz/~ml/weka/.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-som-r33-0.3-5.1-1 (Self-Organizing Map)
Self-Organizing Map (with application in gene clustering)

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcmdrplugin.ma-r32-0.0-2-1 (GUI for Conducting Meta-Analyses in R)
This is an R-Commander plug-in for meta-analysis. This package enables
the user to conduct a meta-analysis in a menu-driven, graphical user
interface environment (e.g., SPSS). It uses recommended procedures as
described in The Handbook of Research Synthesis and Meta-Analysis
(Cooper, Hedges, & Valentine, 2009).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcppprogress-r31-0.4.1-1 (Interruptible Progress Bar)
Allows to display a progress bar in the R console for long running
computations taking place in c++ code, and support for interrupting
those computations even in multithreaded code, typically using OpenMP.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rann-r34-2.6.1-1 (Fast Nearest Neighbour Search)
Finds the k nearest neighbours for every point in a given dataset
in O(N log N) time using Arya and Mount's ANN library (v1.1.3).
There is support for approximate as well as exact searches,
fixed radius searches and bd as well as kd trees.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tensor-r32-1.5-1 (Tensor product of arrays)
The tensor product of two arrays is notionally an outer product
of the arrays collapsed in specific extents by summing along
the appropriate diagonals.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-pspline-r36-1.0-18-3 (Penalized Smoothing Splines)
Smoothing splines with penalties on order m derivatives.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-runit-r31-0.4.32-1 (R Unit test framework)
R functions implementing a standard Unit Testing framework,
with additional code inspection and report generation tools

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rmpfr-r36-0.7-2-1 (Multiple Precision Floating-Point Reliable)
Rmpfr provides (S4 classes and methods for) arithmetic including transcendental
("special") functions for arbitrary precision floating point numbers. To this
end, it interfaces to the LGPL'ed MPFR (Multiple Precision Floating-Point
Reliable) Library which itself is based on the GMP (GNU Multiple Precision)
Library.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rjsonio-r36-1.3-1.3-1 (Serialize R objects to JSON)
This is a package that allows conversion to and from data in Javascript
object notation (JSON) format. This allows R objects to be inserted into
Javascript/ECMAScript/ActionScript code and allows R programmers to read
and convert JSON content to R objects. This is an alternative to rjson
package. That version was too slow for converting large R objects to JSON
and is not extensible, but a very useful prototype. It is fast for parsing.
This package uses methods, vectorized operations and C code and callbacks
to R functions for deserializing JSON objects to R. Verison 0.4 of this
package uses a new native parser, implements the transformation code in
C and allocates memory efficiently (rather than concatenating because
of event driven parsing). The result is a significantly faster parsing
of large JSON documents.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcmdrplugin.ezr-r32-1.40-1 (Easy R for medical statistics)
Easy R for medical statistics

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rggobi-r32-2.1.22-1 (Interface between R and GGobi)
The rggobi package provides a command-line interface to GGobi, an
interactive and dynamic graphics package. Rggobi complements GGobi's
graphical user interface, providing a way to fluidly transition
between analysis and exploration, as well as automating common tasks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tframe-r34-2015.12-1.1-1 (Time Frame coding kernel)
The tframe package provides a kernel of functions for programming
time series methods in a way that is relatively independently of
the representation of time. It also provides plotting, time
windowing, and some other utility functions which are specifically
intended for time series. See the Guide distributed as a vignette,
or ?tframe.Intro for more details. (User utilities other than the
programming kernel have been moved into package tfplot.)

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tsa-r35-1.2-1 (Time Series Analysis)
Contains R functions and datasets detailed in the book "Time
Series Analysis with Applications in R (second edition)" by
Jonathan Cryer and Kung-Sik Chan

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-randomfieldsutils-r31-0.1.0-3 (Utilities for Random Fields)
Various utilities are provided that might be used in 
spatial statistics and elsewhere. It delivers a method 
for solving linear equations that checks the sparsity 
of the matrix before any algorithm is used. Furthermore, 
it includes the Struve functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-tester-r34-0.1.7-1 (Tests and checks characteristics of R objects)
tester allows you to test characteristics of common R objects.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-xopen-r36-1.0.0-1 (Open System Files, 'URLs', Anything)
Cross platform solution to open files, directories or 'URLs' with their
associated programs.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rann-r35-2.6.1-1 (Fast Nearest Neighbour Search)
Finds the k nearest neighbours for every point in a given dataset
in O(N log N) time using Arya and Mount's ANN library (v1.1.3).
There is support for approximate as well as exact searches,
fixed radius searches and bd as well as kd trees.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rex-r32-1.1.2-1 (Friendly Regular Expressions)
A friendly interface for the construction of regular expressions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcmdrplugin.bca-r34-0.9-8-1 (Business and Customer Analytics Rcmdr Plug-In)
This package provides an Rcmdr "plug-in" to accompany the book Customer
and Business Analytics: Applied Data Mining for Business Decision Making
Using R by Daniel S. Putler and Robert E. Krider.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-setrng-r35-2013.9-1-1 (Random Number Generator and Seed)
SetRNG provides utilities to help set and record the setting of
the seed and the uniform and normal generators used when a random
experiment is run. The utilities can be used in other functions
that do random experiments to simplify recording and/or setting
all the necessary information for reproducibility.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-vim-r36-4.8.0-1 (Missing Values Visualization and Imputation)
This package introduces new tools for the visualization of missing and/or
imputed values, which can be used for exploring the data and the structure
of the missing and/or imputed values. Depending on this structure of the
missing values, the corresponding methods may help to identify the
mechanism generating the missing values and allows to explore the data
including missing values. In addition, the quality of imputation can be
visually explored using various univariate, bivariate, multiple and
multivariate plot methods. A graphical user interface available in the
separate package VIMGUI allows an easy handling of the implemented plot
methods.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-png-r36-0.1-7-2 (Read and write PNG images)
This package provides an easy and simple way to read, write and
display bitmap images stored in the PNG format. It can read and
write both files and in-memory raw vectors.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-spatial-r34-7.3-11-1 (Kriging and Point Pattern Analysis Functions)
Functions for kriging and point pattern analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rematch-r33-1.0.1-1 (Match Regular Expressions with a Nicer API)
A small wrapper on 'regexpr' to extract the matches
and captured groups from the match of a regular expression
to a character vector.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sensominer-r36-1.23-1 (Sensory data analysis with R)
an R package for analysing sensory data

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-readstata13-r31-0.9.2-2 (Import 'Stata' Data Files)
Function to read and write the 'Stata' file format.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-shiny-r34-1.3.2-1 (Web Application Framework for R)
Makes it incredibly easy to build interactive web applications with R. 
Automatic "reactive" binding between inputs and outputs and extensive 
pre-built widgets make it possible to build beautiful, responsive, 
and powerful applications with minimal effort.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-testthat-r36-2.2.1-1 (Testthat code)
A testing package specifically tailored for R that's fun,
flexible and easy to set up.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-smatr-r33-3.4-8-1 (Major Axis Estimation and Testing Routines)
s package provides methods of fitting bivariate lines in allometry using
the major axis (MA) or standardised major axis (SMA), and for making
inferences about such lines. The available methods of inference include
confidence intervals and one-sample tests for slope and elevation, testing
for a common slope or elevation amongst several allometric lines,
constructing a confidence interval for a common slope or elevation, and
testing for no shift along a common axis, amongst several samples.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rbenchmark-r35-1.0.0-1 (Benchmarking routine for R)
rbenchmark is inspired by the Perl module Benchmark, and is intended
to facilitate benchmarking of arbitrary R code. The library consists
of just one function, benchmark, which is a simple wrapper around
system.time. Given a specification of the benchmarking process
(counts of replications, evaluation environment) and an arbitrary
number of expressions, benchmark evaluates each of the expressions
in the specified environment, replicating the evaluation as many
times as specified, and returning the results conveniently wrapped
into a data frame.

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2020-01-16: cran-timp-r32-1.13.2-1 (Fitting separable nonlinear models)
TIMP is a problem solving environment for fitting separable nonlinear
models to measurements arising in physics and chemistry experiments,
and has been extensively applied to time-resolved spectroscopy and
FLIM-FRET data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-r.methodss3-r31-1.7.1-1 (Utility function for defining S3 methods)
Methods that simplify the setup of S3 generic functions and S3 methods.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tinytex-r32-0.16-1 (Functions to Maintain 'TeX Live')
Helper functions to install and maintain the 'LaTeX' distribution named
'TinyTeX' (<https://yihui.name/tinytex/>), a lightweight,
cross-platform, portable, and easy-to-maintain version of 'TeX Live'.
This package also contains helper functions to compile 'LaTeX'
documents, and install missing 'LaTeX' packages automatically.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-usethis-r32-1.5.0-1 (Automate Package and Project Setup)
Automate package and project setup tasks that are otherwise performed
manually. This includes setting up unit testing, test coverage,
continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio'
projects, and more.

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2020-01-16: cran-quantmod-r33-0.4-15-2 (Quantitative Financial Modelling Framework)
Specify, build, trade, and analyse quantitative financial trading strategies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-spatial-r31-7.3-11-1 (Kriging and Point Pattern Analysis Functions)
Functions for kriging and point pattern analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-randomfieldsutils-r35-0.5.3-2 (Utilities for Random Fields)
Various utilities are provided that might be used in 
spatial statistics and elsewhere. It delivers a method 
for solving linear equations that checks the sparsity 
of the matrix before any algorithm is used. Furthermore, 
it includes the Struve functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rvmmin-r31-2018-4.17-1 (Variable Metric Nonlinear Mininization)
Variable metric nonlinear function minimization with bounds constraints.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcmdrmisc-r33-1.0-9-1 (R Commander Miscellaneous Functions)
Various statistical, graphics, and data-management functions
used by the Rcmdr package in the R Commander GUI for R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-zeallot-r31-0.1.0-1 (Multiple/Unpacking/Destructuring Assignment)
Provides a %<-% operator to perform multiple, unpacking, and 
destructuring assignment in R. The operator unpacks the right-hand 
side of an assignment into multiple values and assigns these 
values to variables on the left-hand side of the assignment.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-survey-r36-3.36-1 (Analysis of complex survey samples)
Summary statistics, two-sample tests, generalised linear models,
cumulative link models, Cox models, loglinear models, and general
maximum pseudolikelihood estimation for multistage stratified,
cluster-sampled, unequally weighted survey samples. Variances by
Taylor series linearisation or replicate weights. Post-stratification,
calibration, and raking. Two-phase subsampling designs. Graphics.
Predictive margins by direct standardization. PPS sampling without
replacement. Principal components, factor analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-prospectr-r31-0.1.3-4 (Processing and sample selection of vis-NIR)
The package provides functions for pretreatment and sample selection
of visible and near infrared diffuse reflectance spectra

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-sroc-r34-0.1-2-3 (Nonparametric Smooth ROC Curves)
This package contains a collection of functions to perform
 nonparametric estimation of receiver operating 
 characteristic (ROC) curves for continuous data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-polca-r35-1.4.1-1 (Polytomous variable Latent Class Analysis)
Latent class analysis and latent class regression models for
polytomous outcome variables. Also known as latent structure
analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-slam-r35-0.1-45-2 (Sparse Lightweight Arrays and Matrices)
Data structures and algorithms for sparse arrays and matrices,
based on index arrays and simple triplet representations, respectively.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-st-r36-1.2.5-1 (Shrinkage t Statistic and CAT Score)
This package implements the "shrinkage t" statistic introduced in
Opgen-Rhein and Strimmer (2007) and a shrinkage estimate of the
"correlation-adjusted t-score" (CAT score) described in Zuber
and Strimmer (2009). It also offers a convenient interface to
a number of other regularized t-statistics commonly employed in
high-dimensional case-control studies.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-zeallot-r34-0.1.0-1 (Multiple/Unpacking/Destructuring Assignment)
Provides a %<-% operator to perform multiple, unpacking, and 
destructuring assignment in R. The operator unpacks the right-hand 
side of an assignment into multiple values and assigns these 
values to variables on the left-hand side of the assignment.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-reshape2-r32-1.4.3-1 (Flexibly reshape data)
Reshape lets you flexibly restructure and aggregate data using
just two functions: melt and cast.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-xfun-r34-0.10-1 (Misc. functions by Yihui Xie)
Miscellaneous functions commonly used in other packages maintained
by 'Yihui Xie'.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-promises-r33-1.1.0-1 (Promise-Based Asynchronous Programming)
Provides fundamental abstractions for doing asynchronous programming in
R using promises. Asynchronous programming is useful for allowing a
single R process to orchestrate multiple tasks in the background while
also attending to something else. Semantics are similar to 'JavaScript'
promises, but with a syntax that is idiomatic R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-xlconnect-r34-0.2-15-1 (Excel Connector for R)
Manipulate Excel files from R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-ranger-r34-0.11.2-1 (Manage Life Cycle of Package)
This package can be used to solve Linear Programming / Linear 
Optimization problems by using the simplex algorithm.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-reshape-r36-0.8.8-1 (Flexibly reshape data)
Reshape lets you flexibly restructure and aggregate data
using just two functions: melt and cast.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-setrng-r32-2013.9-1-1 (Random Number Generator and Seed)
SetRNG provides utilities to help set and record the setting of
the seed and the uniform and normal generators used when a random
experiment is run. The utilities can be used in other functions
that do random experiments to simplify recording and/or setting
all the necessary information for reproducibility.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sm-r36-2.2-5.6-2 (Smoothing methods)
This is software linked to the book 'Applied Smoothing Techniques for
Data Analysis - The Kernel Approach with S-Plus Illustrations' Oxford
University Press.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rrcov-r32-1.4-7-2 (Scalable Robust Estimators)
Robust Location and Scatter Estimation and Robust Multivariate
Analysis with High Breakdown Point.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-spam-r33-2.3-0-2 (SPArse Matrix)
Set of functions for sparse matrix algebra. Differences with SparseM/Matrix
are: (1) we only support (essentially) one sparse matrix format, (2) based
on transparent and simple structure(s), (3) tailored for MCMC calculations
within GMRF. (4) S3 and S4 like-"compatible" ... and it is fast.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-trimcluster-r32-0.1-2.1-1 (Cluster analysis with trimming)
Trimmed k-means clustering.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rlang-r33-0.4.0-2 (Functions for Base Types and Core R)
A toolbox for working with base types, core R features like 
the condition system, and core `Tidyverse' features like tidy evaluation.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-randomfieldsutils-r34-0.5.3-2 (Utilities for Random Fields)
Various utilities are provided that might be used in 
spatial statistics and elsewhere. It delivers a method 
for solving linear equations that checks the sparsity 
of the matrix before any algorithm is used. Furthermore, 
it includes the Struve functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-quantreg-r36-5.51-2 (Quantile Regression)
Quantile regression and related methods.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-xlconnect-r36-0.2-15-1 (Excel Connector for R)
Manipulate Excel files from R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-prospectr-r35-0.1.3-4 (Processing and sample selection of vis-NIR)
The package provides functions for pretreatment and sample selection
of visible and near infrared diffuse reflectance spectra

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-wilcoxcv-r33-1.0-2-1 (Wilcoxon-based variable selection in cv)
This package provides functions to perform fast variable selection
based on the Wilcoxon rank sum test in the cross-validation or
Monte-Carlo cross-validation settings, for use in microarray-based
binary classification.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tcltk2-r33-1.2-11-1 (Tcl/Tk Additions)
A series of additional Tcl commands and Tk widgets with style and
various functions (under Windows: DDE exchange, access to the
registry and icon manipulation) to supplement the tcltk package

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rmarkdown-r36-1.16-1 (Dynamic Documents for R)
Convert R Markdown documents into a variety of formats.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rggobi-r35-2.1.22-1 (Interface between R and GGobi)
The rggobi package provides a command-line interface to GGobi, an
interactive and dynamic graphics package. Rggobi complements GGobi's
graphical user interface, providing a way to fluidly transition
between analysis and exploration, as well as automating common tasks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-praise-r34-1.0.0-1 (Praise Users)
Build friendly R packages that praise their users if they have 
done something good, or they just need it to feel better.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tables-r36-0.8.8-1 (Formula-driven table generation)
Computes and displays complex tables of summary statistics

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcppprogress-r36-0.4.1-1 (Interruptible Progress Bar)
Allows to display a progress bar in the R console for long running
computations taking place in c++ code, and support for interrupting
those computations even in multithreaded code, typically using OpenMP.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-psych-r36-1.8.12-1 (Procedures for Psychological Research)
A number of routines for personality, psychometrics and experimental
psychology. Functions are primarily for scale construction using
factor analysis, cluster analysis and reliability analysis, although
others provide basic descriptive statistics. Item Response Theory is
done using factor analysis of tetrachoric and polychoric correlations.
Functions for simulating particular item and test structures are
included. Several functions serve as a useful front end for structural
equation modeling. Graphical displays of path diagrams, factor analysis
and structural equation models are created using basic graphics. Some
of the functions are written to support a book on psychometrics as well
as publications in personality research. For more information, see the
personality-project.org/r webpage.

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2020-01-16: cran-tensor-r35-1.5-1 (Tensor product of arrays)
The tensor product of two arrays is notionally an outer product
of the arrays collapsed in specific extents by summing along
the appropriate diagonals.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rngtools-r35-1.3.1-1 (Utility for Random Number Generators)
This package contains a set of functions for working with Random 
Number Generators (RNGs). In particular, it defines a generic S4 
framework for getting/setting the current RNG, or RNG data that 
are embedded into objects for reproducibility. Notably, convenient 
default methods greatly facilitate the way current RNG settings 
can be changed.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rmarkdown-r34-1.16-1 (Dynamic Documents for R)
Convert R Markdown documents into a variety of formats.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rcdk-r31-3.4.7.1-1 (Interface to the CDK Libraries)
This package allows the user to access functionality in the CDK,
a Java framework for cheminformatics. This allows the user to load
molecules, evaluate fingerprints, calculate molecular descriptors
and so on. In addition the CDK API allows the user to view structures
in 2D.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-speaq-r31-2.0.0-1 (NMR Spectrum Alignment Tools)
We introduce a novel suite of informatics tools for the quantitative analysis
of NMR metabolomic profile data. The core of the processing cascade is a novel
peak alignment algorithm, called hierarchical Cluster-based Peak Alignment
(CluPA). The algorithm aligns a target spectrum to the reference spectrum in
a top-down fashion by building a hierarchical cluster tree from peak lists of
reference and target spectra and then dividing the spectra into smaller
segments based on the most distant clusters of the tree. To reduce the
computational time to estimate the spectral misalignment, the method makes
use of Fast Fourier Transformation (FFT) cross-correlation. Since the method
returns a high-quality alignment, we can propose a simple methodology to study
the variability of the NMR spectra. For each aligned NMR data point the ratio
of the between-group and within-group sum of squares (BW-ratio) is calculated
to quantify the difference in variability between and within predefined groups
of NMR spectra. This differential analysis is related to the calculation of
the F-statistic or a one-way ANOVA, but without distributional assumptions.
Statistical inference based on the BW-ratio is achieved by bootstrapping the
null distribution from the experimental data. Related publication is
available at http://www.biomedcentral.com/1471-2105/12/405/.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-slam-r34-0.1-45-2 (Sparse Lightweight Arrays and Matrices)
Data structures and algorithms for sparse arrays and matrices,
based on index arrays and simple triplet representations, respectively.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-sroc-r35-0.1-2-3 (Nonparametric Smooth ROC Curves)
This package contains a collection of functions to perform
 nonparametric estimation of receiver operating 
 characteristic (ROC) curves for continuous data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-spam-r36-2.3-0-2 (SPArse Matrix)
Set of functions for sparse matrix algebra. Differences with SparseM/Matrix
are: (1) we only support (essentially) one sparse matrix format, (2) based
on transparent and simple structure(s), (3) tailored for MCMC calculations
within GMRF. (4) S3 and S4 like-"compatible" ... and it is fast.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-xfun-r35-0.10-1 (Misc. functions by Yihui Xie)
Miscellaneous functions commonly used in other packages maintained
by 'Yihui Xie'.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tsa-r34-1.2-1 (Time Series Analysis)
Contains R functions and datasets detailed in the book "Time
Series Analysis with Applications in R (second edition)" by
Jonathan Cryer and Kung-Sik Chan

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-vrmlgen-r34-1.4.9-1 (Generate 3D visualizations)
vrmlgen creates 3D scatter and bar plots, visualizations of 3D meshes,
parametric functions and height maps in web-formats like the Virtual
Reality Markup Language (VRML, filetype .wrl) and the LiveGraphics3D format.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sp-r36-1.3-1-1 (GNU R classes and methods for spatial data)
GNU R classes and methods for spatial data

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-scatterplot3d-r32-0.3-41-1 (3D Scatter Plot)
Plots a three dimensional (3D) point cloud.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-randomfields-r33-3.1.12-2 (Simulation and Analysis of Random Fields)
Simulation of Gaussian and extreme value random fields; conditional
simulation; kriging; maximum likelihood estimation

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-sna-r32-2.4-1 (Tools for Social Network Analysis)
A range of tools for social network analysis, including node and graph-level
indices, structural distance and covariance methods, structural equivalence
detection, network regression, random graph generation, and 2D/3D network
visualization.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-robustbase-r34-0.93-5-2 (GNU R Tools for robust methods)
"Essential" Robust Statistics.
The goal is to provide tools allowing to analyze data with robust methods.
This includes regression methodology including model selections and
multivariate statistics where we strive to cover the book
"Robust Statistics, Theory and Methods" by Maronna, Martin and Yohai;
Wiley 2006.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-robcompositions-r36-2.0.10-1 (Robust Estimation for Compositional Data)
The package includes methods for imputation of compositional data
including robust methods, methods to impute rounded zeros, (robust)
outlier detection for compositional data, (robust) principal component
analysis for compositional data, (robust) factor analysis for
compositional data, (robust) discriminant analysis for compositional
data (Fisher rule), robust regression with compositional predictors and
(robust) Anderson-Darling normality tests for compositional data as well
as popular log-ratio transformations (addLR, cenLR, isomLR, and their
inverse transformations). In addition, visualisation and diagnostic
tools are implemented as well as high and low-level plot functions for
the ternary diagram.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sparsem-r32-1.77-2 (Sparse Linear Algebra)
Basic linear algebra for sparse matrices

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-statip-r35-0.2.0-1 (Functions for Distributions and Regression)
A collection of miscellaneous statistical functions for probability
distributions: dbern(), pbern(), qbern(), rbern() for the Bernoulli
distribution, and distr2name(), name2distr() for distribution names;
probability density estimation: densityfun(); most frequent value
estimation: mfv(), mfv1(); calculation of the Hellinger distance:
hellinger(); use of classical kernels: kernelfun(), kernel_properties();
univariate piecewise-constant regression: picor().

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-ranger-r33-0.11.2-1 (Manage Life Cycle of Package)
This package can be used to solve Linear Programming / Linear 
Optimization problems by using the simplex algorithm.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rserve-r31-1.7-3.1-1 (Binary R server)
Rserve acts as a socket server (TCP/IP or local sockets) which allows binary
requests to be sent to R. Every connection has a separate workspace and
working directory. Client-side implementations are available for popular
languages such as C/C++ and Java, allowing any application to use facilities
of R without the need of linking to R code. Rserve supports remote connection,
user authentication and file transfer. A simple R client is included in this
package as well.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-ttr-r32-0.23-5-1 (Technical Trading Rules)
Technical analysis and other functions to construct technical trading 
rules with R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rfast-r35-1.9.5-2 (Efficient and Extremely Fast R Functions)
A collection of fast (utility) functions for data analysis. Column- and
row- wise means, medians, variances, minimums, maximums, many t, F and
G-square tests, many regressions (normal, logistic, Poisson), are some
of the many fast functions. Reference: Tsagris M, Papadakis M. (2018).
Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1
.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-xlsxjars-r32-0.6.1-1 (Package required POI jars for xlsx package)
The xlsxjars package collects all the external jars required for the
xlxs package. These external jars are quite large in size (15MB) and
have a slow release cycle. By separating the Java and R development,
the storage footprint on CRAN is reduced. This release corresponds
to POI 3.10.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-polca-r32-1.4.1-1 (Polytomous variable Latent Class Analysis)
Latent class analysis and latent class regression models for
polytomous outcome variables. Also known as latent structure
analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-psm-r31-0.8-12-2 (Non-Linear Mixed-Effects modelling)
This package provides functions for estimation of linear and non-linear
mixed-effects models using stochastic differential equations. Moreover
it provides functions for finding smoothed estimates of model states
and for simulation. The package allows for any multivariate non-linear
time-variant model to be specified, and it also handles multidimensional
input, co-variates, missing observations and specification of dosage regimen.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-xml-r36-3.98-1.20-1 (Tools for parsing and generating XML within R)
Tools for parsing and generating XML within R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-yaml-r32-2.2.0-1 (Libyaml YAML 1.1 parser and emitter for R)
This package implements the libyaml YAML 1.1 parser and emitter 
(http://pyyaml.org/wiki/LibYAML) for R.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-zip-r34-2.0.4-1 (Cross-Platform 'zip' Compression)
Cross-Platform 'zip' Compression Library. A replacement for the 'zip'
function, that does not require any additional external tools on any
platform.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sde-r31-2.0.15-1 (Stochastic Differential Equations)
Companion package to the book Simulation and Inference for Stochastic
Differential Equations With R Examples, ISBN 978-0-387-75838-1, Springer, NY.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tm-r33-0.7-6-1 (Text Mining Package)
A framework for text mining applications within R.

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2020-01-16: cran-vegan-r36-2.5-6-2 (Community Ecology Package)
Ordination methods, diversity analysis and other functions
for community and vegetation ecologists.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-sourcetools-r34-0.1.7-1 (Reading, Tokenizing and Parsing R Code)
Tools for the reading and tokenization of R code. The 'sourcetools'
package provides both an R and C++ interface for the tokenization of 
R code, and helpers for interacting with the tokenized representation
of R code.

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2020-01-16: cran-vrmlgen-r31-1.4.9-1 (Generate 3D visualizations)
vrmlgen creates 3D scatter and bar plots, visualizations of 3D meshes,
parametric functions and height maps in web-formats like the Virtual
Reality Markup Language (VRML, filetype .wrl) and the LiveGraphics3D format.

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2020-01-16: cran-proxy-r33-0.4-17-1 (Distance and Similarity Measures)
Provides an extensible framework for the efficient calculation of
auto- and cross-proximities, along with implementations of the
most popular ones.

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2020-01-16: cran-rjava-r34-0.9-8-2 (Low-level R to Java interface)
Low-level interface to Java VM very much like .C/.Call and friends.
Allows creation of objects, calling methods and accessing fields.

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2020-01-16: cran-xml2-r34-1.2.2-2 (Parse XML)
Work with XML files using a simple, consistent interface. Built on top of 
the 'libxml2' C library.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-polyclip-r32-1.10-0-1 (Polygon Clipping)
R port of the Clipper library. Performs polygon clipping operations
(intersection, union, set minus, set difference) for polygonal regions
of arbitrary complexity, including holes. Also computes offset polygons
(spatial buffer zones, morphological dilations, Minkowski dilations)
for polygonal regions and polygonal lines.

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2020-01-16: cran-trimcluster-r36-0.1-2.1-1 (Cluster analysis with trimming)
Trimmed k-means clustering.

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2020-01-16: cran-stringi-r33-1.4.3-1 (Character String Processing Facilities)
Allows for fast, correct, consistent, portable, as well as 
convenient character string/text processing in every locale 
and any native encoding. Owing to the use of the ICU library, 
the package provides R users with platform-independent 
functions known to Java, Perl, Python, PHP, and Ruby 
programmers. Among available features there are: pattern 
searching (e.g., with ICU Java-like regular expressions 
or the Unicode Collation Algorithm), random string generation, 
case mapping, string transliteration, concatenation, Unicode 
normalization, date-time formatting and parsing, etc.

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2020-01-16: cran-rrcov-r35-1.4-7-2 (Scalable Robust Estimators)
Robust Location and Scatter Estimation and Robust Multivariate
Analysis with High Breakdown Point.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-sys-r33-3.3-1 (Tools for Running System Commands in R)
Drop-in replacements for the base system2() function with fine control
and consistent behavior across platforms. Supports clean interruption,
timeout, background tasks, and streaming STDIN / STDOUT / STDERR over
binary or text connections. Arguments on Windows automatically get
encoded and quoted to work on different locales.

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2020-01-16: cran-randomforest-r34-4.6-12-1 (GNU R Tools for random forest class/regress)
Classification and regression based on a forest of trees using random inputs.

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2020-01-16: cran-rda-r32-1.0.2-2.1-1 (Shrunken Centroids RDA)
Shrunken Centroids Regularized Discriminant Analysis
for the classification purpose in high dimensional data.

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2020-01-16: cran-usingr-r31-2.0-6-1 (GNU R data sets for "Using R for Intro Stats")
A collection of datasets to accompany the textbook
"Using R for Introductory Statistics."

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2020-01-16: cran-svunit-r35-0.7-12-1 (SciViews GUI API - Unit testing)
A complete unit test system and functions to implement its GUI part

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2020-01-16: cran-rcdklibs-r35-2.0-1 (CDK libraries packaged for R)
This package provides the CDK libraries for use in the R environment.
Given the size of the library itself, this package is not expected to
change very frequently. To make use of the CDK within R, it is suggested
that you use the rcdk package. Note that it is possible to directly
interact with the CDK using rJava. However rcdk exposes functionality
in a more idiomatic way

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2020-01-16: cran-proto-r34-1.0.0-1 (Prototype object-based programming)
An object oriented system using object-based, also called
prototype-based, rather than class-based object oriented ideas.

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2020-01-16: cran-stepplr-r31-0.93-2 (L2 penalized logistic regression)
L2 penalized logistic regression for both continuous and discrete
predictors, with forward stagewise/forward stepwise variable
selection procedure.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-xml-r31-3.98-1.20-1 (Tools for parsing and generating XML within R)
Tools for parsing and generating XML within R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rhpcblasctl-r34-0.18-205-1 (Control the Number of Threads on 'BLAS')
Control the number of threads on 'BLAS' (Aka 'GotoBLAS', 'OpenBLAS',
'ACML', 'BLIS' and 'MKL'). And possible to control the number of threads
in 'OpenMP'. Get a number of logical cores and physical cores if
feasible.

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2020-01-16: cran-sde-r36-2.0.15-1 (Stochastic Differential Equations)
Companion package to the book Simulation and Inference for Stochastic
Differential Equations With R Examples, ISBN 978-0-387-75838-1, Springer, NY.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-psm-r36-0.8-12-2 (Non-Linear Mixed-Effects modelling)
This package provides functions for estimation of linear and non-linear
mixed-effects models using stochastic differential equations. Moreover
it provides functions for finding smoothed estimates of model states
and for simulation. The package allows for any multivariate non-linear
time-variant model to be specified, and it also handles multidimensional
input, co-variates, missing observations and specification of dosage regimen.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rsnns-r31-0.4-12-1 (Stuttgart Neural Network Simulator in R)
The Stuttgart Neural Network Simulator (SNNS) is a library containing many
standard implementations of neural networks. This package wraps the SNNS
functionality to make it available from within R. Using the RSNNS low-level
interface, all of the algorithmic functionality and flexibility of SNNS can
be accessed. Furthermore, the package contains a convenient high-level
interface, so that the most common neural network topologies and learning
algorithms integrate seamlessly into R.

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2020-01-16: cran-rbenchmark-r32-1.0.0-1 (Benchmarking routine for R)
rbenchmark is inspired by the Perl module Benchmark, and is intended
to facilitate benchmarking of arbitrary R code. The library consists
of just one function, benchmark, which is a simple wrapper around
system.time. Given a specification of the benchmarking process
(counts of replications, evaluation environment) and an arbitrary
number of expressions, benchmark evaluates each of the expressions
in the specified environment, replicating the evaluation as many
times as specified, and returning the results conveniently wrapped
into a data frame.

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2020-01-16: cran-waveslim-r36-1.7.5.1-2 (Basic wavelet routines)
Basic wavelet routines for time series (1D), image (2D) and
array (3D) analysis.The code provided here is based on wavelet
methodology developed in Percival and Walden (2000); Gencay,
Selcuk and Whitcher (2001); the dual-tree complex wavelet 
transform (DTCWT) from Kingsbury (1999, 2001) as implemented
by Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002).

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-xml2-r35-1.2.2-2 (Parse XML)
Work with XML files using a simple, consistent interface. Built on top of 
the 'libxml2' C library.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-th.data-r36-1.0-10-1 (TH's Data Archive)
Contains data sets used in other packages Torsten Hothorn maintains.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcpparmadillo-r36-0.9.800.1.0-2 (Rcpp integration for Armadillo)
R and Armadillo integration using Rcpp Armadillo is a templated
C++ linear algebra library (by Conrad Sanderson) that aims towards
a good balance between speed and ease of use. Integer, floating
point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions
are provided through optional integration with LAPACK and ATLAS
libraries. A delayed evaluation approach is employed (during compile
time) to combine several operations into one, and to reduce (or
eliminate) the need for temporaries. This is accomplished through
recursive templates and template meta-programming. This library is
useful if C++ has been decided as the language of choice (due
to speed and/or integration capabilities), rather than another
language. The RcppArmadillo package includes the header files
from the templated Armadillo library. Thus users do not need to
install Armadillo itself in order to use RcppArmadillo. This
Armadillo integration provides a nice illustration of the
capabilities of the Rcpp package for seamless R and C++
integration. Armadillo is licensed under the MPL 2.0, while
RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is
licensed under the GNU GPL version 2 or later, as is the
rest of Rcpp.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rcompression-r34-0.93-2-1 (R Package for in-memory compression)
This package is a basic R interface to the zlib and bzip2 facilities for 
compressing and uncompressing data that are in memory rather than in files.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-stepplr-r34-0.93-2 (L2 penalized logistic regression)
L2 penalized logistic regression for both continuous and discrete
predictors, with forward stagewise/forward stepwise variable
selection procedure.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-praise-r33-1.0.0-1 (Praise Users)
Build friendly R packages that praise their users if they have 
done something good, or they just need it to feel better.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sparsem-r35-1.77-2 (Sparse Linear Algebra)
Basic linear algebra for sparse matrices

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-trimcluster-r33-0.1-2.1-1 (Cluster analysis with trimming)
Trimmed k-means clustering.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-turner-r35-0.1.7-1 (Turn lists of vectors into indexed structures)
Package designed for working with vectors and lists of vectors,
mainly for turning them into other indexed data structures.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tcltk2-r34-1.2-11-1 (Tcl/Tk Additions)
A series of additional Tcl commands and Tk widgets with style and
various functions (under Windows: DDE exchange, access to the
registry and icon manipulation) to supplement the tcltk package

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-superpc-r36-1.09-1 (Supervised principal components)
Supervised principal components for regression and survival analsysis.
Especially useful for high-dimnesional data, including microarray data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcolorbrewer-r36-1.1-2-1 (GNU R Tools for variable-dependent palettes)
The packages provides palettes for drawing nice maps shaded 
according to a variable.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-psy-r34-1.1-1 (Various procedures used in psychometry)
Kappa, ICC, Cronbach alpha, screeplot, mtmm

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rprojroot-r36-1.3-2-1 (Finding Files in Project Subdirectories)
Robust, reliable and flexible paths to files below a project root. 
The 'root' of a project is defined as a directory that matches 
a certain criterion, e.g., it contains a certain regular file.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sandwich-r34-2.5-1-1 (GNU R std err estimators for time-series data)
sandwich: Robust Covariance Matrix Estimators
Model-robust standard error estimators for cross-sectional, 
time series, and longitudinal data.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sn-r32-1.5-4-1 (Skew-normal and skew-t distributions)
Define and manipulate probability distributions of the skew-normal
family and some related ones (notably the skew-t family) and provide
related statistical methods for data fitting and diagnostics, in the
univariate and in the multivariate case.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sda-r33-1.3.7-1 (Shrinkage Discriminant Analysis)
This package provides an efficient framework for high-dimensional
linear and diagonal discriminant analysis with variable selection.
The classifier is trained using James-Stein-type shrinkage estimators
and predictor variables are ranked using correlation-adjusted t-scores
(CAT scores). Variable selection error is controlled using false
non-discovery rates or higher criticism.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-recipes-r34-0.1.7-1 (Preprocessing Tools to Create Design Matrices)
An extensible framework to create and preprocess design matrices.
Recipes consist of one or more data manipulation and analysis "steps".
Statistical parameters for the steps can be estimated from an initial
data set and then applied to other data sets. The resulting design
matrices can then be used as inputs into statistical or machine learning
models.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-utf8-r31-1.1.4-1 (Unicode Text Processing)
Process and print 'UTF-8' encoded international text (Unicode). Input,
validate, normalize, encode, format, and display.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Revert revision numbers
2020-01-16: cran-rprojroot-r34-1.3-2-1 (Finding Files in Project Subdirectories)
Robust, reliable and flexible paths to files below a project root. 
The 'root' of a project is defined as a directory that matches 
a certain criterion, e.g., it contains a certain regular file.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tsp-r36-1.1-7-1 (Traveling Salesperson Problem)
Basic infrastructure and some algorithms for the traveling salesperson
problem (also traveling salesman problem; TSP). The package provides
some simple algorithms and an interface to Concorde, the currently
fastest TSP solver. Concorde itself is not included in the package
and has to be obtained separately.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sensominer-r33-1.23-1 (Sensory data analysis with R)
an R package for analysing sensory data

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-vctrs-r35-0.2.0-2 (Vector Helpers)
Defines new notions of prototype and size that are used to provide 
tools for consistent and well-founded type-coercion and size-recycling, 
and are in turn connected to ideas of type- and size-stability useful 
for analyzing function interfaces.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-recipes-r31-0.1.5-1 (Preprocessing Tools to Create Design Matrices)
An extensible framework to create and preprocess design matrices.
Recipes consist of one or more data manipulation and analysis "steps".
Statistical parameters for the steps can be estimated from an initial
data set and then applied to other data sets. The resulting design
matrices can then be used as inputs into statistical or machine learning
models.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tidyr-r34-1.0.0-2 (Easily Tidy Data)
An evolution of 'reshape2'. It's designed specifically for data 
tidying (not general reshaping or aggregating) and works well 
with 'dplyr' data pipelines.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-tframe-r33-2015.12-1.1-1 (Time Frame coding kernel)
The tframe package provides a kernel of functions for programming
time series methods in a way that is relatively independently of
the representation of time. It also provides plotting, time
windowing, and some other utility functions which are specifically
intended for time series. See the Guide distributed as a vignette,
or ?tframe.Intro for more details. (User utilities other than the
programming kernel have been moved into package tfplot.)

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rgenoud-r32-5.8-3.0-1 (GENetic Optimization Using Derivatives)
A genetic algorithm plus derivative optimizer

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcmdrplugin.bca-r33-0.9-8-1 (Business and Customer Analytics Rcmdr Plug-In)
This package provides an Rcmdr "plug-in" to accompany the book Customer
and Business Analytics: Applied Data Mining for Business Decision Making
Using R by Daniel S. Putler and Robert E. Krider.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcmdrplugin.bca-r31-0.9-8-1 (Business and Customer Analytics Rcmdr Plug-In)
This package provides an Rcmdr "plug-in" to accompany the book Customer
and Business Analytics: Applied Data Mining for Business Decision Making
Using R by Daniel S. Putler and Robert E. Krider.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-profilemodel-r32-0.6.0-1 (Inference functions profiling tools)
profileModel provides tools that can be used to calculate, evaluate, plot
and use for inference the profiles of *arbitrary* inference functions for
for *arbitrary* 'glm'-like fitted models with linear predictors.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-turner-r32-0.1.7-1 (Turn lists of vectors into indexed structures)
Package designed for working with vectors and lists of vectors,
mainly for turning them into other indexed data structures.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-signal-r31-0.7-6-2 (Signal processing)
A set of signal processing R functions originally written for Matlab/Octave.
Includes filter generation utilities, filtering functions, resampling
routines, and visualization of filter models. It also includes interpolation
functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-rweka-r32-0.4-40-1 (R/Weka interface)
An R interface to Weka (Version 3.7.11). Weka is a collection of machine
learning algorithms for data mining tasks written in Java, containing
tools for data pre-processing, classification, regression, clustering,
association rules, and visualization. Package RWeka contains the interface
code, the Weka jar is in a separate package RWekajars. For more information
on Weka see http://www.cs.waikato.ac.nz/~ml/weka/.

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2020-01-16: cran-tfplot-r31-2015.12-1-1 (Time Frame User Utilities)
Utilities in this package are for simple manipulation and quick
plotting of time series data. These utilities use the tframe
package which provides a programming kernel for time series.
Extensions to tframe provided in tframePlus can also be used.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-polycor-r31-0.7-8-2 (Polychoric and Polyserial Correlations)
Computes polychoric and polyserial correlations by quick "two-step"
methods or ML, optionally with standard errors; tetrachoric
and biserial correlations are special cases.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-ptak-r34-1.3-34-1 (Principal Tensor Analysis on k modes)
A multiway method to decompose a tensor (array) of any order, as a
generalisation of SVD also supporting non-identity metrics and
penalisations. 2-way SVD with these extensions is also available.
The package includes also some other multiway methods: PCAn
(Tucker-n) and PARAFAC/CANDECOMP with these extensions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-roughsets-r34-1.3-0-2 (Rough Set and Fuzzy Rough Set Analysis)
This package provides comprehensive implementations of the rough set
theory (RST) and the fuzzy rough set theory (FRST), and integrates
these two theories into a single package. It provides implementations,
not only for the basic concepts of RST and FRST, but also most common
methods based on them for handling some tasks such as discretization,
feature selection, instance selection, rule induction, and prediction.
RST was introduced by Zdzislaw Pawlak in 1982 as a sophisticated
mathematical tool based on indiscernibility relations to model and
process imprecise or incomplete information. It works on symbolic-
valued datasets for tackling the data analysis problems. By using th
indiscernibility relation for objects/instances, RST does not require
additional parameters to analyze the data. FRST is an extension of RST.
The FRST combines concepts of vagueness and indiscernibility that are
expressed with fuzzy sets (as proposed by Zadeh, in 1965) and RST.

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2020-01-16: cran-sgeostat-r35-1.0-27-3 (Framework for Geostatistical Modeling in S+)
An Object-oriented Framework for Geostatistical Modeling in S+

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-visnetwork-r31-2.0.8-1 (Network Visualization)
Provides an R interface to the 'vis.js' JavaScript charting library. It
allows an interactive visualization of networks.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-timedate-r36-3043.102-1 (Rmetrics - Chronological and Calendar Objects)
Environment for teaching "Financial Engineering and Computational Finance"

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rcmdrplugin.ma-r31-0.0-2-1 (GUI for Conducting Meta-Analyses in R)
This is an R-Commander plug-in for meta-analysis. This package enables
the user to conduct a meta-analysis in a menu-driven, graphical user
interface environment (e.g., SPSS). It uses recommended procedures as
described in The Handbook of Research Synthesis and Meta-Analysis
(Cooper, Hedges, & Valentine, 2009).

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2020-01-16: cran-varselrf-r35-0.7-8-1 (Variable selection using random forests)
Variable selection from random forests using both backwards variable
elimination (for the selection of small sets of non-redundant variables)
and selection based on the importance spectrum (somewhat similar to
scree plots; for the selection of large, potentially highly-correlated
variables). Main applications in high-dimensional data (e.g., microarray
data, and other genomics and proteomics applications). You can use rpvm
instead of Rmpi if you want but I've only tested with Rmpi.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rgdal-r33-1.4-6-1 (GNU R Bindings for GDAL)
GNU R Bindings for GDAL

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-roughsets-r36-1.3-0-2 (Rough Set and Fuzzy Rough Set Analysis)
This package provides comprehensive implementations of the rough set
theory (RST) and the fuzzy rough set theory (FRST), and integrates
these two theories into a single package. It provides implementations,
not only for the basic concepts of RST and FRST, but also most common
methods based on them for handling some tasks such as discretization,
feature selection, instance selection, rule induction, and prediction.
RST was introduced by Zdzislaw Pawlak in 1982 as a sophisticated
mathematical tool based on indiscernibility relations to model and
process imprecise or incomplete information. It works on symbolic-
valued datasets for tackling the data analysis problems. By using th
indiscernibility relation for objects/instances, RST does not require
additional parameters to analyze the data. FRST is an extension of RST.
The FRST combines concepts of vagueness and indiscernibility that are
expressed with fuzzy sets (as proposed by Zadeh, in 1965) and RST.

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2020-01-16: cran-rcolorbrewer-r31-1.1-2-1 (GNU R Tools for variable-dependent palettes)
The packages provides palettes for drawing nice maps shaded 
according to a variable.

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2020-01-16: cran-vgamdata-r33-1.0-3-1 (Data supporting the VGAM package)
Data sets to accompany the VGAM package. These are used to illustrate
vector generalized linear and additive models, and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column Interaction Models,
and constrained ordination models in ecology.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rodbc-r36-1.3-16-1 (ODBC Database Access for R)
An ODBC database interface

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2020-01-16: cran-sandwich-r31-2.5-1-1 (GNU R std err estimators for time-series data)
sandwich: Robust Covariance Matrix Estimators
Model-robust standard error estimators for cross-sectional, 
time series, and longitudinal data.

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2020-01-16: cran-rcpproll-r35-0.3.0-1 (Efficient Rolling / Windowed Operations)
Provides fast and efficient routines for common rolling / windowed
operations. Routines for the efficient computation of windowed mean,
median, sum, product, minimum, maximum, standard deviation and variance
are provided.

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2020-01-16: cran-polycor-r34-0.7-10-1 (Polychoric and Polyserial Correlations)
Computes polychoric and polyserial correlations by quick "two-step"
methods or ML, optionally with standard errors; tetrachoric
and biserial correlations are special cases.

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2020-01-16: cran-psy-r35-1.1-1 (Various procedures used in psychometry)
Kappa, ICC, Cronbach alpha, screeplot, mtmm

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2020-01-16: cran-svunit-r32-0.7-12-1 (SciViews GUI API - Unit testing)
A complete unit test system and functions to implement its GUI part

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2020-01-16: cran-tsp-r31-1.1-7-1 (Traveling Salesperson Problem)
Basic infrastructure and some algorithms for the traveling salesperson
problem (also traveling salesman problem; TSP). The package provides
some simple algorithms and an interface to Concorde, the currently
fastest TSP solver. Concorde itself is not included in the package
and has to be obtained separately.

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2020-01-16: cran-survival-r34-2.44-1.1-1 (GNU R Tools for survival analysis)
survival analysis: descriptive statistics, two-sample tests,
parametric accelerated failure models, Cox model.
Delayed entry (truncation) allowed for all models;
interval censoring for parametric models. Case-cohort designs.

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2020-01-16: cran-ptak-r35-1.3-34-1 (Principal Tensor Analysis on k modes)
A multiway method to decompose a tensor (array) of any order, as a
generalisation of SVD also supporting non-identity metrics and
penalisations. 2-way SVD with these extensions is also available.
The package includes also some other multiway methods: PCAn
(Tucker-n) and PARAFAC/CANDECOMP with these extensions.

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2020-01-16: cran-zip-r35-2.0.4-1 (Cross-Platform 'zip' Compression)
Cross-Platform 'zip' Compression Library. A replacement for the 'zip'
function, that does not require any additional external tools on any
platform.

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2020-01-16: cran-prim-r32-1.0.16-1 (Patient Rule Induction Method)
PRIM for bump hunting in high-dimensional data

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2020-01-16: cran-xlsx-r31-0.6.1-1 (Excel 2007 and Excel 97/2000/XP/2003 support)
Provide R functions to read/write/format Excel 2007 and
Excel 97/2000/XP/2003 file formats.

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2020-01-16: cran-qtl-r33-1.44-9-1 (Quantitative trait loci)
Analysis of experimental crosses to identify genes 
(called quantitative trait loci, QTLs) contributing 
to variation in quantitative traits.

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2020-01-16: cran-tester-r33-0.1.7-1 (Tests and checks characteristics of R objects)
tester allows you to test characteristics of common R objects.

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2020-01-16: cran-prodlim-r31-2018.04.18-1 (GNU R Tools for estimation of survival)
Fast and user friendly nonparametric estimation in 
censored survival (event history) analysis.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-tidyselect-r33-0.2.5-1 (Select from a Set of Strings)
A backend for the selecting functions of the 'tidyverse'. It makes it
easy to implement select-like functions in your own packages in a way
that is consistent with other 'tidyverse' interfaces for selection.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-survival-r31-2.44-1.1-1 (GNU R Tools for survival analysis)
survival analysis: descriptive statistics, two-sample tests,
parametric accelerated failure models, Cox model.
Delayed entry (truncation) allowed for all models;
interval censoring for parametric models. Case-cohort designs.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-registry-r33-0.5-1-1 (Infrastructure for R Package Registries)
Provides a generic infrastructure for creating and using registries.

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2020-01-16: cran-rgenoud-r35-5.8-3.0-1 (GENetic Optimization Using Derivatives)
A genetic algorithm plus derivative optimizer

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-prodlim-r34-2018.04.18-1 (GNU R Tools for estimation of survival)
Fast and user friendly nonparametric estimation in 
censored survival (event history) analysis.

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2020-01-16: cran-statip-r32-0.2.0-1 (Functions for Distributions and Regression)
A collection of miscellaneous statistical functions for probability
distributions: dbern(), pbern(), qbern(), rbern() for the Bernoulli
distribution, and distr2name(), name2distr() for distribution names;
probability density estimation: densityfun(); most frequent value
estimation: mfv(), mfv1(); calculation of the Hellinger distance:
hellinger(); use of classical kernels: kernelfun(), kernel_properties();
univariate piecewise-constant regression: picor().

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2020-01-16: cran-stable-r33-1.1.4-1 (Functions and Models for Stable Distributions)
Density, distribution, quantile and hazard functions of a stable
variate; generalized regression models for the parameters of a stable
distribution. See the README for how to make equivalent calls to those
of 'stabledist'. See github for Journal article.

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2020-01-16: cran-rex-r33-1.1.2-1 (Friendly Regular Expressions)
A friendly interface for the construction of regular expressions.

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2020-01-16: cran-th.data-r35-1.0-10-1 (TH's Data Archive)
Contains data sets used in other packages Torsten Hothorn maintains.

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2020-01-16: cran-relaimpo-r31-2.2-3-1 (Relative importance of regressors)
relaimpo provides several metrics for assessing relative importance
in linear models. These can be printed, plotted and bootstrapped.
The recommended metric is lmg, which provides a decomposition of
the model explained variance into non-negative contributions.

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2020-01-16: cran-rcdklibs-r32-2.0-1 (CDK libraries packaged for R)
This package provides the CDK libraries for use in the R environment.
Given the size of the library itself, this package is not expected to
change very frequently. To make use of the CDK within R, it is suggested
that you use the rcdk package. Note that it is possible to directly
interact with the CDK using rJava. However rcdk exposes functionality
in a more idiomatic way

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2020-01-16: cran-psych-r34-1.8.12-1 (Procedures for Psychological Research)
A number of routines for personality, psychometrics and experimental
psychology. Functions are primarily for scale construction using
factor analysis, cluster analysis and reliability analysis, although
others provide basic descriptive statistics. Item Response Theory is
done using factor analysis of tetrachoric and polychoric correlations.
Functions for simulating particular item and test structures are
included. Several functions serve as a useful front end for structural
equation modeling. Graphical displays of path diagrams, factor analysis
and structural equation models are created using basic graphics. Some
of the functions are written to support a book on psychometrics as well
as publications in personality research. For more information, see the
personality-project.org/r webpage.

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2020-01-16: cran-polyclip-r35-1.10-0-1 (Polygon Clipping)
R port of the Clipper library. Performs polygon clipping operations
(intersection, union, set minus, set difference) for polygonal regions
of arbitrary complexity, including holes. Also computes offset polygons
(spatial buffer zones, morphological dilations, Minkowski dilations)
for polygonal regions and polygonal lines.

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2020-01-16: cran-xml-r34-3.98-1.20-1 (Tools for parsing and generating XML within R)
Tools for parsing and generating XML within R

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-rattle-r34-5.2.0-1 (Graphical user interface for data mining in R)
Rattle (the R Analytic Tool To Learn Easily) provides a Gnome
(RGtk2) based interface to R functionality for data mining.
The aim is to provide a simple and intuitive interface that
allows a user to quickly load data from a CSV file (or via ODBC),
transform and explore the data, build and evaluate models, and
export models as PMML (predictive modelling markup language) or
as scores. All of this with knowing little about R. All R
commands are logged and commented through the log tab. Thus
they are available to the user as a script file or as an aide
for the user to learn R or to copy-and-paste directly into R
itself. Rattle also exports a number of utility functions and
the graphical user interface, invoked as rattle(), does not
need to be run to deploy these.

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2020-01-16: cran-zip-r36-2.0.4-1 (Cross-Platform 'zip' Compression)
Cross-Platform 'zip' Compression Library. A replacement for the 'zip'
function, that does not require any additional external tools on any
platform.

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2020-01-16: cran-tfplot-r32-2015.12-1-1 (Time Frame User Utilities)
Utilities in this package are for simple manipulation and quick
plotting of time series data. These utilities use the tframe
package which provides a programming kernel for time series.
Extensions to tframe provided in tframePlus can also be used.

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2020-01-16: cran-reshapegui-r36-0.1.0-1 (GUI for the reshape2 and plyr packages)
A tool for learning how to use the functions, melt, acast/dcast, and ddply.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-turner-r31-0.1.7-1 (Turn lists of vectors into indexed structures)
Package designed for working with vectors and lists of vectors,
mainly for turning them into other indexed data structures.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-signal-r32-0.7-6-2 (Signal processing)
A set of signal processing R functions originally written for Matlab/Octave.
Includes filter generation utilities, filtering functions, resampling
routines, and visualization of filter models. It also includes interpolation
functions.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-xlsxjars-r35-0.6.1-1 (Package required POI jars for xlsx package)
The xlsxjars package collects all the external jars required for the
xlxs package. These external jars are quite large in size (15MB) and
have a slow release cycle. By separating the Java and R development,
the storage footprint on CRAN is reduced. This release corresponds
to POI 3.10.

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2020-01-16: cran-vgamdata-r36-1.0-3-1 (Data supporting the VGAM package)
Data sets to accompany the VGAM package. These are used to illustrate
vector generalized linear and additive models, and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column Interaction Models,
and constrained ordination models in ecology.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-superpc-r35-1.09-1 (Supervised principal components)
Supervised principal components for regression and survival analsysis.
Especially useful for high-dimnesional data, including microarray data.

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2020-01-16: cran-simecol-r33-0.8-13-1 (Simulation of ecological dynamic systems)
simecol is an object oriented framework to simulate ecological (and other)
dynamic systems. It can be used for differential equations, individual-based
(or agent-based) and other models as well. The package helps to organize
scenarios (avoids copy and paste) and improves readability and usability of
code.

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2020-01-16: cran-psy-r31-1.1-1 (Various procedures used in psychometry)
Kappa, ICC, Cronbach alpha, screeplot, mtmm

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

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2020-01-16: cran-sparsem-r36-1.77-2 (Sparse Linear Algebra)
Basic linear algebra for sparse matrices

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    CRAN and Bioconductor for R 3.6
2020-01-16: cran-timedate-r33-3043.102-1 (Rmetrics - Chronological and Calendar Objects)
Environment for teaching "Financial Engineering and Computational Finance"

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2020-01-16: cran-rsnns-r33-0.4-12-1 (Stuttgart Neural Network Simulator in R)
The Stuttgart Neural Network Simulator (SNNS) is a library containing many
standard implementations of neural networks. This package wraps the SNNS
functionality to make it available from within R. Using the RSNNS low-level
interface, all of the algorithmic functionality and flexibility of SNNS can
be accessed. Furthermore, the package contains a convenient high-level
interface, so that the most common neural network topologies and learning
algorithms integrate seamlessly into R.

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2020-01-16: cran-sfsmisc-r33-1.1-4-1 (Utilities from Statistik ETH Zurich seminar)
Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich,
quite a few related to graphics; many ported from S-plus times.

commit log from BABA Yoshihiko (babayoshihiko@mac.com):

    Rev