Recent Package Updates
2019-04-16: gd3-2.2.5-2 (Graphics generation library)
The GD library is useful for creating graphics like hit counters on
the fly. This version supports the PNG, JPEG and WBMP formats and lets
you use TrueType fonts rendered via freetype2.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Apply several fixes for CVEs2019-04-16: nano-cur-2.9.2+git20180125142845-2 (OBSOLETE: use package 'nano')
GNU nano is a free replacement for Pico, the default Pine editor. GNU nano
is an effort to provide a Pico-like editor, but also includes some features
that were missing in the original, such as 'search and replace', 'goto line'
or internationalization support.
.
This is the current development version of nano.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
nano-4.1.
Remove the nano-cur package and turn it into an upgrade bundle.2019-04-16: nano-small-4.1-1 (Free Pico clone with some new features)
GNU nano is an easy-to-use text editor originally designed as a replacement
for Pico, the ncurses-based editor from the non-free mailer package Pine
(itself now available under the Apache License as Alpine).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
nano-4.1.
Remove the nano-cur package and turn it into an upgrade bundle.2019-04-16: nano-4.1-1 (Free Pico clone with some new features)
GNU nano is an easy-to-use text editor originally designed as a replacement
for Pico, the ncurses-based editor from the non-free mailer package Pine
(itself now available under the Apache License as Alpine).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
nano-4.1.
Remove the nano-cur package and turn it into an upgrade bundle.2019-04-16: nano-noutf8-4.1-1 (Free Pico clone with some new features)
GNU nano is an easy-to-use text editor originally designed as a replacement
for Pico, the ncurses-based editor from the non-free mailer package Pine
(itself now available under the Apache License as Alpine).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
nano-4.1.
Remove the nano-cur package and turn it into an upgrade bundle.2019-04-15: nginx-cur-1.13.8-2 (OBSOLETE: use package 'nginx')
Nginx ("engine X") is a high-performance web and reverse proxy server
created by Igor Sysoev. It can be used both as a standalone web server
and as a proxy to reduce the load on back-end HTTP or mail servers.
.
This package provides a version of nginx with the complete set of
standard modules included (but omitting some of those included in
nginx-extra).
.
STANDARD HTTP MODULES: Core, Access, Auth Basic, Auto Index, Browser,
Charset, Empty GIF, FastCGI, Geo, Gzip, Headers, Index, Limit Requests,
Limit Zone, Log, Map, Memcached, Proxy, Referer, Rewrite, SCGI,
Split Clients, SSI, Upstream, User ID, UWSGI.
.
OPTIONAL HTTP MODULES: Addition, Debug, GeoIP, Gzip Precompression,
HTTP Sub, Image Filter, IPv6, Real IP, SSL, Stub Status, Substitution,
WebDAV, XSLT.
.
MAIL MODULES: Mail Core, IMAP, POP3, SMTP, SSL.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Turn this variant into an upgrade package2019-04-14: nginx-1.14.2-1 (Small, powerful, scalable web/proxy server)
Nginx ("engine X") is a high-performance web and reverse proxy server
created by Igor Sysoev. It can be used both as a standalone web server
and as a proxy to reduce the load on back-end HTTP or mail servers.
.
This package provides a version of nginx with the complete set of
standard modules included (but omitting some of those included in
nginx-extra).
.
STANDARD HTTP MODULES: Core, Access, Auth Basic, Auto Index, Browser,
Charset, Empty GIF, FastCGI, Geo, Gzip, Headers, Index, Limit Requests,
Limit Zone, Log, Map, Memcached, Proxy, Referer, Rewrite, SCGI,
Split Clients, SSI, Upstream, User ID, UWSGI.
.
OPTIONAL HTTP MODULES: Addition, Debug, GeoIP, Gzip Precompression,
HTTP Sub, Image Filter, IPv6, Real IP, SSL, Stub Status, Substitution,
WebDAV, XSLT.
.
MAIL MODULES: Mail Core, IMAP, POP3, SMTP, SSL.
commit log from nieder (nieder@users.sourceforge.net):
nginx 1.14.2
Update to latest stable nginx release.
Fix library detection so that it doesn't search/#include /usr/include headers but then link %p libraries.
Fixes #395.2019-04-14: help2man-perl5162-1.47.9-1 (Generates man pages from program output)
help2man is intended to provide an easy way for software authors to
include a manual page in their distribution without having to maintain
that document. Given a program which produces resonably standard --help
and --version outputs, help2man will attempt to re-arrange that output
into something which resembles a manual page.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
help2man 1.47.92019-04-14: help2man-perl5182-1.47.9-1 (Generates man pages from program output)
help2man is intended to provide an easy way for software authors to
include a manual page in their distribution without having to maintain
that document. Given a program which produces resonably standard --help
and --version outputs, help2man will attempt to re-arrange that output
into something which resembles a manual page.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
help2man 1.47.92019-04-14: bowtie2-2.3.5-1 (Ultrafast memory-efficient short read aligner)
An ultrafast and memory-efficient tool for aligning sequencing reads
to long reference sequences. It is particularly good at aligning reads
of about 50 up to 100s or 1,000s of characters, and particularly good
at aligning to relatively long (e.g. mammalian) genomes.
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint
small: for the human genome, its memory footprint is typically
around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2.
Nature Methods. 2012, 9:357-359.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
bowtie2 2.3.52019-04-13: vim-8.1.1170-1 (Improved version of the editor "vi")
VIM adds many of the features that you would expect in an editor:
Unlimited undo, syntax coloring, split windows, visual selection,
graphical user interface (read: menus, mouse control, scrollbars,
text selection), and much much more.
commit log from Hisashi T Fujinaka (htodd@twofifty.com):
Vim: Welcome to Vim-8.1.1170.2019-04-13: vim-nox-8.1.1170-1 (Improved version of the editor "vi")
VIM adds many of the features that you would expect in an editor:
Unlimited undo, syntax coloring, split windows, visual selection,
graphical user interface (read: menus, mouse control, scrollbars,
text selection), and much much more.
commit log from Hisashi T Fujinaka (htodd@twofifty.com):
Vim: Welcome to Vim-8.1.1170.2019-04-13: cran-chemometrics-r31-1.4.2-1 (Multivariate Statistical Analysis)
This package is the R companion to the book "Introduction to Multivariate
Statistical Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-kohonen-r33-3.0.8-1 (Supervised/unsupervised self-organising maps)
Supervised and unsupervised self-organising maps
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-hms-r33-0.4.2-1 (Pretty Time of Day)
Implements an S3 class for storing and formatting time-of-day values,
based on the 'difftime' class.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rpart-r34-4.1-13-1 (GNU R Tools for recursive partitioning)
Recursive partitioning and regression trees
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gower-r35-0.2.0-1 (Gower's Distance)
Compute Gower's distance (or similarity) coefficient between records.
Compute the top-n matches between records. Core algorithms are executed
in parallel on systems supporting OpenMP.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-rcpparmadillo-r34-0.9.300.2.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-akima-r31-0.6-2-1 (Interpolation of irregularly spaced data)
Linear or cubic spline interpolation for irregular gridded data
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-dichromat-r34-2.0-0-1 (Color Schemes for Dichromats)
Collapse red-green or green-blue distinctions to simulate the
effects of different types of color-blindness.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-analyzefmri-r32-1.1-17-1 (Functions for analysis of fMRI datasets)
Functions for I/O, visualisation and analysis of functional Magnetic
Resonance Imaging (fMRI) datasets stored in the ANALYZE or NIFTI format.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-adimpro-r31-0.8.2-1 (Adaptive Smoothing of Digital Images)
s package implements tools for manipulation of digital images and the
Propagation Separation approach by Polzehl and Spokoiny (2006) for
smoothing digital images.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-clustercrit-r35-1.2.8-1 (Clustering Indices)
compute clustering validation indices
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-checkmate-r32-1.9.1-1 (Fast and Versatile Argument Checks)
Tests and assertions to perform frequent argument checks.
A substantial part of the package was written in C to minimize
any worries about execution time overhead.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ape-r33-3.5-2 (Analyses of Phylogenetics and Evolution)
ape provides functions for reading, writing, plotting, and manipulating
phylogenetic trees, analyses of comparative data in a phylogenetic
framework, ancestral character analyses, analyses of diversification
and macroevolution, computing distances from allelic and nucleotide data,
reading and writing nucleotide sequences, and several tools such as
Mantel's test, generalized skyline plots, graphical exploration of
phylogenetic data (alex, trex, kronoviz), estimation of absolute
evolutionary rates and clock-like trees using mean path lengths and
penalized likelihood. Phylogeny estimation can be done with the NJ,
BIONJ, ME, MVR, SDM, and triangle methods, and several methods
handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the
corresponding triangle method). Some functions call external
applications (PhyML, Clustal, T-Coffee, Muscle) whose results are
returned into R.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-visnetwork-r33-2.0.6-1 (Network Visualization)
Provides an R interface to the 'vis.js' JavaScript charting library. It
allows an interactive visualization of networks.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-hyperspec-r33-0.98-20150304-2 (Interface for hyperspectral data)
This package is an interface to handle hyperspectral data sets in R.
I.e. spatially or time-resolved spectra, or spectra with any other
kind of information associated with each of the spectra. The spectra
can be data as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR,
Raman, NMR, MS, etc. More generally, any data that is recorded over
a discretized variable, e.g. absorbance = f (wavelength), stored as
a vector of absorbance values for discrete wavelengths is suitable.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-globaltest-r34-5.28.0-1 (Testing Association of Groups of Genes)
Testing whether sets of genes (e.g. KEGG pathways of GO terms) are
significantly associated with a clinical variable of interest.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-pspline-r34-1.0-18-2 (Penalized Smoothing Splines)
Smoothing splines with penalties on order m derivatives.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-magick-r32-2.0-1 (Advanced Graphics and Image-Processing in R)
Bindings to 'ImageMagick': the most comprehensive open-source image
processing library available. Supports many common formats (png, jpeg,
tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip,
blur, etc). All operations are vectorized via the Magick++ STL meaning
they operate either on a single frame or a series of frames for working
with layers, collages, or animation. In RStudio images are automatically
previewed when printed to the console, resulting in an interactive
editing environment. The latest version of the package includes a native
graphics device for creating in-memory graphics or drawing onto images
using pixel coordinates.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-laeken-r33-0.5.0-1 (Indicators on social exclusion and poverty)
Estimation of indicators on social exclusion and poverty,
as well as Pareto tail modeling for empirical income distributions.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-sparsem-r32-1.77-1 (Sparse Linear Algebra)
Basic linear algebra for sparse matrices
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clustvarsel-r31-2.1-1 (Variable Selection for Model-Based Clustering)
A function which implements variable selection methodology for
model-based clustering which allows to find the (locally) optimal
subset of variables in a dataset that have group/cluster information.
A greedy or headlong search can be used, either in a forward-backward
or backward-forward direction, with or without sub-sampling at the
hierarchical clustering stage for starting Mclust models. By default
the algorithm uses a sequential search, but parallelization is also
available.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gtable-r31-0.2.0-1 (Arrange grobs in tables)
Tools to make it easier to work with "tables" of grobs.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-formatr-r31-1.5-1 (GNU R Tools for formatting R source code)
This package provides a function tidy.source() and optionally a GUI
(by gWidgets and preferably gWidgetsRGtk2) to format R source code.
Spaces and indent will be added to the code automatically, and comments
will be preserved under certain conditions, so that R code will be more
human-readable and tidy.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gridextra-r33-2.3-2 (Grid graphics functions)
misc. high-level Grid functions
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-laeken-r35-0.5.0-1 (Indicators on social exclusion and poverty)
Estimation of indicators on social exclusion and poverty,
as well as Pareto tail modeling for empirical income distributions.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bayesm-r34-3.1-1-1 (Various R programming tools)
bayesm covers many important models used in marketing and micro-
econometrics applications. The package includes: Bayes Regression
(univariate or multivariate dep var), Bayes Seemingly Unrelated
Regression (SUR), Binary and Ordinal Probit, Multinomial Logit
(MNL) and Multinomial Probit (MNP), Multivariate Probit, Negative
Binomial (Poisson) Regression, Multivariate Mixtures of Normals
(including clustering), Dirichlet Process Prior Density Estimation
with normal base, Hierarchical Linear Models with normal prior and
covariates, Hierarchical Linear Models with a mixture of normals
prior and covariates, Hierarchical Multinomial Logits with a
mixture of normals prior and covariates, Hierarchical Multinomial
Logits with a Dirichlet Process prior and covariates, Hierarchical
Negative Binomial Regression Models, Bayesian analysis of choice-
ased conjoint data, Bayesian treatment of linear instrumental
variables models, and Analysis of Multivariate Ordinal survey
data with scale usage heterogeneity (as in Rossi et al, JASA (01)).
For further reference, consult our book, Bayesian Statistics and
Marketing by Rossi, Allenby and McCulloch.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-fansi-r35-0.4.0-1 (ANSI Control Sequence Aware Functions)
Counterparts to R string manipulation functions that account for the
effects of ANSI text formatting control sequences.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-dichromat-r31-2.0-0-1 (Color Schemes for Dichromats)
Collapse red-green or green-blue distinctions to simulate the
effects of different types of color-blindness.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-als-r34-0.0.6-1 (MCR-ALS)
Alternating least squares is often used to resolve components contributing
to data with a bilinear structure; the basic technique may be extended to
alternating constrained least squares. Commonly applied constraints include
unimodality, non-negativity, and normalization of components. Several data
matrices may be decomposed simultaneously by assuming that one of the two
matrices in the bilinear decomposition is shared between datasets.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: bioconductor-qvalue-r31-2.6.0-1 (Q-value estimation)
This package takes a list of p-values resulting from the simultaneous
testing of many hypotheses and estimates their q-values and local FDR
values. The q-value of a test measures the proportion of false positives
incurred (called the false discovery rate) when that particular test is
called significant. The local FDR measures the posterior probability
the null hypothesis is true given the test's p-value. Various plots
are automatically generated, allowing one to make sensible significance
cut-offs. Several mathematical results have recently been shown on the
conservative accuracy of the estimated q-values from this software.
The software can be applied to problems in genomics, brain imaging,
astrophysics, and data mining.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-prettyunits-r31-1.0.2-3 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-yaletoolkit-r35-4.2.2-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-cellranger-r33-1.1.0-1 (Translate Spreadsheet Cell Ranges)
Helper functions to work with spreadsheets and
the A1:D10 style of cell range specification.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-sys-r35-3.1-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bma-r35-3.18.9-1 (Bayesian Model Averaging)
Package for Bayesian model averaging for linear models, generalizable
linear models and survival models (cox regression).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-withr-r31-2.1.2-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rcpparmadillo-r32-0.7.960.1.1-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-caret-r32-6.0-68-1 (Classification and Regression Training)
Misc functions for training and plotting classification and regression models
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-data.table-r32-1.12.0-1 (Extension of data.frame)
Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins,
fast add/modify/delete of columns by group using no copies at all, list
columns and a fast file reader (fread). Offers a natural and flexible
syntax, for faster development.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-pillar-r35-1.3.1-1 (Coloured Formatting for Columns)
Provides a 'pillar' generic designed for formatting columns of data
using the full range of colours provided by modern terminals.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rgtk2-r34-2.20.31-3 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bayestree-r31-0.3-1.4-1 (Bayesian Methods for Tree Based Models)
Implementation of BART:Bayesian Additive Regression Trees,
Chipman, George, McCulloch (2009)
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-pillar-r33-1.3.1-1 (Coloured Formatting for Columns)
Provides a 'pillar' generic designed for formatting columns of data
using the full range of colours provided by modern terminals.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gwidgetstcltk-r33-0.0-55-1 (Toolkit implementation of gWidgets for tcltk)
Port of the gWidgets API to the tcltk package. Requires TK 8.5 or
greater for the tile (ttk)widgets http://www.tcl.tk/software/tcltk/8.5.tml.
This is the default on Windows. Under linux, Tk must be installed.
Under Mac OS X (10.5) there are two options: native Tk or X11.
For the native one, Tk must be upgraded. See www.tcl.tk to download
source. Under the Mac it compiles and installs cleanly. For X11,
tcltk libraries can be downloaded to augment the R binary package.
See http://cran.r-project.org/bin/macosx/tools/. The gdf function
requires the add on Tk package TkTable (http://tktable.sourceforge.net/).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-atelier-r31-0.24-1 (GTK GUI for statistical tools)
A collection of statistical simulation and computation tools with a
GTK GUI, to help teach statistical concepts and compute probabilities.
Two domains are covered: I. Understanding (Central-Limit Theorem and
the Normal Distribution, Distribution of a sample mean, Distribution
of a sample variance, Probability calculator for common distributions),
and II. Elementary Bayesian Statistics (bayesian inference on proportions,
contingency tables, means and variances, with informative and
oninformative priors).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-cairodevice-r32-2.24-1 (Cairo-based antialiased graphics driver)
Cairo/GTK graphics device driver with output to screen, file
(png, svg, pdf, and ps) or memory (arbitrary GdkDrawable or
Cairo context). The screen device may be embedded into RGtk2
interfaces. Supports all interactive features of other graphics
devices, including getGraphicsEvent().
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-htmltools-r35-0.3.6-1 (Tools for HTML)
Tools for HTML generation and output.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ca-r31-0.71-1 (Correspondence Analysis)
A package for computation and visualization of simple, multiple
and joint correspondence analysis.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-xts-r35-0.11-2-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-matrixmodels-r31-0.4-1-1 (Modelling with Sparse And Dense Matrices)
Modelling with sparse and dense 'Matrix' matrices,
using modular prediction and response module classes.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bayestree-r34-0.3-1.4-1 (Bayesian Methods for Tree Based Models)
Implementation of BART:Bayesian Additive Regression Trees,
Chipman, George, McCulloch (2009)
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-utf8-r33-1.1.4-1 (Unicode Text Processing)
Process and print 'UTF-8' encoded international text (Unicode). Input,
validate, normalize, encode, format, and display.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rlang-r32-0.3.2-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rcpproll-r32-0.3.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-adaptivetau-r35-2.2-3-1 (Tau-leaping stochastic simulation)
Implements adaptive tau leaping to approximate the trajectory of a
continuous-time stochastic process as described by Cao et al. (2007)
The Journal of Chemical Physics. This package is based upon work
supported by NSF DBI-0906041 and NIH K99-GM104158 to Philip Johnson
and NIH R01-AI049334 to Rustom Antia.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-minqa-r33-1.2.4-3 (Derivative-free optimization by quadratic)
Derivative-free optimization by quadratic approximation based
on an interface to Fortran implementations by M. J. D. Powell.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-plyr-r32-1.8.4-1 (Splitting, applying and combining data)
plyr is a set of tools that solves a common set of problems: you need to
break a big problem down into manageable pieces, operate on each pieces
and then put all the pieces back together. For example, you might want
to fit a model to each spatial location or time point in your study,
summarise data by panels or collapse high-dimensional arrays to simpler
summary statistics. The development of plyr has been generously supported
by BD (Becton Dickinson).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-partitions-r32-1.9-19-1 (Additive partitions of integers)
Additive partitions of integers. Enumerates the partitions, unequal partitions,
and restricted partitions of an integer; the three corresponding partition
functions are also given. Set partitions are now included.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-lattice-r34-0.20-38-1 (GNU R Tools for lattice graphics)
Lattice is a powerful and elegant high-level data visualization
system, with an emphasis on multivariate data, that is sufficient
for typical graphics needs, and is also flexible enough to handle
most nonstandard requirements.
See ?Lattice for an introduction.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-data.table-r34-1.12.0-1 (Extension of data.frame)
Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins,
fast add/modify/delete of columns by group using no copies at all, list
columns and a fast file reader (fread). Offers a natural and flexible
syntax, for faster development.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-permute-r35-0.9-4-1 (Generating restricted permutations of data)
The 'permute' package implements a set of restricted permutation designs
for freely exchangeable, line transects (time series), and spatial grid
designs plus permutation of blocks (groups of samples). 'permute' also
allows split-plot designs, in which the whole-plots or split-plots or
both can be freely-exchangeable or one of the restricted designs. The
'permute' package is modelled after the permutation schemes of Canoco
3.1 (and later) by Cajo ter Braak.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-markdown-r35-0.9-1 (GNU R Tools for making web reports from text)
R Markdown is a format that enables easy authoring of reproducible
web reports from R. It combines the core syntax of Markdown
(an easy-to-write plain text format for web content) with embedded
R code chunks that are run so their output can be included in
the final document.
The concept of R Markdown is similar to Sweave (a system built-in
to R for combining R with LaTeX). In Sweave, Rnw files are "weaved"
into TeX files that are then compiled into PDFs. In R Markdown,
Rmd files are similarly "weaved" into plain markdown (.md) files
that are then compiled into HTML documents.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-deoptimr-r32-1.0-8-1 (Differential Evolution Optimization)
An implementation of the jDE variant of the Differential Evolution stochastic
algorithm for global optimization of nonlinear programming problems.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-codetools-r32-0.2-16-1 (Code Analysis Tools for R)
Code analysis tools for R
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bvls-r35-1.4-3 (Stark-Parker algorithm)
An R interface to the Stark-Parker implementation of an algorithm
for bounded-variable least squares
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-gridextra-r34-2.3-2 (Grid graphics functions)
misc. high-level Grid functions
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-pcamethods-r34-1.66.0-1 (Collection of PCA methods)
Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear
PCA and the conventional SVD PCA. A cluster based method for missing
value estimationn is included for comparison. BPCA, PPCA and NipalsPCA
may be used to perform PCA on incomplete data as well as for accurate
missing value estimation. A set of methods for printing and plotting
the results is also provided. All PCA methods make use of the same
data structure (pcaRes) to provide a unique interface to the PCA
results. Developed at the Max-Planck Institute for Molecular Plant
Physiology, Golm, Germany.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-clustergeneration-r33-1.3.4-1 (Random cluster generation)
The package contains functions for generating random clusters, generating
random covariance/correlation matrices, calculating a separation index
(data and population version) for pairs of clusters or cluster distributions,
and 1-D and 2-D projection plots to visualize clusters. The package also
contains a function to generate random clusters based on factorial designs
with factors such as degree of separation, number of clusters, number of
variables, number of noisy variables.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-hyperspec-r31-0.98-20150304-2 (Interface for hyperspectral data)
This package is an interface to handle hyperspectral data sets in R.
I.e. spatially or time-resolved spectra, or spectra with any other
kind of information associated with each of the spectra. The spectra
can be data as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR,
Raman, NMR, MS, etc. More generally, any data that is recorded over
a discretized variable, e.g. absorbance = f (wavelength), stored as
a vector of absorbance values for discrete wavelengths is suitable.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bvls-r31-1.4-3 (Stark-Parker algorithm)
An R interface to the Stark-Parker implementation of an algorithm
for bounded-variable least squares
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-barcode-r31-1.1-1 (Barcode distribution plots)
This package includes the function \code{barcode()}, which produces a
histogram-like plot of a distribution that shows granularity in the data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bvpsolve-r31-1.3.3-1 (Solvers for boundary value problems)
Functions that solve boundary value problems (BVP) of systems
of ordinary differential equations (ODE). The functions provide
an interface to the FORTRAN functionS twpbvpC, colnew/colsys,
and an R-implementation of the shooting method.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-chemospecutils-r32-0.2.211-1 (Functions Supporting ChemoSpec / ChemoSpec2D)
Functions supporting the common needs of packages 'ChemoSpec' and
'ChemoSpec2D'.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-lattice-r32-0.20-38-1 (GNU R Tools for lattice graphics)
Lattice is a powerful and elegant high-level data visualization
system, with an emphasis on multivariate data, that is sufficient
for typical graphics needs, and is also flexible enough to handle
most nonstandard requirements.
See ?Lattice for an introduction.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-keggraph-r35-1.32.0-1 (Graph approach to KEGG PATHWAY in R)
KEGGGraph is an interface between KEGG pathway and graph object as well
as a collection of tools to analyze, dissect and visualize these graphs.
It parses the regularly updated KGML (KEGG XML) files into graph models
maintaining all essential pathway attributes. The package offers
functionalities including parsing, graph operation, visualization and etc.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-chemometricswithr-r32-0.1.13-1 (Chemometrics with R)
The package provides functions and scripts used in the book
"Chemometrics with R - Multivariate Data Analysis in the
Natural Sciences and Life Sciences" by Ron Wehrens, Springer (2011).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-maldiquant-r31-1.11-1 (Quantitative Analysis of Mass Spec Data)
MALDIquant provides a complete analysis pipeline for MALDI-TOF and other
mass spectrometry data. Distinctive features include baseline subtraction
methods such as TopHat or SNIP, peak alignment using warping functions,
handling of replicated measurements as well as allowing spectra with
different resolutions.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gridextra-r31-2.3-2 (Grid graphics functions)
misc. high-level Grid functions
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-partitions-r34-1.9-19-1 (Additive partitions of integers)
Additive partitions of integers. Enumerates the partitions, unequal partitions,
and restricted partitions of an integer; the three corresponding partition
functions are also given. Set partitions are now included.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-htmlwidgets-r32-1.3-1 (HTML Widgets for R)
A framework for creating HTML widgets that render in various
contexts including the R console, 'R Markdown' documents,
and 'Shiny' web applications.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-xlconnectjars-r34-0.2-15-1 (JAR dependencies for the XLConnect)
Provides external JAR dependencies for the XLConnect package.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-dichromat-r33-2.0-0-1 (Color Schemes for Dichromats)
Collapse red-green or green-blue distinctions to simulate the
effects of different types of color-blindness.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bvpsolve-r33-1.3.3-1 (Solvers for boundary value problems)
Functions that solve boundary value problems (BVP) of systems
of ordinary differential equations (ODE). The functions provide
an interface to the FORTRAN functionS twpbvpC, colnew/colsys,
and an R-implementation of the shooting method.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-acepack-r33-1.4.1-1 (ACE and AVAS methods)
ACE and AVAS methods for choosing regression transformations.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-siggenes-r32-1.48.0-1 (Multiple testing using SAM and EBAM)
Identification of differentially expressed genes and estimation of the
False Discovery Rate (FDR) using both the Significance Analysis of
Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-latticeextra-r33-0.6-28-1 (Extra Graphical Utilities)
Extra graphical utilities based on lattice
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bvls-r33-1.4-3 (Stark-Parker algorithm)
An R interface to the Stark-Parker implementation of an algorithm
for bounded-variable least squares
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-clustergeneration-r34-1.3.4-1 (Random cluster generation)
The package contains functions for generating random clusters, generating
random covariance/correlation matrices, calculating a separation index
(data and population version) for pairs of clusters or cluster distributions,
and 1-D and 2-D projection plots to visualize clusters. The package also
contains a function to generate random clusters based on factorial designs
with factors such as degree of separation, number of clusters, number of
variables, number of noisy variables.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-pspline-r32-1.0-18-2 (Penalized Smoothing Splines)
Smoothing splines with penalties on order m derivatives.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-rgraphviz-r34-2.18.0-1 (Plotting capabilities for R graph objects)
nterfaces R with the AT and T graphviz library for plotting R graph
objects from the graph package. Users on all platforms must install
graphviz; see the README file, available in the source distribution
of this file, for details.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-nnet-r31-7.3-12-2 (GNU R Tools for neural networks)
Software for feed-forward neural networks with a single hidden layer,
and for multinomial log-linear models.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bayestree-r33-0.3-1.4-1 (Bayesian Methods for Tree Based Models)
Implementation of BART:Bayesian Additive Regression Trees,
Chipman, George, McCulloch (2009)
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-animation-r32-2.6-1 (Utilities to create animations in statistics)
This package contains a variety of functions for animations in
statistics, covering areas such as probability theory,
mathematical statistics, multivariate statistics, nonparametric
statistics, sampling survey, linear models, time series,
computational statistics, data mining and machine learning.
These functions might be helpful in teaching statistics and
data analysis. Also provided in this package are several
approaches to save animations to various formats, e.g. Flash,
GIF, HTML pages, PDF and videos (saveSWF(), saveGIF(), saveHTML(),
saveLatex(), and saveVideo() respectively). PDF animations
can be inserted into Sweave/knitr easily.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-rpart-r35-4.1-13-1 (GNU R Tools for recursive partitioning)
Recursive partitioning and regression trees
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-nnet-r35-7.3-12-2 (GNU R Tools for neural networks)
Software for feed-forward neural networks with a single hidden layer,
and for multinomial log-linear models.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gower-r34-0.2.0-1 (Gower's Distance)
Compute Gower's distance (or similarity) coefficient between records.
Compute the top-n matches between records. Core algorithms are executed
in parallel on systems supporting OpenMP.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-fansi-r34-0.4.0-1 (ANSI Control Sequence Aware Functions)
Counterparts to R string manipulation functions that account for the
effects of ANSI text formatting control sequences.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-baseline-r34-1.2-1-1 (Baseline Correction of Spectra)
Collection of baseline correction algorithms, along with a
framework and a GUI for optimising baseline algorithm parameters.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-quantreg-r34-5.38-1 (Quantile Regression)
Quantile regression and related methods.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-nnet-r33-7.3-12-2 (GNU R Tools for neural networks)
Software for feed-forward neural networks with a single hidden layer,
and for multinomial log-linear models.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-matrix-r31-1.2-6-1 (Sparse and Dense Matrix Classes and Methods)
Classes and methods for dense and sparse matrices and operations
on them using LAPACK and SuiteSparse.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-xlconnectjars-r32-0.2-15-1 (JAR dependencies for the XLConnect)
Provides external JAR dependencies for the XLConnect package.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-visnetwork-r31-2.0.6-1 (Network Visualization)
Provides an R interface to the 'vis.js' JavaScript charting library. It
allows an interactive visualization of networks.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-recipes-r33-0.1.5-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-histdata-r35-0.8-4-1 (History of statistics data sets)
The HistData package provides a collection of small data sets that
are interesting and important in the history of statistics and data
visualization. The goal of the package is to make these available,
both for instructional use and for historical research. Some of
these present interesting challenges for graphics or analysis in R.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-sparsem-r34-1.77-1 (Sparse Linear Algebra)
Basic linear algebra for sparse matrices
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-care-r32-1.1.10-1 (Regression and CAR Score Variable Selection)
The "care" package implements the regression approach of Zuber and
Strimmer (2011) "High-dimensional regression and variable selection
using CAR scores" SAGMB 10: 34. CAR scores measure the correlation
between the response and the Mahalanobis-decorrelated predictors.
The squared CAR score is a natural measure of variable importance
and provides a canonical ordering of variables. This package
provides functions for estimating CAR scores, for variable
selection using CAR scores, and for estimating corresponding
regression coefficients. Both shrinkage as well as empirical
estimators are available.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-bh-r32-1.69.0-1-1 (Boost C++ header files)
Boost provides free peer-reviewed portable C++ source libraries.
A large part of Boost is provided as C++ template code which is
resolved entirely at compile-time without linking. This package
aims to provide the most useful subset of Boost libraries for
template use among CRAN package. By placing these libraries in
this package, we offer a more efficient distribution system for
CRAN as replication of this code in the sources of other
packages is avoided.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-chemometrics-r33-1.4.2-1 (Multivariate Statistical Analysis)
This package is the R companion to the book "Introduction to Multivariate
Statistical Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-progress-r34-1.2.0-1 (Statnet project common scripts and utilities)
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rcppeigen-r33-0.3.3.5.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-nnet-r34-7.3-12-2 (GNU R Tools for neural networks)
Software for feed-forward neural networks with a single hidden layer,
and for multinomial log-linear models.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ncal-r33-2015.3-3-2 (Nonlinear Calibration)
nCal is a package that performs nonlinear calibration and curve fitting for
data from Luminex, RT-PCR, ELISA, RPPA etc. Its precursor is Ruminex.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-prettyunits-r33-1.0.2-3 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-randomforest-r34-4.6-12-2 (GNU R Tools for random forest class/regress)
Classification and regression based on a forest of trees using random inputs.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-waveslim-r33-1.7.5-3 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-atelier-r34-0.24-1 (GTK GUI for statistical tools)
A collection of statistical simulation and computation tools with a
GTK GUI, to help teach statistical concepts and compute probabilities.
Two domains are covered: I. Understanding (Central-Limit Theorem and
the Normal Distribution, Distribution of a sample mean, Distribution
of a sample variance, Probability calculator for common distributions),
and II. Elementary Bayesian Statistics (bayesian inference on proportions,
contingency tables, means and variances, with informative and
oninformative priors).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-arules-r32-1.4-1-2 (Mining Association Rules)
Provides the infrastructure for representing, manipulating and analyzing
transaction data and patterns (frequent itemsets and association rules).
Also provides interfaces to C implementations of the association mining
algorithms Apriori and Eclat by C. Borgelt.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-plogr-r34-0.2.0-1 (Parametrized Active Bindings)
Provides a simple interface for creating active bindings where
the bound function accepts additional arguments.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-lattice-r31-0.20-38-1 (GNU R Tools for lattice graphics)
Lattice is a powerful and elegant high-level data visualization
system, with an emphasis on multivariate data, that is sufficient
for typical graphics needs, and is also flexible enough to handle
most nonstandard requirements.
See ?Lattice for an introduction.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-survival-r34-2.43-3-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-visnetwork-r32-2.0.6-1 (Network Visualization)
Provides an R interface to the 'vis.js' JavaScript charting library. It
allows an interactive visualization of networks.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-cairo-r35-1.5-9-2 (Graphics device using cairo graphics library)
This package provides a Cairo graphics device that can be use to
create high-quality vector (PDF, PostScript and SVG) and bitmap output
(PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32).
Since it uses the same back-end for all output, copying across formats
is WYSIWYG. Files are created without the dependence on X11 or other
external programs. This device supports alpha channel (semi-transparent
drawing) and resulting images can contain transparent and semi-transparent
regions. It is ideal for use in server environments (file output) and as
a replacement for other devices that don't have Cairo's capabilities
such as alpha support or anti-aliasing. Backends are modular such that
any subset of backends is supported.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-waveslim-r31-1.7.5-3 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-chemometricswithrdata-r31-0.1.3-1 (Data for package ChemometricsWithR)
The package provides data sets used in the book "Chemometrics with R
- Multivariate Data Analysis in the Natural Sciences and Life Sciences"
by Ron Wehrens, Springer (2011).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: bioconductor-sspa-r34-2.14.0-1 (General Sample Size and Power Analysis)
General Sample size and power analysis for microarray and
next-generation sequencing data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-rcpparmadillo-r33-0.9.300.2.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clustvarsel-r33-2.3.1-1 (Variable Selection for Model-Based Clustering)
A function which implements variable selection methodology for
model-based clustering which allows to find the (locally) optimal
subset of variables in a dataset that have group/cluster information.
A greedy or headlong search can be used, either in a forward-backward
or backward-forward direction, with or without sub-sampling at the
hierarchical clustering stage for starting Mclust models. By default
the algorithm uses a sequential search, but parallelization is also
available.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-globalancova-r34-3.42.0-1 (Global test for differential gene expression)
We give the following arguments in support of the GlobalAncova approach: After
appropriate normalisation, gene-expression-data appear rather symmetrical and
outliers are no real problem, so least squares should be rather robust. ANCOVA
with interaction yields saturated data modelling e.g. different means per group
and gene. Covariate adjustment can help to correct for possible selection bias.
Variance homogeneity and uncorrelated residuals cannot be expected. Application
of ordinary least squares gives unbiased, but no longer optimal estimates
(Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate,
due to correlation. The test statistic however mirrors deviations from the null
hypothesis. In combination with a permutation approach, empirical significance
levels can be approximated. Alternatively, an approximation yields asymptotic
p-values. This work was supported by the NGFN grant 01 GR 0459, BMBF, Germany.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-openxlsx-r33-4.1.0-1 (Read, Write and Edit XLSX Files)
Simplifies the creation of Excel .xlsx files by providing a high level
interface to writing, styling and editing worksheets. Through the use
of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect'
packages with the added benefit of removing the dependency on Java.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ncal-r31-2015.3-3-2 (Nonlinear Calibration)
nCal is a package that performs nonlinear calibration and curve fitting for
data from Luminex, RT-PCR, ELISA, RPPA etc. Its precursor is Ruminex.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gtable-r34-0.2.0-1 (Arrange grobs in tables)
Tools to make it easier to work with "tables" of grobs.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-checkmate-r35-1.9.1-1 (Fast and Versatile Argument Checks)
Tests and assertions to perform frequent argument checks.
A substantial part of the package was written in C to minimize
any worries about execution time overhead.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-reshape2-r35-1.4.3-1 (Flexibly reshape data)
Reshape lets you flexibly restructure and aggregate data using
just two functions: melt and cast.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-class-r35-7.3-15-1 (GNU R Tools for classification)
Various functions for classification.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-barcode-r32-1.1-1 (Barcode distribution plots)
This package includes the function \code{barcode()}, which produces a
histogram-like plot of a distribution that shows granularity in the data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-binda-r32-1.0.3-2 (Multi-Class Discriminant Analysis)
The "binda" package implements functions for multi-class discriminant
analysis using binary predictors, for corresponding variable selection,
and for dichotomizing continuous data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-openxlsx-r31-3.0.0-1 (Read, Write and Edit XLSX Files)
Simplifies the creation of Excel .xlsx files by providing a high level
interface to writing, styling and editing worksheets. Through the use
of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect'
packages with the added benefit of removing the dependency on Java.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gwidgetstcltk-r32-0.0-55-1 (Toolkit implementation of gWidgets for tcltk)
Port of the gWidgets API to the tcltk package. Requires TK 8.5 or
greater for the tile (ttk)widgets http://www.tcl.tk/software/tcltk/8.5.tml.
This is the default on Windows. Under linux, Tk must be installed.
Under Mac OS X (10.5) there are two options: native Tk or X11.
For the native one, Tk must be upgraded. See www.tcl.tk to download
source. Under the Mac it compiles and installs cleanly. For X11,
tcltk libraries can be downloaded to augment the R binary package.
See http://cran.r-project.org/bin/macosx/tools/. The gdf function
requires the add on Tk package TkTable (http://tktable.sourceforge.net/).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-hmisc-r32-3.17-4-1 (Harrell Miscellaneous)
The Hmisc library contains many functions useful for data analysis,
high-level graphics, utility operations, functions for computing sample size
and power, importing datasets, imputing missing values, advanced table making,
variable clustering, character string manipulation, conversion of S objects
to LaTeX code, and recoding variables.
Please submit bug reports to 'http://biostat.mc.vanderbilt.edu/trac/Hmisc'.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-cocorresp-r35-0.3-0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-bayesm-r31-3.0-2-1 (Various R programming tools)
bayesm covers many important models used in marketing and micro-
econometrics applications. The package includes: Bayes Regression
(univariate or multivariate dep var), Bayes Seemingly Unrelated
Regression (SUR), Binary and Ordinal Probit, Multinomial Logit
(MNL) and Multinomial Probit (MNP), Multivariate Probit, Negative
Binomial (Poisson) Regression, Multivariate Mixtures of Normals
(including clustering), Dirichlet Process Prior Density Estimation
with normal base, Hierarchical Linear Models with normal prior and
covariates, Hierarchical Linear Models with a mixture of normals
prior and covariates, Hierarchical Multinomial Logits with a
mixture of normals prior and covariates, Hierarchical Multinomial
Logits with a Dirichlet Process prior and covariates, Hierarchical
Negative Binomial Regression Models, Bayesian analysis of choice-
ased conjoint data, Bayesian treatment of linear instrumental
variables models, and Analysis of Multivariate Ordinal survey
data with scale usage heterogeneity (as in Rossi et al, JASA (01)).
For further reference, consult our book, Bayesian Statistics and
Marketing by Rossi, Allenby and McCulloch.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-genomeinfodb-r33-1.10.3-1 (Manipulating chromosome/'seqname' identifiers)
The Seqnames package contains data and functions that define and allow
translation between different chromosome sequence naming conventions
(e.g., "chr1" versus "1"), including a function that attempts to place
sequence names in their natural, rather than lexicographic, order.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-formatr-r34-1.5-1 (GNU R Tools for formatting R source code)
This package provides a function tidy.source() and optionally a GUI
(by gWidgets and preferably gWidgetsRGtk2) to format R source code.
Spaces and indent will be added to the code automatically, and comments
will be preserved under certain conditions, so that R code will be more
human-readable and tidy.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-vim-r33-4.7.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bca-r31-0.9-3-1 (Business and Customer Analytics)
Underlying support functions for RcmdrPlugin.BCA and a companion to 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-ada-r35-2.0-5-1 (R package for stochastic boosting)
Performs discrete, real, and gentle boost under both exponential
and logistic loss on a given data set. The package ada provides
a straightforward, well-documented, and broad boosting routine
for classification, ideally suited for small to moderate-sized
data sets.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-cellranger-r32-1.1.0-1 (Translate Spreadsheet Cell Ranges)
Helper functions to work with spreadsheets and
the A1:D10 style of cell range specification.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-maldiquant-r32-1.11-1 (Quantitative Analysis of Mass Spec Data)
MALDIquant provides a complete analysis pipeline for MALDI-TOF and other
mass spectrometry data. Distinctive features include baseline subtraction
methods such as TopHat or SNIP, peak alignment using warping functions,
handling of replicated measurements as well as allowing spectra with
different resolutions.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-rgraphviz-r32-2.18.0-1 (Plotting capabilities for R graph objects)
nterfaces R with the AT and T graphviz library for plotting R graph
objects from the graph package. Users on all platforms must install
graphviz; see the README file, available in the source distribution
of this file, for details.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-bvls-r34-1.4-3 (Stark-Parker algorithm)
An R interface to the Stark-Parker implementation of an algorithm
for bounded-variable least squares
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-htmltools-r32-0.3.6-1 (Tools for HTML)
Tools for HTML generation and output.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clipr-r32-0.5.0-1 (Read and Write from the System Clipboard)
Simple utility functions to read from and write to the Windows, OS X,
and X11 clipboards.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-lubridate-r31-1.7.4-1 (Make Dealing with Dates a Little Easier)
Functions to work with date-times and time-spans: fast and user friendly
parsing of date-time data, extraction and updating of components of a
date-time (years, months, days, hours, minutes, and seconds), algebraic
manipulation on date-time and time-span objects. The 'lubridate' package
has a consistent and memorable syntax that makes working with dates easy
and fun. Parts of the 'CCTZ' source code, released under the Apache 2.0
License, are included in this package. See
<https://github.com/google/cctz> for more details.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-data.table-r33-1.12.0-1 (Extension of data.frame)
Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins,
fast add/modify/delete of columns by group using no copies at all, list
columns and a fast file reader (fread). Offers a natural and flexible
syntax, for faster development.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-kohonen-r35-3.0.8-1 (Supervised/unsupervised self-organising maps)
Supervised and unsupervised self-organising maps
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-lubridate-r34-1.7.4-1 (Make Dealing with Dates a Little Easier)
Functions to work with date-times and time-spans: fast and user friendly
parsing of date-time data, extraction and updating of components of a
date-time (years, months, days, hours, minutes, and seconds), algebraic
manipulation on date-time and time-span objects. The 'lubridate' package
has a consistent and memorable syntax that makes working with dates easy
and fun. Parts of the 'CCTZ' source code, released under the Apache 2.0
License, are included in this package. See
<https://github.com/google/cctz> for more details.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-pbkrtest-r33-0.4-7-1 (Kenward-Roger-based methods)
Test in linear mixed effects models. Attention is on linear mixed
effects models as implemented in the lme4 package. The package
implements a parametric bootstrap test. The package implements a
Kenward-Roger modification of F-tests.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-matrixmodels-r33-0.4-1-1 (Modelling with Sparse And Dense Matrices)
Modelling with sparse and dense 'Matrix' matrices,
using modular prediction and response module classes.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-pbkrtest-r31-0.4-2-1 (Kenward-Roger-based methods)
Test in linear mixed effects models. Attention is on linear mixed
effects models as implemented in the lme4 package. The package
implements a parametric bootstrap test. The package implements a
Kenward-Roger modification of F-tests.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-partitions-r33-1.9-19-1 (Additive partitions of integers)
Additive partitions of integers. Enumerates the partitions, unequal partitions,
and restricted partitions of an integer; the three corresponding partition
functions are also given. Set partitions are now included.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-pspline-r31-1.0-18-2 (Penalized Smoothing Splines)
Smoothing splines with penalties on order m derivatives.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gwidgetstcltk-r34-0.0-55-1 (Toolkit implementation of gWidgets for tcltk)
Port of the gWidgets API to the tcltk package. Requires TK 8.5 or
greater for the tile (ttk)widgets http://www.tcl.tk/software/tcltk/8.5.tml.
This is the default on Windows. Under linux, Tk must be installed.
Under Mac OS X (10.5) there are two options: native Tk or X11.
For the native one, Tk must be upgraded. See www.tcl.tk to download
source. Under the Mac it compiles and installs cleanly. For X11,
tcltk libraries can be downloaded to augment the R binary package.
See http://cran.r-project.org/bin/macosx/tools/. The gdf function
requires the add on Tk package TkTable (http://tktable.sourceforge.net/).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bca-r32-0.9-3-1 (Business and Customer Analytics)
Underlying support functions for RcmdrPlugin.BCA and a companion to 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-adimpro-r34-0.8.2-1 (Adaptive Smoothing of Digital Images)
s package implements tools for manipulation of digital images and the
Propagation Separation approach by Polzehl and Spokoiny (2006) for
smoothing digital images.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rcppeigen-r31-0.3.3.5.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-rgraphviz-r33-2.18.0-1 (Plotting capabilities for R graph objects)
nterfaces R with the AT and T graphviz library for plotting R graph
objects from the graph package. Users on all platforms must install
graphviz; see the README file, available in the source distribution
of this file, for details.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-lme4-r31-1.1-13-1 (Various R programming tools)
Fit linear and generalized linear mixed-effects models. The models
and their components are represented using S4 classes and methods.
The core computational algorithms are implemented using the Eigen
C++ library for numerical linear algebra and RcppEigen "glue".
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-recipes-r35-0.1.5-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-partitions-r31-1.9-19-1 (Additive partitions of integers)
Additive partitions of integers. Enumerates the partitions, unequal partitions,
and restricted partitions of an integer; the three corresponding partition
functions are also given. Set partitions are now included.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-chron-r33-2.3-53-1 (Chronological objects)
Chronological objects which can handle dates and times
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-sparsem-r31-1.77-1 (Sparse Linear Algebra)
Basic linear algebra for sparse matrices
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-cellranger-r34-1.1.0-1 (Translate Spreadsheet Cell Ranges)
Helper functions to work with spreadsheets and
the A1:D10 style of cell range specification.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-formatr-r32-1.5-1 (GNU R Tools for formatting R source code)
This package provides a function tidy.source() and optionally a GUI
(by gWidgets and preferably gWidgetsRGtk2) to format R source code.
Spaces and indent will be added to the code automatically, and comments
will be preserved under certain conditions, so that R code will be more
human-readable and tidy.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ca-r33-0.71-1 (Correspondence Analysis)
A package for computation and visualization of simple, multiple
and joint correspondence analysis.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-adimpro-r32-0.8.2-1 (Adaptive Smoothing of Digital Images)
s package implements tools for manipulation of digital images and the
Propagation Separation approach by Polzehl and Spokoiny (2006) for
smoothing digital images.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-brglm-r31-0.6.2-1 (Bias reduction in binomial-response)
Fit generalized linear models with binomial responses using either
an adjusted-score approach to bias reduction or maximum penalized
likelihood where penalization is by Jeffreys invariant prior.
These procedures return estimates with improved frequentist properties
(bias, mean squared error) that are always finite even in cases where
the maximum likelihood estimates are infinite (data separation).
Fitting takes place by fitting generalized linear models on iteratively
updated pseudo-data. The interface is essentially the same as 'glm'.
More flexibility is provided by the fact that custom pseudo-data
representations can be specified and used for model fitting. Functions
are provided for the construction of confidence intervals for the
reduced-bias estimates.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-chemometricswithrdata-r34-0.1.3-1 (Data for package ChemometricsWithR)
The package provides data sets used in the book "Chemometrics with R
- Multivariate Data Analysis in the Natural Sciences and Life Sciences"
by Ron Wehrens, Springer (2011).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-car-r35-3.0-2-1 (Companion to Applied Regression)
This package accompanies J. Fox and S. Weisberg, An R Companion to
Applied Regression, Second Edition, Sage, 2011.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-histdata-r32-0.8-4-1 (History of statistics data sets)
The HistData package provides a collection of small data sets that
are interesting and important in the history of statistics and data
visualization. The goal of the package is to make these available,
both for instructional use and for historical research. Some of
these present interesting challenges for graphics or analysis in R.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-chemospecutils-r33-0.2.211-1 (Functions Supporting ChemoSpec / ChemoSpec2D)
Functions supporting the common needs of packages 'ChemoSpec' and
'ChemoSpec2D'.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-aer-r35-1.2-6-1 (Applied Econometrics with R)
Functions, data sets, examples, demos, and vignettes for the book
Christian Kleiber and Achim Zeileis (2008), Applied Econometrics
with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-abind-r33-1.4-5-1 (Combine multi-dimensional arrays)
Combine multi-dimensional arrays into a single array. This is a
generalization of cbind and rbind. Works with vectors, matrices,
and higher-dimensional arrays. Also provides functions adrop,
asub, and afill for manipulating, extracting and replacing data
in arrays.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-numderiv-r34-2016.8-1-1 (Accurate Numerical Derivatives)
This package provide methods for calculating (usually) accurate numerical
first and second order derivatives. Accurate calculations are done using
Richardson's extrapolation or, when applicable, a complex step derivative
is available. A simple difference method is also provided. Simple difference
is (usually) less accurate but is much quicker than Richardson's extrapolation
and provides a useful cross-check. Methods are provided for real scalar and
vector valued functions.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-data.table-r31-1.12.0-1 (Extension of data.frame)
Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins,
fast add/modify/delete of columns by group using no copies at all, list
columns and a fast file reader (fread). Offers a natural and flexible
syntax, for faster development.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-xlconnectjars-r33-0.2-15-1 (JAR dependencies for the XLConnect)
Provides external JAR dependencies for the XLConnect package.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-codetools-r35-0.2-16-1 (Code Analysis Tools for R)
Code analysis tools for R
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rcppeigen-r34-0.3.3.5.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-latticeextra-r31-0.6-28-1 (Extra Graphical Utilities)
Extra graphical utilities based on lattice
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-biglm-r33-0.9-1-3 (Bounded memory linear/generalized models)
Regression for data too large to fit in memory
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-plogr-r35-0.2.0-1 (Parametrized Active Bindings)
Provides a simple interface for creating active bindings where
the bound function accepts additional arguments.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-visnetwork-r34-2.0.6-1 (Network Visualization)
Provides an R interface to the 'vis.js' JavaScript charting library. It
allows an interactive visualization of networks.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-clv-r32-0.3-2.1-1 (Cluster Validation Techniques)
Package contains most of the popular internal and external cluster validation
methods ready to use for the most of the outputs produced by functions coming
from package "cluster". Package contains also functions and examples of usage
for cluster stability approach that might be applied to algorithms implemented
in "cluster" package as well as user defined clustering algorithms.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: bioconductor-globaltest-r31-5.28.0-1 (Testing Association of Groups of Genes)
Testing whether sets of genes (e.g. KEGG pathways of GO terms) are
significantly associated with a clinical variable of interest.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-cairo-r34-1.5-9-2 (Graphics device using cairo graphics library)
This package provides a Cairo graphics device that can be use to
create high-quality vector (PDF, PostScript and SVG) and bitmap output
(PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32).
Since it uses the same back-end for all output, copying across formats
is WYSIWYG. Files are created without the dependence on X11 or other
external programs. This device supports alpha channel (semi-transparent
drawing) and resulting images can contain transparent and semi-transparent
regions. It is ideal for use in server environments (file output) and as
a replacement for other devices that don't have Cairo's capabilities
such as alpha support or anti-aliasing. Backends are modular such that
any subset of backends is supported.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-chemometricswithr-r31-0.1.13-1 (Chemometrics with R)
The package provides functions and scripts used in the book
"Chemometrics with R - Multivariate Data Analysis in the
Natural Sciences and Life Sciences" by Ron Wehrens, Springer (2011).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-atelier-r32-0.24-1 (GTK GUI for statistical tools)
A collection of statistical simulation and computation tools with a
GTK GUI, to help teach statistical concepts and compute probabilities.
Two domains are covered: I. Understanding (Central-Limit Theorem and
the Normal Distribution, Distribution of a sample mean, Distribution
of a sample variance, Probability calculator for common distributions),
and II. Elementary Bayesian Statistics (bayesian inference on proportions,
contingency tables, means and variances, with informative and
oninformative priors).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-markdown-r32-0.9-1 (GNU R Tools for making web reports from text)
R Markdown is a format that enables easy authoring of reproducible
web reports from R. It combines the core syntax of Markdown
(an easy-to-write plain text format for web content) with embedded
R code chunks that are run so their output can be included in
the final document.
The concept of R Markdown is similar to Sweave (a system built-in
to R for combining R with LaTeX). In Sweave, Rnw files are "weaved"
into TeX files that are then compiled into PDFs. In R Markdown,
Rmd files are similarly "weaved" into plain markdown (.md) files
that are then compiled into HTML documents.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-preprocesscore-r34-1.36.0-1 (Collection of pre-processing functions)
A library of core preprocessing routines
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-lubridate-r33-1.7.4-1 (Make Dealing with Dates a Little Easier)
Functions to work with date-times and time-spans: fast and user friendly
parsing of date-time data, extraction and updating of components of a
date-time (years, months, days, hours, minutes, and seconds), algebraic
manipulation on date-time and time-span objects. The 'lubridate' package
has a consistent and memorable syntax that makes working with dates easy
and fun. Parts of the 'CCTZ' source code, released under the Apache 2.0
License, are included in this package. See
<https://github.com/google/cctz> for more details.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-jsonlite-r34-1.6-1 (JSON Parser and Generator for R)
A fast JSON parser and generator optimized for statistical data and the web.
Started out as a fork of RJSONIO, but has been completely rewritten in
recent versions. The package offers flexible, robust, high performance
tools for working with JSON in R and is particularly powerful for building
pipelines and interacting with web APIs. The implementation is based on the
mapping described in the vignette of the package (Ooms, 2014). In addition
to drop-in replacements for toJSON and fromJSON, jsonlite contains functions
to stream, validate, and prettify JSON data. The unit tests included with
the package verify that all edge cases are encoded and decoded consistently
for use with dynamic data in systems and applications.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-acepack-r35-1.4.1-1 (ACE and AVAS methods)
ACE and AVAS methods for choosing regression transformations.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-deoptimr-r35-1.0-8-1 (Differential Evolution Optimization)
An implementation of the jDE variant of the Differential Evolution stochastic
algorithm for global optimization of nonlinear programming problems.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-digest-r32-0.6.18-1 (GNU R Tools for string function wrappers)
The digest package provides a function 'digest()' for the creation of
hash digests of arbitrary R objects (using the md5, sha-1, sha-256 and
crc32 algorithms) permitting easy comparison of R language objects,
as well as a function 'hmac()' to create hash-based message
authentication code. The md5 algorithm by Ron Rivest is specified in
RFC 1321, the sha-1 and sha-256 algorithms are specified in FIPS-180-1
and FIPS-180-2, and the crc32 algorithm is described in
ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt.
For md5, sha-1, sha-256 and aes, this package uses a small standalone
implementations that were provided by Christophe Devine.
For crc32, code from the zlib library is used.
For sha-512, an implementation by Aaron D. Gifford is used.
Please note that this package is not meant to be deployed for
cryptographic purposes for which more comprehensive (and widely tested)
libraries such as OpenSSL should be used.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-matrix-r34-1.2-6-1 (Sparse and Dense Matrix Classes and Methods)
Classes and methods for dense and sparse matrices and operations
on them using LAPACK and SuiteSparse.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-animation-r35-2.6-1 (Utilities to create animations in statistics)
This package contains a variety of functions for animations in
statistics, covering areas such as probability theory,
mathematical statistics, multivariate statistics, nonparametric
statistics, sampling survey, linear models, time series,
computational statistics, data mining and machine learning.
These functions might be helpful in teaching statistics and
data analysis. Also provided in this package are several
approaches to save animations to various formats, e.g. Flash,
GIF, HTML pages, PDF and videos (saveSWF(), saveGIF(), saveHTML(),
saveLatex(), and saveVideo() respectively). PDF animations
can be inserted into Sweave/knitr easily.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-permute-r33-0.9-4-1 (Generating restricted permutations of data)
The 'permute' package implements a set of restricted permutation designs
for freely exchangeable, line transects (time series), and spatial grid
designs plus permutation of blocks (groups of samples). 'permute' also
allows split-plot designs, in which the whole-plots or split-plots or
both can be freely-exchangeable or one of the restricted designs. The
'permute' package is modelled after the permutation schemes of Canoco
3.1 (and later) by Cajo ter Braak.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ash-r35-1.0-15-1 (David Scott's ASH routines)
David Scott's ASH routines
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-inline-r32-0.3.15-1 (Inline C, C++, Fortran function calls)
Functionality to dynamically define R functions and S4 methods
with in-lined C, C++ or Fortran code supporting .C and .Call
calling conventions.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-barcode-r34-1.1-1 (Barcode distribution plots)
This package includes the function \code{barcode()}, which produces a
histogram-like plot of a distribution that shows granularity in the data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clv-r31-0.3-2.1-1 (Cluster Validation Techniques)
Package contains most of the popular internal and external cluster validation
methods ready to use for the most of the outputs produced by functions coming
from package "cluster". Package contains also functions and examples of usage
for cluster stability approach that might be applied to algorithms implemented
in "cluster" package as well as user defined clustering algorithms.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-class-r34-7.3-15-1 (GNU R Tools for classification)
Various functions for classification.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-inline-r33-0.3.15-1 (Inline C, C++, Fortran function calls)
Functionality to dynamically define R functions and S4 methods
with in-lined C, C++ or Fortran code supporting .C and .Call
calling conventions.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-cairo-r33-1.5-9-2 (Graphics device using cairo graphics library)
This package provides a Cairo graphics device that can be use to
create high-quality vector (PDF, PostScript and SVG) and bitmap output
(PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32).
Since it uses the same back-end for all output, copying across formats
is WYSIWYG. Files are created without the dependence on X11 or other
external programs. This device supports alpha channel (semi-transparent
drawing) and resulting images can contain transparent and semi-transparent
regions. It is ideal for use in server environments (file output) and as
a replacement for other devices that don't have Cairo's capabilities
such as alpha support or anti-aliasing. Backends are modular such that
any subset of backends is supported.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-inline-r35-0.3.15-1 (Inline C, C++, Fortran function calls)
Functionality to dynamically define R functions and S4 methods
with in-lined C, C++ or Fortran code supporting .C and .Call
calling conventions.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-biglm-r34-0.9-1-3 (Bounded memory linear/generalized models)
Regression for data too large to fit in memory
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-foreach-r31-1.4.4-1 (Foreach looping construct for R)
Support for the foreach looping construct. Foreach is an idiom that
allows for iterating over elements in a collection, without the use
of an explicit loop counter. This package in particular is intended
to be used for its return value, rather than for its side effects.
In that sense, it is similar to the standard lapply function, but
doesn't require the evaluation of a function. Using foreach without
side effects also facilitates executing the loop in parallel.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-withr-r32-2.1.2-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-caret-r31-6.0-68-1 (Classification and Regression Training)
Misc functions for training and plotting classification and regression models
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-nlme-r32-3.1-128-1 (Linear and Nonlinear Mixed Effects Models)
Fit and compare Gaussian linear and nonlinear mixed-effects models.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-htmlwidgets-r31-1.3-1 (HTML Widgets for R)
A framework for creating HTML widgets that render in various
contexts including the R console, 'R Markdown' documents,
and 'Shiny' web applications.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-tkrplot-r35-0.0-24-1 (TK Rplot)
simple mechanism for placing R graphics in a Tk widget
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-vgamdata-r35-1.0-3-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rcppeigen-r32-0.3.3.5.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-class-r33-7.3-15-1 (GNU R Tools for classification)
Various functions for classification.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-foreign-r33-0.8-71-1 (Read Data Stored by Minitab, S, etc)
Functions for reading and writing data stored by some versions of Epi Info,
Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and writing
some dBase files.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gridextra-r35-2.3-2 (Grid graphics functions)
misc. high-level Grid functions
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-labeling-r32-0.3-1 (Axis Labeling)
Provides a range of axis labeling algorithms
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-digest-r33-0.6.18-1 (GNU R Tools for string function wrappers)
The digest package provides a function 'digest()' for the creation of
hash digests of arbitrary R objects (using the md5, sha-1, sha-256 and
crc32 algorithms) permitting easy comparison of R language objects,
as well as a function 'hmac()' to create hash-based message
authentication code. The md5 algorithm by Ron Rivest is specified in
RFC 1321, the sha-1 and sha-256 algorithms are specified in FIPS-180-1
and FIPS-180-2, and the crc32 algorithm is described in
ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt.
For md5, sha-1, sha-256 and aes, this package uses a small standalone
implementations that were provided by Christophe Devine.
For crc32, code from the zlib library is used.
For sha-512, an implementation by Aaron D. Gifford is used.
Please note that this package is not meant to be deployed for
cryptographic purposes for which more comprehensive (and widely tested)
libraries such as OpenSSL should be used.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bca-r34-0.9-3-1 (Business and Customer Analytics)
Underlying support functions for RcmdrPlugin.BCA and a companion to 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-rlang-r31-0.3.2-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-digest-r35-0.6.18-1 (GNU R Tools for string function wrappers)
The digest package provides a function 'digest()' for the creation of
hash digests of arbitrary R objects (using the md5, sha-1, sha-256 and
crc32 algorithms) permitting easy comparison of R language objects,
as well as a function 'hmac()' to create hash-based message
authentication code. The md5 algorithm by Ron Rivest is specified in
RFC 1321, the sha-1 and sha-256 algorithms are specified in FIPS-180-1
and FIPS-180-2, and the crc32 algorithm is described in
ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt.
For md5, sha-1, sha-256 and aes, this package uses a small standalone
implementations that were provided by Christophe Devine.
For crc32, code from the zlib library is used.
For sha-512, an implementation by Aaron D. Gifford is used.
Please note that this package is not meant to be deployed for
cryptographic purposes for which more comprehensive (and widely tested)
libraries such as OpenSSL should be used.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-munsell-r32-0.5.0-1 (Munsell colour system)
Functions for exploring and using the Munsell colour system
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-latticeextra-r32-0.6-28-1 (Extra Graphical Utilities)
Extra graphical utilities based on lattice
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bradleyterry2-r35-1.0-9-1 (Bradley-Terry Models)
Specify and fit the Bradley-Terry model, including structured versions
in which the parameters are related to explanatory variables through a
linear predictor and versions with contest-specific effects, such as a
home advantage.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-gwidgets-r32-0.0-54-1 (R interfaces to gWidgets API)
gWidgets provides a toolkit-independent API for building interactive
GUIs. At least one of the 'gWidgetsXXX packages', such as gWidgetstcltk,
needs to be installed. Some icons are on loan from the scigraphica
project http://scigraphica.sourceforge.net.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-formula-r33-1.2-3-1 (Extended Model Formulas)
Infrastructure for extended formulas with multiple parts on the
right-hand side and/or multiple responses on the left-hand side.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-askpass-r35-1.1-1 (Safe Password Entry for R, Git, and SSH)
Cross-platform utilities for prompting the user for credentials or a
passphrase, for example to authenticate with a server or read a
protected key. Includes native programs for MacOS and Windows, hence no
'tcltk' is required. Password entry can be invoked in two different
ways: directly from R via the askpass() function, or indirectly as
password-entry back-end for 'ssh-agent' or 'git-credential' via the
SSH_ASKPASS and GIT_ASKPASS environment variables. Thereby the user can
be prompted for credentials or a passphrase if needed when R calls out
to git or ssh.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-randomforest-r35-4.6-12-2 (GNU R Tools for random forest class/regress)
Classification and regression based on a forest of trees using random inputs.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-crayon-r34-1.3.4-1 (Colored Terminal Output)
Colored terminal output on terminals that support 'ANSI'
color and highlight codes. It also works in 'Emacs' 'ESS'.
'ANSI' color support is automatically detected. Colors
and highlighting can be combined and nested. New styles
can also be created easily. This package was inspired by
the 'chalk' 'JavaScript' project.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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>.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-chron-r34-2.3-53-1 (Chronological objects)
Chronological objects which can handle dates and times
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-sspa-r35-2.14.0-1 (General Sample Size and Power Analysis)
General Sample size and power analysis for microarray and
next-generation sequencing data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-biomark-r35-0.4.5-1 (Find biomarkers in two-class discrimination)
The package provides biomarker selection for several classification
methods: the lasso/elastic net, PCLDA, PLSDA, and several t-tests.
Two approaches are provided, one based on the stability of model
coefficients under perturbation, and the other on higher criticism.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-akima-r32-0.6-2-1 (Interpolation of irregularly spaced data)
Linear or cubic spline interpolation for irregular gridded data
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-cardata-r34-3.0-2-1 (Companion to Applied Regression Data Sets)
Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied
Regression, Third Edition, Sage (forthcoming).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-nloptr-r31-1.2.1-1 (R interface to NLopt)
nloptr is an R interface to NLopt. NLopt is a free/open-source library
for nonlinear optimization, providing a common interface for a number
of different free optimization routines available online as well as
original implementations of various other algorithms. See
http://ab-initio.mit.edu/wiki/index.php/NLopt_Introduction for more
information on the available algorithms. During installation on Unix
the NLopt code is downloaded and compiled from the NLopt website.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-abind-r34-1.4-5-1 (Combine multi-dimensional arrays)
Combine multi-dimensional arrays into a single array. This is a
generalization of cbind and rbind. Works with vectors, matrices,
and higher-dimensional arrays. Also provides functions adrop,
asub, and afill for manipulating, extracting and replacing data
in arrays.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-cluster-r31-2.0.6-1 (Cluster Analysis Extended Rousseeuw et al)
Cluster Analysis Extended Rousseeuw et al
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-htmltools-r33-0.3.6-1 (Tools for HTML)
Tools for HTML generation and output.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-cardata-r32-3.0-2-1 (Companion to Applied Regression Data Sets)
Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied
Regression, Third Edition, Sage (forthcoming).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-analyzefmri-r31-1.1-17-1 (Functions for analysis of fMRI datasets)
Functions for I/O, visualisation and analysis of functional Magnetic
Resonance Imaging (fMRI) datasets stored in the ANALYZE or NIFTI format.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-boot-r35-1.3-20-1 (GNU R Tools for bootstrap methods)
functions and datasets for bootstrapping from the book
"Bootstrap Methods and Their Applications"
by A. C. Davison and D. V. Hinkley (1997, CUP).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-baseline-r33-1.2-1-1 (Baseline Correction of Spectra)
Collection of baseline correction algorithms, along with a
framework and a GUI for optimising baseline algorithm parameters.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-quantreg-r33-5.38-1 (Quantile Regression)
Quantile regression and related methods.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-pmml-r31-1.5.7-1 (Generate PMML for various models)
The Predictive Model Markup Language (PMML) is an XML-based language
which provides a way for applications to define statistical and data
mining models and to share models between PMML compliant applications.
More information about PMML and the Data Mining Group can be found at
http://www.dmg.org. The generated PMML can be imported into any PMML
consuming application, such as the Zementis ADAPA and UPPI scoring engines
which allow for predictive models built in R to be deployed and executed
on site, in the cloud (Amazon, IBM, and FICO), in-database (IBM Netezza,
Pivotal, Sybase IQ, Teradata and Teradata Aster) or Hadoop (Datameer and Hive).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-classint-r32-0.3-1-1 (Choose Univariate Class Intervals)
Selected commonly used methods for choosing univariate class intervals
for mapping or other graphics purposes.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clv-r34-0.3-2.1-1 (Cluster Validation Techniques)
Package contains most of the popular internal and external cluster validation
methods ready to use for the most of the outputs produced by functions coming
from package "cluster". Package contains also functions and examples of usage
for cluster stability approach that might be applied to algorithms implemented
in "cluster" package as well as user defined clustering algorithms.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-chron-r35-2.3-53-1 (Chronological objects)
Chronological objects which can handle dates and times
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-baseline-r31-1.2-1-1 (Baseline Correction of Spectra)
Collection of baseline correction algorithms, along with a
framework and a GUI for optimising baseline algorithm parameters.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-quantreg-r31-5.38-1 (Quantile Regression)
Quantile regression and related methods.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-pmml-r35-1.5.7-1 (Generate PMML for various models)
The Predictive Model Markup Language (PMML) is an XML-based language
which provides a way for applications to define statistical and data
mining models and to share models between PMML compliant applications.
More information about PMML and the Data Mining Group can be found at
http://www.dmg.org. The generated PMML can be imported into any PMML
consuming application, such as the Zementis ADAPA and UPPI scoring engines
which allow for predictive models built in R to be deployed and executed
on site, in the cloud (Amazon, IBM, and FICO), in-database (IBM Netezza,
Pivotal, Sybase IQ, Teradata and Teradata Aster) or Hadoop (Datameer and Hive).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-magrittr-r32-1.5-2 (Forward-pipe operator for R)
Provides a mechanism for chaining commands with a new
forward-pipe operator, %>%. This operator will forward
a value, or the result of an expression, into the next
function call/expression. There is flexible support
for the type of right-hand side expressions. For more
information, see package vignette. To quote Rene Magritte,
"Ceci n'est pas un pipe."
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-boot-r31-1.3-20-1 (GNU R Tools for bootstrap methods)
functions and datasets for bootstrapping from the book
"Bootstrap Methods and Their Applications"
by A. C. Davison and D. V. Hinkley (1997, CUP).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-hms-r35-0.4.2-1 (Pretty Time of Day)
Implements an S3 class for storing and formatting time-of-day values,
based on the 'difftime' class.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-speaq-r33-2.0.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-munsell-r34-0.5.0-1 (Munsell colour system)
Functions for exploring and using the Munsell colour system
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clustercrit-r34-1.2.8-1 (Clustering Indices)
compute clustering validation indices
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-pmml-r33-1.5.7-1 (Generate PMML for various models)
The Predictive Model Markup Language (PMML) is an XML-based language
which provides a way for applications to define statistical and data
mining models and to share models between PMML compliant applications.
More information about PMML and the Data Mining Group can be found at
http://www.dmg.org. The generated PMML can be imported into any PMML
consuming application, such as the Zementis ADAPA and UPPI scoring engines
which allow for predictive models built in R to be deployed and executed
on site, in the cloud (Amazon, IBM, and FICO), in-database (IBM Netezza,
Pivotal, Sybase IQ, Teradata and Teradata Aster) or Hadoop (Datameer and Hive).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clustvarsel-r32-2.3.1-1 (Variable Selection for Model-Based Clustering)
A function which implements variable selection methodology for
model-based clustering which allows to find the (locally) optimal
subset of variables in a dataset that have group/cluster information.
A greedy or headlong search can be used, either in a forward-backward
or backward-forward direction, with or without sub-sampling at the
hierarchical clustering stage for starting Mclust models. By default
the algorithm uses a sequential search, but parallelization is also
available.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-dichromat-r35-2.0-0-1 (Color Schemes for Dichromats)
Collapse red-green or green-blue distinctions to simulate the
effects of different types of color-blindness.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-limma-r34-3.30.13-1 (Linear Models for Microarray Data)
Data analysis, linear models and differential expression for microarray data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-mime-r34-0.6-1 (Map Filenames to MIME Types)
Guesses the MIME type from a filename extension using the data
derived from /etc/mime.types in UNIX-type systems.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-protgenerics-r34-1.6.0-1 (S4 generic functions for proteomics)
S4 generic functions for Bioconductor proteomics infrastructure.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-abind-r35-1.4-5-1 (Combine multi-dimensional arrays)
Combine multi-dimensional arrays into a single array. This is a
generalization of cbind and rbind. Works with vectors, matrices,
and higher-dimensional arrays. Also provides functions adrop,
asub, and afill for manipulating, extracting and replacing data
in arrays.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-boot-r33-1.3-20-1 (GNU R Tools for bootstrap methods)
functions and datasets for bootstrapping from the book
"Bootstrap Methods and Their Applications"
by A. C. Davison and D. V. Hinkley (1997, CUP).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-prettyunits-r32-1.0.2-3 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-adaptivetau-r34-2.2-3-1 (Tau-leaping stochastic simulation)
Implements adaptive tau leaping to approximate the trajectory of a
continuous-time stochastic process as described by Cao et al. (2007)
The Journal of Chemical Physics. This package is based upon work
supported by NSF DBI-0906041 and NIH K99-GM104158 to Philip Johnson
and NIH R01-AI049334 to Rustom Antia.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-htmltools-r34-0.3.6-1 (Tools for HTML)
Tools for HTML generation and output.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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>.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-graph-r34-1.52.0-1 (Package to handle graph data structures)
A package that implements some simple graph handling capabilities.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-ade4-r32-1.7-13-1 (Analysis of Ecological Data)
Multivariate data analysis and graphical display.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-bayestree-r35-0.3-1.4-1 (Bayesian Methods for Tree Based Models)
Implementation of BART:Bayesian Additive Regression Trees,
Chipman, George, McCulloch (2009)
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: bioconductor-protgenerics-r35-1.6.0-1 (S4 generic functions for proteomics)
S4 generic functions for Bioconductor proteomics infrastructure.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-varselrf-r33-0.7-8-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-chemospecutils-r34-0.2.211-1 (Functions Supporting ChemoSpec / ChemoSpec2D)
Functions supporting the common needs of packages 'ChemoSpec' and
'ChemoSpec2D'.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-rio-r34-0.5.16-2 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-whisker-r35-0.3-2-1 ({{mustache}} for R, logicless templating)
logicless templating, reuse templates in many programming
languages including R
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bvpsolve-r34-1.3.3-1 (Solvers for boundary value problems)
Functions that solve boundary value problems (BVP) of systems
of ordinary differential equations (ODE). The functions provide
an interface to the FORTRAN functionS twpbvpC, colnew/colsys,
and an R-implementation of the shooting method.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-qvcalc-r31-0.9-1-1 (Quasi Variances for Effects in Stat Models)
Functions to compute quasi variances and associated measures of
approximation error.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-plogr-r33-0.2.0-1 (Parametrized Active Bindings)
Provides a simple interface for creating active bindings where
the bound function accepts additional arguments.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-sys-r33-3.1-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bma-r33-3.18.9-1 (Bayesian Model Averaging)
Package for Bayesian model averaging for linear models, generalizable
linear models and survival models (cox regression).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-biglm-r35-0.9-1-3 (Bounded memory linear/generalized models)
Regression for data too large to fit in memory
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-bradleyterry2-r31-1.0-9-1 (Bradley-Terry Models)
Specify and fit the Bradley-Terry model, including structured versions
in which the parameters are related to explanatory variables through a
linear predictor and versions with contest-specific effects, such as a
home advantage.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-mass-r32-7.3-51.1-1 (GNU R data sets for "Modern App. Stat", 4ed)
Functions and datasets to support Venables and Ripley,
'Modern Applied Statistics with S' (4th edition, 2002).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-cairodevice-r31-2.24-1 (Cairo-based antialiased graphics driver)
Cairo/GTK graphics device driver with output to screen, file
(png, svg, pdf, and ps) or memory (arbitrary GdkDrawable or
Cairo context). The screen device may be embedded into RGtk2
interfaces. Supports all interactive features of other graphics
devices, including getGraphicsEvent().
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-yaletoolkit-r34-4.2.2-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-candisc-r31-0.8-0-1 (Shrunken Centroids RDA)
This package includes functions for computing and visualizing
generalized canonical discriminant analyses and canonical
correlation analysis for a multivariate linear model.
Traditional canonical discriminant analysis is restricted
to a one-way MANOVA design and is equivalent to canonical
correlation analysis between a set of quantitative response
variables and a set of dummy variables coded from the factor
variable. The candisc package generalizes this to multi-way
MANOVA designs for all factors in a multivariate linear model,
computing canonical scores and vectors for each term. The
graphic functions provide low-rank (1D, 2D, 3D) visualizations
of terms in an mlm via the plot.candisc and heplot.candisc
methods. Related plots are now provided for canonical
correlation analysis when all predictors are quantitative.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-arules-r35-1.6-3-1 (Mining Association Rules)
Provides the infrastructure for representing, manipulating and analyzing
transaction data and patterns (frequent itemsets and association rules).
Also provides interfaces to C implementations of the association mining
algorithms Apriori and Eclat by C. Borgelt.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-openssl-r31-1.3-1 (Encryption, Signatures and Certificates)
Bindings to OpenSSL libssl and libcrypto, plus custom SSH
pubkey parsers. Supports RSA, DSA and EC curves P-256,
P-384 and P-521. Cryptographic signatures can either be
created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric
encryption; RSA for asymmetric (public key) encryption or
EC for Diffie Hellman. High-level envelope functions combine
RSA and AES for encrypting arbitrary sized data. Other
utilities include key generators, hash functions (md5,
sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually
performing crypto calculations on large multibyte integers.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-lubridate-r32-1.7.4-1 (Make Dealing with Dates a Little Easier)
Functions to work with date-times and time-spans: fast and user friendly
parsing of date-time data, extraction and updating of components of a
date-time (years, months, days, hours, minutes, and seconds), algebraic
manipulation on date-time and time-span objects. The 'lubridate' package
has a consistent and memorable syntax that makes working with dates easy
and fun. Parts of the 'CCTZ' source code, released under the Apache 2.0
License, are included in this package. See
<https://github.com/google/cctz> for more details.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-readjdx-r32-0.3.250-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-arules-r33-1.4-1-2 (Mining Association Rules)
Provides the infrastructure for representing, manipulating and analyzing
transaction data and patterns (frequent itemsets and association rules).
Also provides interfaces to C implementations of the association mining
algorithms Apriori and Eclat by C. Borgelt.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-htmltools-r31-0.3.6-1 (Tools for HTML)
Tools for HTML generation and output.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-lmtest-r34-0.9-36-1 (Testing Linear Regression Models)
A collection of tests, data sets, and examples for diagnostic checking
in linear regression models. Furthermore, some generic tools for
inference in parametric models are provided
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-xts-r33-0.11-2-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clipr-r31-0.5.0-1 (Read and Write from the System Clipboard)
Simple utility functions to read from and write to the Windows, OS X,
and X11 clipboards.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gridextra-r32-2.3-2 (Grid graphics functions)
misc. high-level Grid functions
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-wccsom-r34-1.2.11-1 (SOM networks for patterns with peak shifts)
SOM networks for comparing patterns with peak shifts.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-pbkrtest-r34-0.4-7-1 (Kenward-Roger-based methods)
Test in linear mixed effects models. Attention is on linear mixed
effects models as implemented in the lme4 package. The package
implements a parametric bootstrap test. The package implements a
Kenward-Roger modification of F-tests.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-chemometricswithr-r35-0.1.13-1 (Chemometrics with R)
The package provides functions and scripts used in the book
"Chemometrics with R - Multivariate Data Analysis in the
Natural Sciences and Life Sciences" by Ron Wehrens, Springer (2011).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-gower-r33-0.2.0-1 (Gower's Distance)
Compute Gower's distance (or similarity) coefficient between records.
Compute the top-n matches between records. Core algorithms are executed
in parallel on systems supporting OpenMP.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-cluster-r34-2.0.7-1-1 (Cluster Analysis Extended Rousseeuw et al)
Cluster Analysis Extended Rousseeuw et al
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-htmlwidgets-r33-1.3-1 (HTML Widgets for R)
A framework for creating HTML widgets that render in various
contexts including the R console, 'R Markdown' documents,
and 'Shiny' web applications.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-curl-r32-3.3-1 (Connection Interface to Libcurl)
The curl() function provides a drop-in replacement for base url() with better
performance and support for http 2.0, ssl (https://, ftps://), gzip, deflate
and other libcurl goodies. This interface is implemented using the RConnection
API in order to support incremental processing of both binary and text streams.
If you are looking for a more-user-friendly http client, try the RCurl or httr
packages instead.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gwidgets-r35-0.0-54-1 (R interfaces to gWidgets API)
gWidgets provides a toolkit-independent API for building interactive
GUIs. At least one of the 'gWidgetsXXX packages', such as gWidgetstcltk,
needs to be installed. Some icons are on loan from the scigraphica
project http://scigraphica.sourceforge.net.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-codetools-r34-0.2-16-1 (Code Analysis Tools for R)
Code analysis tools for R
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rcppeigen-r35-0.3.3.5.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-codetools-r31-0.2-16-1 (Code Analysis Tools for R)
Code analysis tools for R
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-chemospecutils-r35-0.2.211-1 (Functions Supporting ChemoSpec / ChemoSpec2D)
Functions supporting the common needs of packages 'ChemoSpec' and
'ChemoSpec2D'.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-fansi-r33-0.4.0-1 (ANSI Control Sequence Aware Functions)
Counterparts to R string manipulation functions that account for the
effects of ANSI text formatting control sequences.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-formula-r35-1.2-3-1 (Extended Model Formulas)
Infrastructure for extended formulas with multiple parts on the
right-hand side and/or multiple responses on the left-hand side.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gwidgetsrgtk2-r35-0.0-86-1 (Toolkit implementation of gWidgets for RGtk2)
Port of gWidgets API to RGtk2
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-askpass-r33-1.1-1 (Safe Password Entry for R, Git, and SSH)
Cross-platform utilities for prompting the user for credentials or a
passphrase, for example to authenticate with a server or read a
protected key. Includes native programs for MacOS and Windows, hence no
'tcltk' is required. Password entry can be invoked in two different
ways: directly from R via the askpass() function, or indirectly as
password-entry back-end for 'ssh-agent' or 'git-credential' via the
SSH_ASKPASS and GIT_ASKPASS environment variables. Thereby the user can
be prompted for credentials or a passphrase if needed when R calls out
to git or ssh.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-globaltest-r33-5.28.0-1 (Testing Association of Groups of Genes)
Testing whether sets of genes (e.g. KEGG pathways of GO terms) are
significantly associated with a clinical variable of interest.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-hyperspec-r32-0.98-20150304-2 (Interface for hyperspectral data)
This package is an interface to handle hyperspectral data sets in R.
I.e. spatially or time-resolved spectra, or spectra with any other
kind of information associated with each of the spectra. The spectra
can be data as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR,
Raman, NMR, MS, etc. More generally, any data that is recorded over
a discretized variable, e.g. absorbance = f (wavelength), stored as
a vector of absorbance values for discrete wavelengths is suitable.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-rgraphviz-r31-2.18.0-1 (Plotting capabilities for R graph objects)
nterfaces R with the AT and T graphviz library for plotting R graph
objects from the graph package. Users on all platforms must install
graphviz; see the README file, available in the source distribution
of this file, for details.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-aer-r33-1.2-6-1 (Applied Econometrics with R)
Functions, data sets, examples, demos, and vignettes for the book
Christian Kleiber and Achim Zeileis (2008), Applied Econometrics
with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-car-r33-3.0-2-1 (Companion to Applied Regression)
This package accompanies J. Fox and S. Weisberg, An R Companion to
Applied Regression, Second Edition, Sage, 2011.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-checkmate-r33-1.9.1-1 (Fast and Versatile Argument Checks)
Tests and assertions to perform frequent argument checks.
A substantial part of the package was written in C to minimize
any worries about execution time overhead.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-biomark-r33-0.4.5-1 (Find biomarkers in two-class discrimination)
The package provides biomarker selection for several classification
methods: the lasso/elastic net, PCLDA, PLSDA, and several t-tests.
Two approaches are provided, one based on the stability of model
coefficients under perturbation, and the other on higher criticism.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-candisc-r32-0.8-0-1 (Shrunken Centroids RDA)
This package includes functions for computing and visualizing
generalized canonical discriminant analyses and canonical
correlation analysis for a multivariate linear model.
Traditional canonical discriminant analysis is restricted
to a one-way MANOVA design and is equivalent to canonical
correlation analysis between a set of quantitative response
variables and a set of dummy variables coded from the factor
variable. The candisc package generalizes this to multi-way
MANOVA designs for all factors in a multivariate linear model,
computing canonical scores and vectors for each term. The
graphic functions provide low-rank (1D, 2D, 3D) visualizations
of terms in an mlm via the plot.candisc and heplot.candisc
methods. Related plots are now provided for canonical
correlation analysis when all predictors are quantitative.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-crayon-r31-1.3.4-1 (Colored Terminal Output)
Colored terminal output on terminals that support 'ANSI'
color and highlight codes. It also works in 'Emacs' 'ESS'.
'ANSI' color support is automatically detected. Colors
and highlighting can be combined and nested. New styles
can also be created easily. This package was inspired by
the 'chalk' 'JavaScript' project.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-mime-r33-0.6-1 (Map Filenames to MIME Types)
Guesses the MIME type from a filename extension using the data
derived from /etc/mime.types in UNIX-type systems.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-animation-r34-2.6-1 (Utilities to create animations in statistics)
This package contains a variety of functions for animations in
statistics, covering areas such as probability theory,
mathematical statistics, multivariate statistics, nonparametric
statistics, sampling survey, linear models, time series,
computational statistics, data mining and machine learning.
These functions might be helpful in teaching statistics and
data analysis. Also provided in this package are several
approaches to save animations to various formats, e.g. Flash,
GIF, HTML pages, PDF and videos (saveSWF(), saveGIF(), saveHTML(),
saveLatex(), and saveVideo() respectively). PDF animations
can be inserted into Sweave/knitr easily.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-openxlsx-r34-4.1.0-1 (Read, Write and Edit XLSX Files)
Simplifies the creation of Excel .xlsx files by providing a high level
interface to writing, styling and editing worksheets. Through the use
of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect'
packages with the added benefit of removing the dependency on Java.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-openssl-r32-1.3-1 (Encryption, Signatures and Certificates)
Bindings to OpenSSL libssl and libcrypto, plus custom SSH
pubkey parsers. Supports RSA, DSA and EC curves P-256,
P-384 and P-521. Cryptographic signatures can either be
created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric
encryption; RSA for asymmetric (public key) encryption or
EC for Diffie Hellman. High-level envelope functions combine
RSA and AES for encrypting arbitrary sized data. Other
utilities include key generators, hash functions (md5,
sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually
performing crypto calculations on large multibyte integers.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-tkrplot-r33-0.0-24-1 (TK Rplot)
simple mechanism for placing R graphics in a Tk widget
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bh-r35-1.69.0-1-1 (Boost C++ header files)
Boost provides free peer-reviewed portable C++ source libraries.
A large part of Boost is provided as C++ template code which is
resolved entirely at compile-time without linking. This package
aims to provide the most useful subset of Boost libraries for
template use among CRAN package. By placing these libraries in
this package, we offer a more efficient distribution system for
CRAN as replication of this code in the sources of other
packages is avoided.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-als-r31-0.0.6-1 (MCR-ALS)
Alternating least squares is often used to resolve components contributing
to data with a bilinear structure; the basic technique may be extended to
alternating constrained least squares. Commonly applied constraints include
unimodality, non-negativity, and normalization of components. Several data
matrices may be decomposed simultaneously by assuming that one of the two
matrices in the bilinear decomposition is shared between datasets.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-pmml-r34-1.5.7-1 (Generate PMML for various models)
The Predictive Model Markup Language (PMML) is an XML-based language
which provides a way for applications to define statistical and data
mining models and to share models between PMML compliant applications.
More information about PMML and the Data Mining Group can be found at
http://www.dmg.org. The generated PMML can be imported into any PMML
consuming application, such as the Zementis ADAPA and UPPI scoring engines
which allow for predictive models built in R to be deployed and executed
on site, in the cloud (Amazon, IBM, and FICO), in-database (IBM Netezza,
Pivotal, Sybase IQ, Teradata and Teradata Aster) or Hadoop (Datameer and Hive).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-foreign-r35-0.8-71-1 (Read Data Stored by Minitab, S, etc)
Functions for reading and writing data stored by some versions of Epi Info,
Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and writing
some dBase files.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-boot-r34-1.3-20-1 (GNU R Tools for bootstrap methods)
functions and datasets for bootstrapping from the book
"Bootstrap Methods and Their Applications"
by A. C. Davison and D. V. Hinkley (1997, CUP).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-survival-r31-2.43-3-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-progress-r33-1.2.0-1 (Statnet project common scripts and utilities)
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-labeling-r35-0.3-1 (Axis Labeling)
Provides a range of axis labeling algorithms
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-hmisc-r31-3.17-4-1 (Harrell Miscellaneous)
The Hmisc library contains many functions useful for data analysis,
high-level graphics, utility operations, functions for computing sample size
and power, importing datasets, imputing missing values, advanced table making,
variable clustering, character string manipulation, conversion of S objects
to LaTeX code, and recoding variables.
Please submit bug reports to 'http://biostat.mc.vanderbilt.edu/trac/Hmisc'.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-mime-r31-0.6-1 (Map Filenames to MIME Types)
Guesses the MIME type from a filename extension using the data
derived from /etc/mime.types in UNIX-type systems.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-minqa-r35-1.2.4-3 (Derivative-free optimization by quadratic)
Derivative-free optimization by quadratic approximation based
on an interface to Fortran implementations by M. J. D. Powell.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-waveslim-r34-1.7.5-3 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-nloptr-r34-1.2.1-1 (R interface to NLopt)
nloptr is an R interface to NLopt. NLopt is a free/open-source library
for nonlinear optimization, providing a common interface for a number
of different free optimization routines available online as well as
original implementations of various other algorithms. See
http://ab-initio.mit.edu/wiki/index.php/NLopt_Introduction for more
information on the available algorithms. During installation on Unix
the NLopt code is downloaded and compiled from the NLopt website.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-mime-r35-0.6-1 (Map Filenames to MIME Types)
Guesses the MIME type from a filename extension using the data
derived from /etc/mime.types in UNIX-type systems.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-als-r32-0.0.6-1 (MCR-ALS)
Alternating least squares is often used to resolve components contributing
to data with a bilinear structure; the basic technique may be extended to
alternating constrained least squares. Commonly applied constraints include
unimodality, non-negativity, and normalization of components. Several data
matrices may be decomposed simultaneously by assuming that one of the two
matrices in the bilinear decomposition is shared between datasets.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-survival-r33-2.43-3-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-progress-r31-1.2.0-1 (Statnet project common scripts and utilities)
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-animation-r31-2.6-1 (Utilities to create animations in statistics)
This package contains a variety of functions for animations in
statistics, covering areas such as probability theory,
mathematical statistics, multivariate statistics, nonparametric
statistics, sampling survey, linear models, time series,
computational statistics, data mining and machine learning.
These functions might be helpful in teaching statistics and
data analysis. Also provided in this package are several
approaches to save animations to various formats, e.g. Flash,
GIF, HTML pages, PDF and videos (saveSWF(), saveGIF(), saveHTML(),
saveLatex(), and saveVideo() respectively). PDF animations
can be inserted into Sweave/knitr easily.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-foreach-r34-1.4.4-1 (Foreach looping construct for R)
Support for the foreach looping construct. Foreach is an idiom that
allows for iterating over elements in a collection, without the use
of an explicit loop counter. This package in particular is intended
to be used for its return value, rather than for its side effects.
In that sense, it is similar to the standard lapply function, but
doesn't require the evaluation of a function. Using foreach without
side effects also facilitates executing the loop in parallel.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-binda-r31-1.0.3-2 (Multi-Class Discriminant Analysis)
The "binda" package implements functions for multi-class discriminant
analysis using binary predictors, for corresponding variable selection,
and for dichotomizing continuous data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ash-r33-1.0-15-1 (David Scott's ASH routines)
David Scott's ASH routines
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: bioconductor-biocparallel-r34-1.8.2-1 (Facilities for parallel evaluation)
This package provides modified versions and novel implementation of
functions for parallel evaluation, tailored to use with Bioconductor
objects.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-checkmate-r34-1.9.1-1 (Fast and Versatile Argument Checks)
Tests and assertions to perform frequent argument checks.
A substantial part of the package was written in C to minimize
any worries about execution time overhead.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ca-r34-0.71-1 (Correspondence Analysis)
A package for computation and visualization of simple, multiple
and joint correspondence analysis.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-matrixmodels-r32-0.4-1-1 (Modelling with Sparse And Dense Matrices)
Modelling with sparse and dense 'Matrix' matrices,
using modular prediction and response module classes.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rgtk2-r33-2.20.31-3 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-openssl-r34-1.3-1 (Encryption, Signatures and Certificates)
Bindings to OpenSSL libssl and libcrypto, plus custom SSH
pubkey parsers. Supports RSA, DSA and EC curves P-256,
P-384 and P-521. Cryptographic signatures can either be
created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric
encryption; RSA for asymmetric (public key) encryption or
EC for Diffie Hellman. High-level envelope functions combine
RSA and AES for encrypting arbitrary sized data. Other
utilities include key generators, hash functions (md5,
sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually
performing crypto calculations on large multibyte integers.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-cocorresp-r34-0.3-0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-dichromat-r32-2.0-0-1 (Color Schemes for Dichromats)
Collapse red-green or green-blue distinctions to simulate the
effects of different types of color-blindness.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-candisc-r34-0.8-0-1 (Shrunken Centroids RDA)
This package includes functions for computing and visualizing
generalized canonical discriminant analyses and canonical
correlation analysis for a multivariate linear model.
Traditional canonical discriminant analysis is restricted
to a one-way MANOVA design and is equivalent to canonical
correlation analysis between a set of quantitative response
variables and a set of dummy variables coded from the factor
variable. The candisc package generalizes this to multi-way
MANOVA designs for all factors in a multivariate linear model,
computing canonical scores and vectors for each term. The
graphic functions provide low-rank (1D, 2D, 3D) visualizations
of terms in an mlm via the plot.candisc and heplot.candisc
methods. Related plots are now provided for canonical
correlation analysis when all predictors are quantitative.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-vcd-r33-1.4-4-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-codetools-r33-0.2-16-1 (Code Analysis Tools for R)
Code analysis tools for R
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-foreach-r32-1.4.4-1 (Foreach looping construct for R)
Support for the foreach looping construct. Foreach is an idiom that
allows for iterating over elements in a collection, without the use
of an explicit loop counter. This package in particular is intended
to be used for its return value, rather than for its side effects.
In that sense, it is similar to the standard lapply function, but
doesn't require the evaluation of a function. Using foreach without
side effects also facilitates executing the loop in parallel.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-siggenes-r34-1.48.0-1 (Multiple testing using SAM and EBAM)
Identification of differentially expressed genes and estimation of the
False Discovery Rate (FDR) using both the Significance Analysis of
Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-jsonlite-r31-1.6-1 (JSON Parser and Generator for R)
A fast JSON parser and generator optimized for statistical data and the web.
Started out as a fork of RJSONIO, but has been completely rewritten in
recent versions. The package offers flexible, robust, high performance
tools for working with JSON in R and is particularly powerful for building
pipelines and interacting with web APIs. The implementation is based on the
mapping described in the vignette of the package (Ooms, 2014). In addition
to drop-in replacements for toJSON and fromJSON, jsonlite contains functions
to stream, validate, and prettify JSON data. The unit tests included with
the package verify that all edge cases are encoded and decoded consistently
for use with dynamic data in systems and applications.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-pillar-r32-1.3.1-1 (Coloured Formatting for Columns)
Provides a 'pillar' generic designed for formatting columns of data
using the full range of colours provided by modern terminals.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-whisker-r33-0.3-2-1 ({{mustache}} for R, logicless templating)
logicless templating, reuse templates in many programming
languages including R
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-analyzefmri-r33-1.1-17-1 (Functions for analysis of fMRI datasets)
Functions for I/O, visualisation and analysis of functional Magnetic
Resonance Imaging (fMRI) datasets stored in the ANALYZE or NIFTI format.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-gwidgetsrgtk2-r31-0.0-86-1 (Toolkit implementation of gWidgets for RGtk2)
Port of gWidgets API to RGtk2
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-jsonlite-r33-1.6-1 (JSON Parser and Generator for R)
A fast JSON parser and generator optimized for statistical data and the web.
Started out as a fork of RJSONIO, but has been completely rewritten in
recent versions. The package offers flexible, robust, high performance
tools for working with JSON in R and is particularly powerful for building
pipelines and interacting with web APIs. The implementation is based on the
mapping described in the vignette of the package (Ooms, 2014). In addition
to drop-in replacements for toJSON and fromJSON, jsonlite contains functions
to stream, validate, and prettify JSON data. The unit tests included with
the package verify that all edge cases are encoded and decoded consistently
for use with dynamic data in systems and applications.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-checkmate-r31-1.9.1-1 (Fast and Versatile Argument Checks)
Tests and assertions to perform frequent argument checks.
A substantial part of the package was written in C to minimize
any worries about execution time overhead.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-assertthat-r35-0.2.0-1 (Easy pre and post assertions)
assertthat is an extension to stopifnot() that makes it easy
to declare the pre and post conditions that you code should
satisfy, while also producing friendly error messages so that
your users know what they've done wrong.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-keggraph-r32-1.32.0-1 (Graph approach to KEGG PATHWAY in R)
KEGGGraph is an interface between KEGG pathway and graph object as well
as a collection of tools to analyze, dissect and visualize these graphs.
It parses the regularly updated KGML (KEGG XML) files into graph models
maintaining all essential pathway attributes. The package offers
functionalities including parsing, graph operation, visualization and etc.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-minqa-r34-1.2.4-3 (Derivative-free optimization by quadratic)
Derivative-free optimization by quadratic approximation based
on an interface to Fortran implementations by M. J. D. Powell.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-lubridate-r35-1.7.4-1 (Make Dealing with Dates a Little Easier)
Functions to work with date-times and time-spans: fast and user friendly
parsing of date-time data, extraction and updating of components of a
date-time (years, months, days, hours, minutes, and seconds), algebraic
manipulation on date-time and time-span objects. The 'lubridate' package
has a consistent and memorable syntax that makes working with dates easy
and fun. Parts of the 'CCTZ' source code, released under the Apache 2.0
License, are included in this package. See
<https://github.com/google/cctz> for more details.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-magrittr-r35-1.5-2 (Forward-pipe operator for R)
Provides a mechanism for chaining commands with a new
forward-pipe operator, %>%. This operator will forward
a value, or the result of an expression, into the next
function call/expression. There is flexible support
for the type of right-hand side expressions. For more
information, see package vignette. To quote Rene Magritte,
"Ceci n'est pas un pipe."
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-numderiv-r31-2016.8-1-1 (Accurate Numerical Derivatives)
This package provide methods for calculating (usually) accurate numerical
first and second order derivatives. Accurate calculations are done using
Richardson's extrapolation or, when applicable, a complex step derivative
is available. A simple difference method is also provided. Simple difference
is (usually) less accurate but is much quicker than Richardson's extrapolation
and provides a useful cross-check. Methods are provided for real scalar and
vector valued functions.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-magick-r35-2.0-1 (Advanced Graphics and Image-Processing in R)
Bindings to 'ImageMagick': the most comprehensive open-source image
processing library available. Supports many common formats (png, jpeg,
tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip,
blur, etc). All operations are vectorized via the Magick++ STL meaning
they operate either on a single frame or a series of frames for working
with layers, collages, or animation. In RStudio images are automatically
previewed when printed to the console, resulting in an interactive
editing environment. The latest version of the package includes a native
graphics device for creating in-memory graphics or drawing onto images
using pixel coordinates.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-cluster-r32-2.0.7-1-1 (Cluster Analysis Extended Rousseeuw et al)
Cluster Analysis Extended Rousseeuw et al
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-magick-r33-2.0-1 (Advanced Graphics and Image-Processing in R)
Bindings to 'ImageMagick': the most comprehensive open-source image
processing library available. Supports many common formats (png, jpeg,
tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip,
blur, etc). All operations are vectorized via the Magick++ STL meaning
they operate either on a single frame or a series of frames for working
with layers, collages, or animation. In RStudio images are automatically
previewed when printed to the console, resulting in an interactive
editing environment. The latest version of the package includes a native
graphics device for creating in-memory graphics or drawing onto images
using pixel coordinates.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-laeken-r32-0.5.0-1 (Indicators on social exclusion and poverty)
Estimation of indicators on social exclusion and poverty,
as well as Pareto tail modeling for empirical income distributions.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rpart-r33-4.1-13-1 (GNU R Tools for recursive partitioning)
Recursive partitioning and regression trees
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-classint-r35-0.3-1-1 (Choose Univariate Class Intervals)
Selected commonly used methods for choosing univariate class intervals
for mapping or other graphics purposes.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ada-r33-2.0-5-1 (R package for stochastic boosting)
Performs discrete, real, and gentle boost under both exponential
and logistic loss on a given data set. The package ada provides
a straightforward, well-documented, and broad boosting routine
for classification, ideally suited for small to moderate-sized
data sets.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-numderiv-r33-2016.8-1-1 (Accurate Numerical Derivatives)
This package provide methods for calculating (usually) accurate numerical
first and second order derivatives. Accurate calculations are done using
Richardson's extrapolation or, when applicable, a complex step derivative
is available. A simple difference method is also provided. Simple difference
is (usually) less accurate but is much quicker than Richardson's extrapolation
and provides a useful cross-check. Methods are provided for real scalar and
vector valued functions.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-qvcalc-r34-0.9-1-1 (Quasi Variances for Effects in Stat Models)
Functions to compute quasi variances and associated measures of
approximation error.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-cairodevice-r33-2.24-1 (Cairo-based antialiased graphics driver)
Cairo/GTK graphics device driver with output to screen, file
(png, svg, pdf, and ps) or memory (arbitrary GdkDrawable or
Cairo context). The screen device may be embedded into RGtk2
interfaces. Supports all interactive features of other graphics
devices, including getGraphicsEvent().
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-vim-r35-4.7.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-munsell-r31-0.5.0-1 (Munsell colour system)
Functions for exploring and using the Munsell colour system
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-brglm-r32-0.6.2-1 (Bias reduction in binomial-response)
Fit generalized linear models with binomial responses using either
an adjusted-score approach to bias reduction or maximum penalized
likelihood where penalization is by Jeffreys invariant prior.
These procedures return estimates with improved frequentist properties
(bias, mean squared error) that are always finite even in cases where
the maximum likelihood estimates are infinite (data separation).
Fitting takes place by fitting generalized linear models on iteratively
updated pseudo-data. The interface is essentially the same as 'glm'.
More flexibility is provided by the fact that custom pseudo-data
representations can be specified and used for model fitting. Functions
are provided for the construction of confidence intervals for the
reduced-bias estimates.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-lmtest-r31-0.9-36-1 (Testing Linear Regression Models)
A collection of tests, data sets, and examples for diagnostic checking
in linear regression models. Furthermore, some generic tools for
inference in parametric models are provided
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bayestree-r32-0.3-1.4-1 (Bayesian Methods for Tree Based Models)
Implementation of BART:Bayesian Additive Regression Trees,
Chipman, George, McCulloch (2009)
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-animation-r33-2.6-1 (Utilities to create animations in statistics)
This package contains a variety of functions for animations in
statistics, covering areas such as probability theory,
mathematical statistics, multivariate statistics, nonparametric
statistics, sampling survey, linear models, time series,
computational statistics, data mining and machine learning.
These functions might be helpful in teaching statistics and
data analysis. Also provided in this package are several
approaches to save animations to various formats, e.g. Flash,
GIF, HTML pages, PDF and videos (saveSWF(), saveGIF(), saveHTML(),
saveLatex(), and saveVideo() respectively). PDF animations
can be inserted into Sweave/knitr easily.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-chemometrics-r32-1.4.2-1 (Multivariate Statistical Analysis)
This package is the R companion to the book "Introduction to Multivariate
Statistical Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-gwidgets-r33-0.0-54-1 (R interfaces to gWidgets API)
gWidgets provides a toolkit-independent API for building interactive
GUIs. At least one of the 'gWidgetsXXX packages', such as gWidgetstcltk,
needs to be installed. Some icons are on loan from the scigraphica
project http://scigraphica.sourceforge.net.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-pkgconfig-r31-2.0.2-1 (Private Configuration for R Packages)
Set configuration options on a per-package basis. Options set by
a given package only apply to that package, other packages are unaffected.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-arulesviz-r31-1.0-0-1 (Visualizing Association Rules)
Various visualization techniques for association rules and itemsets.
The packages also includes several interactive visualizations for
rule exploration. This package extends package arules.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ca-r32-0.71-1 (Correspondence Analysis)
A package for computation and visualization of simple, multiple
and joint correspondence analysis.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-foreign-r31-0.8-71-1 (Read Data Stored by Minitab, S, etc)
Functions for reading and writing data stored by some versions of Epi Info,
Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and writing
some dBase files.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-calibrate-r32-1.7.2-1 (Calibration of Scatterplot and Biplot Axes)
Package for drawing calibrated scales with tick marks on
(non-orthogonal) variable vectors in scatterplots and biplots.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-ncal-r32-2015.3-3-2 (Nonlinear Calibration)
nCal is a package that performs nonlinear calibration and curve fitting for
data from Luminex, RT-PCR, ELISA, RPPA etc. Its precursor is Ruminex.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gwidgetsrgtk2-r33-0.0-86-1 (Toolkit implementation of gWidgets for RGtk2)
Port of gWidgets API to RGtk2
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-chemometricswithrdata-r32-0.1.3-1 (Data for package ChemometricsWithR)
The package provides data sets used in the book "Chemometrics with R
- Multivariate Data Analysis in the Natural Sciences and Life Sciences"
by Ron Wehrens, Springer (2011).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-chemometrics-r35-1.4.2-1 (Multivariate Statistical Analysis)
This package is the R companion to the book "Introduction to Multivariate
Statistical Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-tkrplot-r34-0.0-24-1 (TK Rplot)
simple mechanism for placing R graphics in a Tk widget
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gwidgets-r31-0.0-54-1 (R interfaces to gWidgets API)
gWidgets provides a toolkit-independent API for building interactive
GUIs. At least one of the 'gWidgetsXXX packages', such as gWidgetstcltk,
needs to be installed. Some icons are on loan from the scigraphica
project http://scigraphica.sourceforge.net.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-adaptivetau-r33-2.2-3-1 (Tau-leaping stochastic simulation)
Implements adaptive tau leaping to approximate the trajectory of a
continuous-time stochastic process as described by Cao et al. (2007)
The Journal of Chemical Physics. This package is based upon work
supported by NSF DBI-0906041 and NIH K99-GM104158 to Philip Johnson
and NIH R01-AI049334 to Rustom Antia.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-withr-r35-2.1.2-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-xlsx-r33-0.6.1-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-readjdx-r35-0.3.250-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-care-r34-1.1.10-1 (Regression and CAR Score Variable Selection)
The "care" package implements the regression approach of Zuber and
Strimmer (2011) "High-dimensional regression and variable selection
using CAR scores" SAGMB 10: 34. CAR scores measure the correlation
between the response and the Mahalanobis-decorrelated predictors.
The squared CAR score is a natural measure of variable importance
and provides a canonical ordering of variables. This package
provides functions for estimating CAR scores, for variable
selection using CAR scores, and for estimating corresponding
regression coefficients. Both shrinkage as well as empirical
estimators are available.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-hmisc-r33-3.17-4-1 (Harrell Miscellaneous)
The Hmisc library contains many functions useful for data analysis,
high-level graphics, utility operations, functions for computing sample size
and power, importing datasets, imputing missing values, advanced table making,
variable clustering, character string manipulation, conversion of S objects
to LaTeX code, and recoding variables.
Please submit bug reports to 'http://biostat.mc.vanderbilt.edu/trac/Hmisc'.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-foreach-r33-1.4.4-1 (Foreach looping construct for R)
Support for the foreach looping construct. Foreach is an idiom that
allows for iterating over elements in a collection, without the use
of an explicit loop counter. This package in particular is intended
to be used for its return value, rather than for its side effects.
In that sense, it is similar to the standard lapply function, but
doesn't require the evaluation of a function. Using foreach without
side effects also facilitates executing the loop in parallel.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bradleyterry2-r32-1.0-9-1 (Bradley-Terry Models)
Specify and fit the Bradley-Terry model, including structured versions
in which the parameters are related to explanatory variables through a
linear predictor and versions with contest-specific effects, such as a
home advantage.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-binda-r33-1.0.3-2 (Multi-Class Discriminant Analysis)
The "binda" package implements functions for multi-class discriminant
analysis using binary predictors, for corresponding variable selection,
and for dichotomizing continuous data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-crayon-r32-1.3.4-1 (Colored Terminal Output)
Colored terminal output on terminals that support 'ANSI'
color and highlight codes. It also works in 'Emacs' 'ESS'.
'ANSI' color support is automatically detected. Colors
and highlighting can be combined and nested. New styles
can also be created easily. This package was inspired by
the 'chalk' 'JavaScript' project.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-whisker-r32-0.3-2-1 ({{mustache}} for R, logicless templating)
logicless templating, reuse templates in many programming
languages including R
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-keggraph-r34-1.32.0-1 (Graph approach to KEGG PATHWAY in R)
KEGGGraph is an interface between KEGG pathway and graph object as well
as a collection of tools to analyze, dissect and visualize these graphs.
It parses the regularly updated KGML (KEGG XML) files into graph models
maintaining all essential pathway attributes. The package offers
functionalities including parsing, graph operation, visualization and etc.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-pkgconfig-r34-2.0.2-1 (Private Configuration for R Packages)
Set configuration options on a per-package basis. Options set by
a given package only apply to that package, other packages are unaffected.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-arulesviz-r34-1.3-2-1 (Visualizing Association Rules)
Various visualization techniques for association rules and itemsets.
The packages also includes several interactive visualizations for
rule exploration. This package extends package arules.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-cluster-r33-2.0.7-1-1 (Cluster Analysis Extended Rousseeuw et al)
Cluster Analysis Extended Rousseeuw et al
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-chemospecutils-r31-0.2.211-1 (Functions Supporting ChemoSpec / ChemoSpec2D)
Functions supporting the common needs of packages 'ChemoSpec' and
'ChemoSpec2D'.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-iterators-r35-1.0.8-1 (Iterator construct for R)
Support for iterators, which allow a programmer to traverse
through all the elements of a vector, list, or other collection of data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-chemometricswithr-r34-0.1.13-1 (Chemometrics with R)
The package provides functions and scripts used in the book
"Chemometrics with R - Multivariate Data Analysis in the
Natural Sciences and Life Sciences" by Ron Wehrens, Springer (2011).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-clipr-r33-0.5.0-1 (Read and Write from the System Clipboard)
Simple utility functions to read from and write to the Windows, OS X,
and X11 clipboards.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ada-r32-2.0-5-1 (R package for stochastic boosting)
Performs discrete, real, and gentle boost under both exponential
and logistic loss on a given data set. The package ada provides
a straightforward, well-documented, and broad boosting routine
for classification, ideally suited for small to moderate-sized
data sets.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-akima-r35-0.6-2-1 (Interpolation of irregularly spaced data)
Linear or cubic spline interpolation for irregular gridded data
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-gower-r31-0.2.0-1 (Gower's Distance)
Compute Gower's distance (or similarity) coefficient between records.
Compute the top-n matches between records. Core algorithms are executed
in parallel on systems supporting OpenMP.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-wilcoxcv-r35-1.0-2-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clusterfly-r34-0.4-3 (Visualise clustering algorithms with GGobi)
Visualise clustering algorithms with GGobi. Contains both general
code for visualising clustering results and specific visualisations
for model-based, hierarchical and SOM clustering.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-survival-r35-2.43-3-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-labeling-r31-0.3-1 (Axis Labeling)
Provides a range of axis labeling algorithms
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-fansi-r31-0.4.0-1 (ANSI Control Sequence Aware Functions)
Counterparts to R string manipulation functions that account for the
effects of ANSI text formatting control sequences.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bca-r35-0.9-3-1 (Business and Customer Analytics)
Underlying support functions for RcmdrPlugin.BCA and a companion to 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ada-r31-2.0-5-1 (R package for stochastic boosting)
Performs discrete, real, and gentle boost under both exponential
and logistic loss on a given data set. The package ada provides
a straightforward, well-documented, and broad boosting routine
for classification, ideally suited for small to moderate-sized
data sets.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-cardata-r35-3.0-2-1 (Companion to Applied Regression Data Sets)
Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied
Regression, Third Edition, Sage (forthcoming).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clustersim-r31-0.45-2-1 (Searching for optimal clustering procedure)
GDM Distance, Sokal-Michener Distance, Bray-Curtis Distance, Calinski-Harabasz
Index, G2 Index, G3 Index, Silhouette Index, Krzanowski-Lai Index, Hartigan
Index, Gap Index, DB Index, Data Normalization, HINoV method, Replication
analysis for cluster validation, Clustering with several algorithms, distances,
Symbolic interval distances, Plot functions, Random cluster generation, Linear
ordering methods, Comparing partitions, Spectral clustering, Ordinal to metric
scale transformation, Untypical data generation.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-biomark-r34-0.4.5-1 (Find biomarkers in two-class discrimination)
The package provides biomarker selection for several classification
methods: the lasso/elastic net, PCLDA, PLSDA, and several t-tests.
Two approaches are provided, one based on the stability of model
coefficients under perturbation, and the other on higher criticism.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-chemospec-r33-5.0.229-1 (Exploratory Chemometrics for Spectroscopy)
A collection of functions for plotting spectra (NMR, IR etc) and carrying
out various forms of top-down exploratory data analysis, such as HCA, PCA
and model-based clustering. The design allows comparison of data from
samples which fall into groups such as treatment vs. control. Robust
methods appropriate for this type of high-dimensional data are available.
ChemoSpec is designed to be very user friendly and suitable for people
with limited background in R.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-matrix-r33-1.2-6-1 (Sparse and Dense Matrix Classes and Methods)
Classes and methods for dense and sparse matrices and operations
on them using LAPACK and SuiteSparse.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bradleyterry2-r34-1.0-9-1 (Bradley-Terry Models)
Specify and fit the Bradley-Terry model, including structured versions
in which the parameters are related to explanatory variables through a
linear predictor and versions with contest-specific effects, such as a
home advantage.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-formula-r31-1.2-3-1 (Extended Model Formulas)
Infrastructure for extended formulas with multiple parts on the
right-hand side and/or multiple responses on the left-hand side.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-progress-r35-1.2.0-1 (Statnet project common scripts and utilities)
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-labeling-r33-0.3-1 (Axis Labeling)
Provides a range of axis labeling algorithms
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-matrix-r35-1.2-6-1 (Sparse and Dense Matrix Classes and Methods)
Classes and methods for dense and sparse matrices and operations
on them using LAPACK and SuiteSparse.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-htmltable-r33-1.13.1-1 (Advanced Tables for Markdown/HTML)
Tables with state-of-the-art layout elements such as row spanners,
column spanners, table spanners, zebra striping, and more. While
allowing advanced layout, the underlying css-structure is simple
in order to maximize compatibility with word processors such as
'MS Word' or 'LibreOffice'. The package also contains a few text
formatting functions that help outputting text compatible
with HTML/'LaTeX'.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clustercrit-r33-1.2.8-1 (Clustering Indices)
compute clustering validation indices
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-askpass-r34-1.1-1 (Safe Password Entry for R, Git, and SSH)
Cross-platform utilities for prompting the user for credentials or a
passphrase, for example to authenticate with a server or read a
protected key. Includes native programs for MacOS and Windows, hence no
'tcltk' is required. Password entry can be invoked in two different
ways: directly from R via the askpass() function, or indirectly as
password-entry back-end for 'ssh-agent' or 'git-credential' via the
SSH_ASKPASS and GIT_ASKPASS environment variables. Thereby the user can
be prompted for credentials or a passphrase if needed when R calls out
to git or ssh.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-matrixmodels-r35-0.4-1-1 (Modelling with Sparse And Dense Matrices)
Modelling with sparse and dense 'Matrix' matrices,
using modular prediction and response module classes.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-base64enc-r35-0.1-3-1 (Tools for base64 encoding)
This package provides tools for handling base64 encoding.
It is more flexible than the orphaned base64 package.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-keggraph-r31-1.32.0-1 (Graph approach to KEGG PATHWAY in R)
KEGGGraph is an interface between KEGG pathway and graph object as well
as a collection of tools to analyze, dissect and visualize these graphs.
It parses the regularly updated KGML (KEGG XML) files into graph models
maintaining all essential pathway attributes. The package offers
functionalities including parsing, graph operation, visualization and etc.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-lmtest-r32-0.9-36-1 (Testing Linear Regression Models)
A collection of tests, data sets, and examples for diagnostic checking
in linear regression models. Furthermore, some generic tools for
inference in parametric models are provided
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rpart-r31-4.1-13-1 (GNU R Tools for recursive partitioning)
Recursive partitioning and regression trees
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-pkgconfig-r33-2.0.2-1 (Private Configuration for R Packages)
Set configuration options on a per-package basis. Options set by
a given package only apply to that package, other packages are unaffected.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-car-r31-2.0-25-1 (Companion to Applied Regression)
This package accompanies J. Fox and S. Weisberg, An R Companion to
Applied Regression, Second Edition, Sage, 2011.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-arulesviz-r33-1.3-2-1 (Visualizing Association Rules)
Various visualization techniques for association rules and itemsets.
The packages also includes several interactive visualizations for
rule exploration. This package extends package arules.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-data.table-r35-1.12.0-1 (Extension of data.frame)
Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins,
fast add/modify/delete of columns by group using no copies at all, list
columns and a fast file reader (fread). Offers a natural and flexible
syntax, for faster development.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-chron-r32-2.3-53-1 (Chronological objects)
Chronological objects which can handle dates and times
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clusterfly-r32-0.4-3 (Visualise clustering algorithms with GGobi)
Visualise clustering algorithms with GGobi. Contains both general
code for visualising clustering results and specific visualisations
for model-based, hierarchical and SOM clustering.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rio-r35-0.5.16-2 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clustersim-r33-0.45-2-1 (Searching for optimal clustering procedure)
GDM Distance, Sokal-Michener Distance, Bray-Curtis Distance, Calinski-Harabasz
Index, G2 Index, G3 Index, Silhouette Index, Krzanowski-Lai Index, Hartigan
Index, Gap Index, DB Index, Data Normalization, HINoV method, Replication
analysis for cluster validation, Clustering with several algorithms, distances,
Symbolic interval distances, Plot functions, Random cluster generation, Linear
ordering methods, Comparing partitions, Spectral clustering, Ordinal to metric
scale transformation, Untypical data generation.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-varselrf-r32-0.7-8-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-aer-r31-1.2-6-1 (Applied Econometrics with R)
Functions, data sets, examples, demos, and vignettes for the book
Christian Kleiber and Achim Zeileis (2008), Applied Econometrics
with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-akima-r34-0.6-2-1 (Interpolation of irregularly spaced data)
Linear or cubic spline interpolation for irregular gridded data
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-bh-r31-1.69.0-1-1 (Boost C++ header files)
Boost provides free peer-reviewed portable C++ source libraries.
A large part of Boost is provided as C++ template code which is
resolved entirely at compile-time without linking. This package
aims to provide the most useful subset of Boost libraries for
template use among CRAN package. By placing these libraries in
this package, we offer a more efficient distribution system for
CRAN as replication of this code in the sources of other
packages is avoided.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-plyr-r34-1.8.4-1 (Splitting, applying and combining data)
plyr is a set of tools that solves a common set of problems: you need to
break a big problem down into manageable pieces, operate on each pieces
and then put all the pieces back together. For example, you might want
to fit a model to each spatial location or time point in your study,
summarise data by panels or collapse high-dimensional arrays to simpler
summary statistics. The development of plyr has been generously supported
by BD (Becton Dickinson).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-limma-r35-3.30.13-1 (Linear Models for Microarray Data)
Data analysis, linear models and differential expression for microarray data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-askpass-r32-1.1-1 (Safe Password Entry for R, Git, and SSH)
Cross-platform utilities for prompting the user for credentials or a
passphrase, for example to authenticate with a server or read a
protected key. Includes native programs for MacOS and Windows, hence no
'tcltk' is required. Password entry can be invoked in two different
ways: directly from R via the askpass() function, or indirectly as
password-entry back-end for 'ssh-agent' or 'git-credential' via the
SSH_ASKPASS and GIT_ASKPASS environment variables. Thereby the user can
be prompted for credentials or a passphrase if needed when R calls out
to git or ssh.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-partitions-r35-1.9-19-1 (Additive partitions of integers)
Additive partitions of integers. Enumerates the partitions, unequal partitions,
and restricted partitions of an integer; the three corresponding partition
functions are also given. Set partitions are now included.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-munsell-r35-0.5.0-1 (Munsell colour system)
Functions for exploring and using the Munsell colour system
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-deoptimr-r34-1.0-8-1 (Differential Evolution Optimization)
An implementation of the jDE variant of the Differential Evolution stochastic
algorithm for global optimization of nonlinear programming problems.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-jsonlite-r35-1.6-1 (JSON Parser and Generator for R)
A fast JSON parser and generator optimized for statistical data and the web.
Started out as a fork of RJSONIO, but has been completely rewritten in
recent versions. The package offers flexible, robust, high performance
tools for working with JSON in R and is particularly powerful for building
pipelines and interacting with web APIs. The implementation is based on the
mapping described in the vignette of the package (Ooms, 2014). In addition
to drop-in replacements for toJSON and fromJSON, jsonlite contains functions
to stream, validate, and prettify JSON data. The unit tests included with
the package verify that all edge cases are encoded and decoded consistently
for use with dynamic data in systems and applications.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-aer-r32-1.2-6-1 (Applied Econometrics with R)
Functions, data sets, examples, demos, and vignettes for the book
Christian Kleiber and Achim Zeileis (2008), Applied Econometrics
with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-biomark-r32-0.4.5-1 (Find biomarkers in two-class discrimination)
The package provides biomarker selection for several classification
methods: the lasso/elastic net, PCLDA, PLSDA, and several t-tests.
Two approaches are provided, one based on the stability of model
coefficients under perturbation, and the other on higher criticism.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-abind-r32-1.4-5-1 (Combine multi-dimensional arrays)
Combine multi-dimensional arrays into a single array. This is a
generalization of cbind and rbind. Works with vectors, matrices,
and higher-dimensional arrays. Also provides functions adrop,
asub, and afill for manipulating, extracting and replacing data
in arrays.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gtable-r33-0.2.0-1 (Arrange grobs in tables)
Tools to make it easier to work with "tables" of grobs.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-laeken-r31-0.4.6-1 (Indicators on social exclusion and poverty)
Estimation of indicators on social exclusion and poverty,
as well as Pareto tail modeling for empirical income distributions.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-car-r32-3.0-2-1 (Companion to Applied Regression)
This package accompanies J. Fox and S. Weisberg, An R Companion to
Applied Regression, Second Edition, Sage, 2011.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gtable-r35-0.2.0-1 (Arrange grobs in tables)
Tools to make it easier to work with "tables" of grobs.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-magrittr-r31-1.5-2 (Forward-pipe operator for R)
Provides a mechanism for chaining commands with a new
forward-pipe operator, %>%. This operator will forward
a value, or the result of an expression, into the next
function call/expression. There is flexible support
for the type of right-hand side expressions. For more
information, see package vignette. To quote Rene Magritte,
"Ceci n'est pas un pipe."
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-numderiv-r35-2016.8-1-1 (Accurate Numerical Derivatives)
This package provide methods for calculating (usually) accurate numerical
first and second order derivatives. Accurate calculations are done using
Richardson's extrapolation or, when applicable, a complex step derivative
is available. A simple difference method is also provided. Simple difference
is (usually) less accurate but is much quicker than Richardson's extrapolation
and provides a useful cross-check. Methods are provided for real scalar and
vector valued functions.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-quantreg-r32-5.38-1 (Quantile Regression)
Quantile regression and related methods.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-baseline-r32-1.2-1-1 (Baseline Correction of Spectra)
Collection of baseline correction algorithms, along with a
framework and a GUI for optimising baseline algorithm parameters.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-classint-r33-0.3-1-1 (Choose Univariate Class Intervals)
Selected commonly used methods for choosing univariate class intervals
for mapping or other graphics purposes.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-pillar-r31-1.3.1-1 (Coloured Formatting for Columns)
Provides a 'pillar' generic designed for formatting columns of data
using the full range of colours provided by modern terminals.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-htmltable-r34-1.13.1-1 (Advanced Tables for Markdown/HTML)
Tables with state-of-the-art layout elements such as row spanners,
column spanners, table spanners, zebra striping, and more. While
allowing advanced layout, the underlying css-structure is simple
in order to maximize compatibility with word processors such as
'MS Word' or 'LibreOffice'. The package also contains a few text
formatting functions that help outputting text compatible
with HTML/'LaTeX'.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-hms-r34-0.4.2-1 (Pretty Time of Day)
Implements an S3 class for storing and formatting time-of-day values,
based on the 'difftime' class.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ash-r31-1.0-15-1 (David Scott's ASH routines)
David Scott's ASH routines
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-openssl-r33-1.3-1 (Encryption, Signatures and Certificates)
Bindings to OpenSSL libssl and libcrypto, plus custom SSH
pubkey parsers. Supports RSA, DSA and EC curves P-256,
P-384 and P-521. Cryptographic signatures can either be
created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric
encryption; RSA for asymmetric (public key) encryption or
EC for Diffie Hellman. High-level envelope functions combine
RSA and AES for encrypting arbitrary sized data. Other
utilities include key generators, hash functions (md5,
sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually
performing crypto calculations on large multibyte integers.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-tkrplot-r32-0.0-24-1 (TK Rplot)
simple mechanism for placing R graphics in a Tk widget
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-candisc-r33-0.8-0-1 (Shrunken Centroids RDA)
This package includes functions for computing and visualizing
generalized canonical discriminant analyses and canonical
correlation analysis for a multivariate linear model.
Traditional canonical discriminant analysis is restricted
to a one-way MANOVA design and is equivalent to canonical
correlation analysis between a set of quantitative response
variables and a set of dummy variables coded from the factor
variable. The candisc package generalizes this to multi-way
MANOVA designs for all factors in a multivariate linear model,
computing canonical scores and vectors for each term. The
graphic functions provide low-rank (1D, 2D, 3D) visualizations
of terms in an mlm via the plot.candisc and heplot.candisc
methods. Related plots are now provided for canonical
correlation analysis when all predictors are quantitative.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-chemospec-r34-5.0.229-1 (Exploratory Chemometrics for Spectroscopy)
A collection of functions for plotting spectra (NMR, IR etc) and carrying
out various forms of top-down exploratory data analysis, such as HCA, PCA
and model-based clustering. The design allows comparison of data from
samples which fall into groups such as treatment vs. control. Robust
methods appropriate for this type of high-dimensional data are available.
ChemoSpec is designed to be very user friendly and suitable for people
with limited background in R.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-xlconnect-r35-0.2-15-1 (Excel Connector for R)
Manipulate Excel files from R
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-classint-r31-0.3-1-1 (Choose Univariate Class Intervals)
Selected commonly used methods for choosing univariate class intervals
for mapping or other graphics purposes.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clv-r35-0.3-2.1-1 (Cluster Validation Techniques)
Package contains most of the popular internal and external cluster validation
methods ready to use for the most of the outputs produced by functions coming
from package "cluster". Package contains also functions and examples of usage
for cluster stability approach that might be applied to algorithms implemented
in "cluster" package as well as user defined clustering algorithms.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: bioconductor-genomeinfodb-r34-1.10.3-1 (Manipulating chromosome/'seqname' identifiers)
The Seqnames package contains data and functions that define and allow
translation between different chromosome sequence naming conventions
(e.g., "chr1" versus "1"), including a function that attempts to place
sequence names in their natural, rather than lexicographic, order.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-rgtk2-r31-2.20.31-3 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-magrittr-r33-1.5-2 (Forward-pipe operator for R)
Provides a mechanism for chaining commands with a new
forward-pipe operator, %>%. This operator will forward
a value, or the result of an expression, into the next
function call/expression. There is flexible support
for the type of right-hand side expressions. For more
information, see package vignette. To quote Rene Magritte,
"Ceci n'est pas un pipe."
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-qvalue-r32-2.6.0-1 (Q-value estimation)
This package takes a list of p-values resulting from the simultaneous
testing of many hypotheses and estimates their q-values and local FDR
values. The q-value of a test measures the proportion of false positives
incurred (called the false discovery rate) when that particular test is
called significant. The local FDR measures the posterior probability
the null hypothesis is true given the test's p-value. Various plots
are automatically generated, allowing one to make sensible significance
cut-offs. Several mathematical results have recently been shown on the
conservative accuracy of the estimated q-values from this software.
The software can be applied to problems in genomics, brain imaging,
astrophysics, and data mining.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-biglm-r32-0.9-1-3 (Bounded memory linear/generalized models)
Regression for data too large to fit in memory
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-backports-r32-1.1.3-1 (Resolving the function names)
Implementations of functions which have been introduced in R
since version 3.0.0. The backports are conditionally exported
which results in R resolving the function names to the version
shipped with R (if available) and uses the implemented backports
as fallback. This way package developers can make use of the new
functions without worrying about the minimum required R version.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-whisker-r34-0.3-2-1 ({{mustache}} for R, logicless templating)
logicless templating, reuse templates in many programming
languages including R
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-als-r33-0.0.6-1 (MCR-ALS)
Alternating least squares is often used to resolve components contributing
to data with a bilinear structure; the basic technique may be extended to
alternating constrained least squares. Commonly applied constraints include
unimodality, non-negativity, and normalization of components. Several data
matrices may be decomposed simultaneously by assuming that one of the two
matrices in the bilinear decomposition is shared between datasets.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: bioconductor-graph-r35-1.52.0-1 (Package to handle graph data structures)
A package that implements some simple graph handling capabilities.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-chemospec-r31-5.0.229-1 (Exploratory Chemometrics for Spectroscopy)
A collection of functions for plotting spectra (NMR, IR etc) and carrying
out various forms of top-down exploratory data analysis, such as HCA, PCA
and model-based clustering. The design allows comparison of data from
samples which fall into groups such as treatment vs. control. Robust
methods appropriate for this type of high-dimensional data are available.
ChemoSpec is designed to be very user friendly and suitable for people
with limited background in R.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-viridis-r31-0.5.1-2 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ash-r32-1.0-15-1 (David Scott's ASH routines)
David Scott's ASH routines
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-htmltable-r31-1.13.1-1 (Advanced Tables for Markdown/HTML)
Tables with state-of-the-art layout elements such as row spanners,
column spanners, table spanners, zebra striping, and more. While
allowing advanced layout, the underlying css-structure is simple
in order to maximize compatibility with word processors such as
'MS Word' or 'LibreOffice'. The package also contains a few text
formatting functions that help outputting text compatible
with HTML/'LaTeX'.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-cairodevice-r34-2.24-1 (Cairo-based antialiased graphics driver)
Cairo/GTK graphics device driver with output to screen, file
(png, svg, pdf, and ps) or memory (arbitrary GdkDrawable or
Cairo context). The screen device may be embedded into RGtk2
interfaces. Supports all interactive features of other graphics
devices, including getGraphicsEvent().
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-biomark-r31-0.4.5-1 (Find biomarkers in two-class discrimination)
The package provides biomarker selection for several classification
methods: the lasso/elastic net, PCLDA, PLSDA, and several t-tests.
Two approaches are provided, one based on the stability of model
coefficients under perturbation, and the other on higher criticism.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-cardata-r33-3.0-2-1 (Companion to Applied Regression Data Sets)
Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied
Regression, Third Edition, Sage (forthcoming).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-protgenerics-r33-1.6.0-1 (S4 generic functions for proteomics)
S4 generic functions for Bioconductor proteomics infrastructure.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-askpass-r31-1.1-1 (Safe Password Entry for R, Git, and SSH)
Cross-platform utilities for prompting the user for credentials or a
passphrase, for example to authenticate with a server or read a
protected key. Includes native programs for MacOS and Windows, hence no
'tcltk' is required. Password entry can be invoked in two different
ways: directly from R via the askpass() function, or indirectly as
password-entry back-end for 'ssh-agent' or 'git-credential' via the
SSH_ASKPASS and GIT_ASKPASS environment variables. Thereby the user can
be prompted for credentials or a passphrase if needed when R calls out
to git or ssh.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-nloptr-r32-1.2.1-1 (R interface to NLopt)
nloptr is an R interface to NLopt. NLopt is a free/open-source library
for nonlinear optimization, providing a common interface for a number
of different free optimization routines available online as well as
original implementations of various other algorithms. See
http://ab-initio.mit.edu/wiki/index.php/NLopt_Introduction for more
information on the available algorithms. During installation on Unix
the NLopt code is downloaded and compiled from the NLopt website.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gwidgetsrgtk2-r34-0.0-86-1 (Toolkit implementation of gWidgets for RGtk2)
Port of gWidgets API to RGtk2
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-formula-r34-1.2-3-1 (Extended Model Formulas)
Infrastructure for extended formulas with multiple parts on the
right-hand side and/or multiple responses on the left-hand side.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-cluster-r35-2.0.7-1-1 (Cluster Analysis Extended Rousseeuw et al)
Cluster Analysis Extended Rousseeuw et al
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-progress-r32-1.2.0-1 (Statnet project common scripts and utilities)
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-brglm-r34-0.6.2-1 (Bias reduction in binomial-response)
Fit generalized linear models with binomial responses using either
an adjusted-score approach to bias reduction or maximum penalized
likelihood where penalization is by Jeffreys invariant prior.
These procedures return estimates with improved frequentist properties
(bias, mean squared error) that are always finite even in cases where
the maximum likelihood estimates are infinite (data separation).
Fitting takes place by fitting generalized linear models on iteratively
updated pseudo-data. The interface is essentially the same as 'glm'.
More flexibility is provided by the fact that custom pseudo-data
representations can be specified and used for model fitting. Functions
are provided for the construction of confidence intervals for the
reduced-bias estimates.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-adaptivetau-r31-2.2-3-1 (Tau-leaping stochastic simulation)
Implements adaptive tau leaping to approximate the trajectory of a
continuous-time stochastic process as described by Cao et al. (2007)
The Journal of Chemical Physics. This package is based upon work
supported by NSF DBI-0906041 and NIH K99-GM104158 to Philip Johnson
and NIH R01-AI049334 to Rustom Antia.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-survival-r32-2.43-3-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-calibrate-r35-1.7.2-1 (Calibration of Scatterplot and Biplot Axes)
Package for drawing calibrated scales with tick marks on
(non-orthogonal) variable vectors in scatterplots and biplots.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-plyr-r35-1.8.4-1 (Splitting, applying and combining data)
plyr is a set of tools that solves a common set of problems: you need to
break a big problem down into manageable pieces, operate on each pieces
and then put all the pieces back together. For example, you might want
to fit a model to each spatial location or time point in your study,
summarise data by panels or collapse high-dimensional arrays to simpler
summary statistics. The development of plyr has been generously supported
by BD (Becton Dickinson).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-xts-r31-0.10-0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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>.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-cairo-r31-1.5-9-2 (Graphics device using cairo graphics library)
This package provides a Cairo graphics device that can be use to
create high-quality vector (PDF, PostScript and SVG) and bitmap output
(PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32).
Since it uses the same back-end for all output, copying across formats
is WYSIWYG. Files are created without the dependence on X11 or other
external programs. This device supports alpha channel (semi-transparent
drawing) and resulting images can contain transparent and semi-transparent
regions. It is ideal for use in server environments (file output) and as
a replacement for other devices that don't have Cairo's capabilities
such as alpha support or anti-aliasing. Backends are modular such that
any subset of backends is supported.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-base64enc-r32-0.1-3-1 (Tools for base64 encoding)
This package provides tools for handling base64 encoding.
It is more flexible than the orphaned base64 package.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clustercrit-r31-1.2.8-1 (Clustering Indices)
compute clustering validation indices
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-foreach-r35-1.4.4-1 (Foreach looping construct for R)
Support for the foreach looping construct. Foreach is an idiom that
allows for iterating over elements in a collection, without the use
of an explicit loop counter. This package in particular is intended
to be used for its return value, rather than for its side effects.
In that sense, it is similar to the standard lapply function, but
doesn't require the evaluation of a function. Using foreach without
side effects also facilitates executing the loop in parallel.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-plyr-r31-1.8.4-1 (Splitting, applying and combining data)
plyr is a set of tools that solves a common set of problems: you need to
break a big problem down into manageable pieces, operate on each pieces
and then put all the pieces back together. For example, you might want
to fit a model to each spatial location or time point in your study,
summarise data by panels or collapse high-dimensional arrays to simpler
summary statistics. The development of plyr has been generously supported
by BD (Becton Dickinson).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-caret-r33-6.0-68-1 (Classification and Regression Training)
Misc functions for training and plotting classification and regression models
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clustersim-r34-0.45-2-1 (Searching for optimal clustering procedure)
GDM Distance, Sokal-Michener Distance, Bray-Curtis Distance, Calinski-Harabasz
Index, G2 Index, G3 Index, Silhouette Index, Krzanowski-Lai Index, Hartigan
Index, Gap Index, DB Index, Data Normalization, HINoV method, Replication
analysis for cluster validation, Clustering with several algorithms, distances,
Symbolic interval distances, Plot functions, Random cluster generation, Linear
ordering methods, Comparing partitions, Spectral clustering, Ordinal to metric
scale transformation, Untypical data generation.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-sys-r32-3.1-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bma-r32-3.18.9-1 (Bayesian Model Averaging)
Package for Bayesian model averaging for linear models, generalizable
linear models and survival models (cox regression).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-gwidgetsrgtk2-r32-0.0-86-1 (Toolkit implementation of gWidgets for RGtk2)
Port of gWidgets API to RGtk2
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clustergeneration-r31-1.3.4-1 (Random cluster generation)
The package contains functions for generating random clusters, generating
random covariance/correlation matrices, calculating a separation index
(data and population version) for pairs of clusters or cluster distributions,
and 1-D and 2-D projection plots to visualize clusters. The package also
contains a function to generate random clusters based on factorial designs
with factors such as degree of separation, number of clusters, number of
variables, number of noisy variables.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-globaltest-r32-5.28.0-1 (Testing Association of Groups of Genes)
Testing whether sets of genes (e.g. KEGG pathways of GO terms) are
significantly associated with a clinical variable of interest.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-clusterfly-r31-0.4-3 (Visualise clustering algorithms with GGobi)
Visualise clustering algorithms with GGobi. Contains both general
code for visualising clustering results and specific visualisations
for model-based, hierarchical and SOM clustering.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-foreign-r34-0.8-71-1 (Read Data Stored by Minitab, S, etc)
Functions for reading and writing data stored by some versions of Epi Info,
Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and writing
some dBase files.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bradleyterry2-r33-1.0-9-1 (Bradley-Terry Models)
Specify and fit the Bradley-Terry model, including structured versions
in which the parameters are related to explanatory variables through a
linear predictor and versions with contest-specific effects, such as a
home advantage.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bma-r31-3.18.9-1 (Bayesian Model Averaging)
Package for Bayesian model averaging for linear models, generalizable
linear models and survival models (cox regression).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-sys-r31-3.1-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-minqa-r32-1.2.4-3 (Derivative-free optimization by quadratic)
Derivative-free optimization by quadratic approximation based
on an interface to Fortran implementations by M. J. D. Powell.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-analyzefmri-r34-1.1-17-1 (Functions for analysis of fMRI datasets)
Functions for I/O, visualisation and analysis of functional Magnetic
Resonance Imaging (fMRI) datasets stored in the ANALYZE or NIFTI format.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-bh-r33-1.69.0-1-1 (Boost C++ header files)
Boost provides free peer-reviewed portable C++ source libraries.
A large part of Boost is provided as C++ template code which is
resolved entirely at compile-time without linking. This package
aims to provide the most useful subset of Boost libraries for
template use among CRAN package. By placing these libraries in
this package, we offer a more efficient distribution system for
CRAN as replication of this code in the sources of other
packages is avoided.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-plyr-r33-1.8.4-1 (Splitting, applying and combining data)
plyr is a set of tools that solves a common set of problems: you need to
break a big problem down into manageable pieces, operate on each pieces
and then put all the pieces back together. For example, you might want
to fit a model to each spatial location or time point in your study,
summarise data by panels or collapse high-dimensional arrays to simpler
summary statistics. The development of plyr has been generously supported
by BD (Becton Dickinson).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-iterators-r32-1.0.8-1 (Iterator construct for R)
Support for iterators, which allow a programmer to traverse
through all the elements of a vector, list, or other collection of data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rlang-r33-0.3.2-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-tkrplot-r31-0.0-24-1 (TK Rplot)
simple mechanism for placing R graphics in a Tk widget
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-xts-r32-0.11-2-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-readjdx-r33-0.3.250-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-class-r31-7.3-15-1 (GNU R Tools for classification)
Various functions for classification.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-vim-r34-4.7.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clustersim-r32-0.45-2-1 (Searching for optimal clustering procedure)
GDM Distance, Sokal-Michener Distance, Bray-Curtis Distance, Calinski-Harabasz
Index, G2 Index, G3 Index, Silhouette Index, Krzanowski-Lai Index, Hartigan
Index, Gap Index, DB Index, Data Normalization, HINoV method, Replication
analysis for cluster validation, Clustering with several algorithms, distances,
Symbolic interval distances, Plot functions, Random cluster generation, Linear
ordering methods, Comparing partitions, Spectral clustering, Ordinal to metric
scale transformation, Untypical data generation.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clusterfly-r33-0.4-3 (Visualise clustering algorithms with GGobi)
Visualise clustering algorithms with GGobi. Contains both general
code for visualising clustering results and specific visualisations
for model-based, hierarchical and SOM clustering.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-histdata-r34-0.8-4-1 (History of statistics data sets)
The HistData package provides a collection of small data sets that
are interesting and important in the history of statistics and data
visualization. The goal of the package is to make these available,
both for instructional use and for historical research. Some of
these present interesting challenges for graphics or analysis in R.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-whisker-r31-0.3-2-1 ({{mustache}} for R, logicless templating)
logicless templating, reuse templates in many programming
languages including R
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-quantreg-r35-5.38-1 (Quantile Regression)
Quantile regression and related methods.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-baseline-r35-1.2-1-1 (Baseline Correction of Spectra)
Collection of baseline correction algorithms, along with a
framework and a GUI for optimising baseline algorithm parameters.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: bioconductor-siggenes-r33-1.48.0-1 (Multiple testing using SAM and EBAM)
Identification of differentially expressed genes and estimation of the
False Discovery Rate (FDR) using both the Significance Analysis of
Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-cellranger-r35-1.1.0-1 (Translate Spreadsheet Cell Ranges)
Helper functions to work with spreadsheets and
the A1:D10 style of cell range specification.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-mzr-r35-2.8.1-2 (Parser for netCDF, mzXML, mzData and mzML)
mzR provides a unified API to the common file formats and parsers available
for mass spectrometry data. It comes with a wrapper for the ISB random access
parser for mass spectrometry mzXML, mzData and mzML files. The package contains
the original code written by the ISB, and a subset of the proteowizard library
for mzML. The netCDF reading code has previously been used in XCMS.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-plogr-r31-0.2.0-1 (Parametrized Active Bindings)
Provides a simple interface for creating active bindings where
the bound function accepts additional arguments.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-zlibbioc-r34-1.20.0-1 (R packaged zlib-1.2.5)
An R packaged zlib-1.2.5
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-numderiv-r32-2016.8-1-1 (Accurate Numerical Derivatives)
This package provide methods for calculating (usually) accurate numerical
first and second order derivatives. Accurate calculations are done using
Richardson's extrapolation or, when applicable, a complex step derivative
is available. A simple difference method is also provided. Simple difference
is (usually) less accurate but is much quicker than Richardson's extrapolation
and provides a useful cross-check. Methods are provided for real scalar and
vector valued functions.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-viridis-r34-0.5.1-2 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-biocparallel-r35-1.8.2-1 (Facilities for parallel evaluation)
This package provides modified versions and novel implementation of
functions for parallel evaluation, tailored to use with Bioconductor
objects.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-randomforest-r32-4.6-12-2 (GNU R Tools for random forest class/regress)
Classification and regression based on a forest of trees using random inputs.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-qvcalc-r32-0.9-1-1 (Quasi Variances for Effects in Stat Models)
Functions to compute quasi variances and associated measures of
approximation error.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-bayesm-r33-3.0-2-1 (Various R programming tools)
bayesm covers many important models used in marketing and micro-
econometrics applications. The package includes: Bayes Regression
(univariate or multivariate dep var), Bayes Seemingly Unrelated
Regression (SUR), Binary and Ordinal Probit, Multinomial Logit
(MNL) and Multinomial Probit (MNP), Multivariate Probit, Negative
Binomial (Poisson) Regression, Multivariate Mixtures of Normals
(including clustering), Dirichlet Process Prior Density Estimation
with normal base, Hierarchical Linear Models with normal prior and
covariates, Hierarchical Linear Models with a mixture of normals
prior and covariates, Hierarchical Multinomial Logits with a
mixture of normals prior and covariates, Hierarchical Multinomial
Logits with a Dirichlet Process prior and covariates, Hierarchical
Negative Binomial Regression Models, Bayesian analysis of choice-
ased conjoint data, Bayesian treatment of linear instrumental
variables models, and Analysis of Multivariate Ordinal survey
data with scale usage heterogeneity (as in Rossi et al, JASA (01)).
For further reference, consult our book, Bayesian Statistics and
Marketing by Rossi, Allenby and McCulloch.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-genomeinfodb-r35-1.10.3-1 (Manipulating chromosome/'seqname' identifiers)
The Seqnames package contains data and functions that define and allow
translation between different chromosome sequence naming conventions
(e.g., "chr1" versus "1"), including a function that attempts to place
sequence names in their natural, rather than lexicographic, order.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-candisc-r35-0.8-0-1 (Shrunken Centroids RDA)
This package includes functions for computing and visualizing
generalized canonical discriminant analyses and canonical
correlation analysis for a multivariate linear model.
Traditional canonical discriminant analysis is restricted
to a one-way MANOVA design and is equivalent to canonical
correlation analysis between a set of quantitative response
variables and a set of dummy variables coded from the factor
variable. The candisc package generalizes this to multi-way
MANOVA designs for all factors in a multivariate linear model,
computing canonical scores and vectors for each term. The
graphic functions provide low-rank (1D, 2D, 3D) visualizations
of terms in an mlm via the plot.candisc and heplot.candisc
methods. Related plots are now provided for canonical
correlation analysis when all predictors are quantitative.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-bayesm-r35-3.1-1-1 (Various R programming tools)
bayesm covers many important models used in marketing and micro-
econometrics applications. The package includes: Bayes Regression
(univariate or multivariate dep var), Bayes Seemingly Unrelated
Regression (SUR), Binary and Ordinal Probit, Multinomial Logit
(MNL) and Multinomial Probit (MNP), Multivariate Probit, Negative
Binomial (Poisson) Regression, Multivariate Mixtures of Normals
(including clustering), Dirichlet Process Prior Density Estimation
with normal base, Hierarchical Linear Models with normal prior and
covariates, Hierarchical Linear Models with a mixture of normals
prior and covariates, Hierarchical Multinomial Logits with a
mixture of normals prior and covariates, Hierarchical Multinomial
Logits with a Dirichlet Process prior and covariates, Hierarchical
Negative Binomial Regression Models, Bayesian analysis of choice-
ased conjoint data, Bayesian treatment of linear instrumental
variables models, and Analysis of Multivariate Ordinal survey
data with scale usage heterogeneity (as in Rossi et al, JASA (01)).
For further reference, consult our book, Bayesian Statistics and
Marketing by Rossi, Allenby and McCulloch.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-openssl-r35-1.3-1 (Encryption, Signatures and Certificates)
Bindings to OpenSSL libssl and libcrypto, plus custom SSH
pubkey parsers. Supports RSA, DSA and EC curves P-256,
P-384 and P-521. Cryptographic signatures can either be
created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric
encryption; RSA for asymmetric (public key) encryption or
EC for Diffie Hellman. High-level envelope functions combine
RSA and AES for encrypting arbitrary sized data. Other
utilities include key generators, hash functions (md5,
sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually
performing crypto calculations on large multibyte integers.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-latticeextra-r35-0.6-28-1 (Extra Graphical Utilities)
Extra graphical utilities based on lattice
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-xcms-r35-1.50.1-2 (Base functions for Bioconductor)
Framework for processing and visualization of chromatographically separated
and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML,
and mzData files. Preprocesses data for high-throughput, untargeted analyte
profiling.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-sp-r32-1.3-1-1 (GNU R classes and methods for spatial data)
GNU R classes and methods for spatial data
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bvls-r32-1.4-3 (Stark-Parker algorithm)
An R interface to the Stark-Parker implementation of an algorithm
for bounded-variable least squares
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-laeken-r34-0.5.0-1 (Indicators on social exclusion and poverty)
Estimation of indicators on social exclusion and poverty,
as well as Pareto tail modeling for empirical income distributions.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-viridislite-r34-0.3.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-foreign-r32-0.8-71-1 (Read Data Stored by Minitab, S, etc)
Functions for reading and writing data stored by some versions of Epi Info,
Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and writing
some dBase files.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-visnetwork-r35-2.0.6-1 (Network Visualization)
Provides an R interface to the 'vis.js' JavaScript charting library. It
allows an interactive visualization of networks.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-care-r35-1.1.10-1 (Regression and CAR Score Variable Selection)
The "care" package implements the regression approach of Zuber and
Strimmer (2011) "High-dimensional regression and variable selection
using CAR scores" SAGMB 10: 34. CAR scores measure the correlation
between the response and the Mahalanobis-decorrelated predictors.
The squared CAR score is a natural measure of variable importance
and provides a canonical ordering of variables. This package
provides functions for estimating CAR scores, for variable
selection using CAR scores, and for estimating corresponding
regression coefficients. Both shrinkage as well as empirical
estimators are available.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-formula-r32-1.2-3-1 (Extended Model Formulas)
Infrastructure for extended formulas with multiple parts on the
right-hand side and/or multiple responses on the left-hand side.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-pillar-r34-1.3.1-1 (Coloured Formatting for Columns)
Provides a 'pillar' generic designed for formatting columns of data
using the full range of colours provided by modern terminals.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-munsell-r33-0.5.0-1 (Munsell colour system)
Functions for exploring and using the Munsell colour system
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-htmlwidgets-r34-1.3-1 (HTML Widgets for R)
A framework for creating HTML widgets that render in various
contexts including the R console, 'R Markdown' documents,
and 'Shiny' web applications.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-backports-r35-1.1.3-1 (Resolving the function names)
Implementations of functions which have been introduced in R
since version 3.0.0. The backports are conditionally exported
which results in R resolving the function names to the version
shipped with R (if available) and uses the implemented backports
as fallback. This way package developers can make use of the new
functions without worrying about the minimum required R version.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-qvalue-r33-2.6.0-1 (Q-value estimation)
This package takes a list of p-values resulting from the simultaneous
testing of many hypotheses and estimates their q-values and local FDR
values. The q-value of a test measures the proportion of false positives
incurred (called the false discovery rate) when that particular test is
called significant. The local FDR measures the posterior probability
the null hypothesis is true given the test's p-value. Various plots
are automatically generated, allowing one to make sensible significance
cut-offs. Several mathematical results have recently been shown on the
conservative accuracy of the estimated q-values from this software.
The software can be applied to problems in genomics, brain imaging,
astrophysics, and data mining.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-care-r31-1.1.10-1 (Regression and CAR Score Variable Selection)
The "care" package implements the regression approach of Zuber and
Strimmer (2011) "High-dimensional regression and variable selection
using CAR scores" SAGMB 10: 34. CAR scores measure the correlation
between the response and the Mahalanobis-decorrelated predictors.
The squared CAR score is a natural measure of variable importance
and provides a canonical ordering of variables. This package
provides functions for estimating CAR scores, for variable
selection using CAR scores, and for estimating corresponding
regression coefficients. Both shrinkage as well as empirical
estimators are available.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-nnet-r32-7.3-12-2 (GNU R Tools for neural networks)
Software for feed-forward neural networks with a single hidden layer,
and for multinomial log-linear models.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-xlconnect-r32-0.2-15-1 (Excel Connector for R)
Manipulate Excel files from R
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-r6-r32-2.4.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-care-r33-1.1.10-1 (Regression and CAR Score Variable Selection)
The "care" package implements the regression approach of Zuber and
Strimmer (2011) "High-dimensional regression and variable selection
using CAR scores" SAGMB 10: 34. CAR scores measure the correlation
between the response and the Mahalanobis-decorrelated predictors.
The squared CAR score is a natural measure of variable importance
and provides a canonical ordering of variables. This package
provides functions for estimating CAR scores, for variable
selection using CAR scores, and for estimating corresponding
regression coefficients. Both shrinkage as well as empirical
estimators are available.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-markdown-r34-0.9-1 (GNU R Tools for making web reports from text)
R Markdown is a format that enables easy authoring of reproducible
web reports from R. It combines the core syntax of Markdown
(an easy-to-write plain text format for web content) with embedded
R code chunks that are run so their output can be included in
the final document.
The concept of R Markdown is similar to Sweave (a system built-in
to R for combining R with LaTeX). In Sweave, Rnw files are "weaved"
into TeX files that are then compiled into PDFs. In R Markdown,
Rmd files are similarly "weaved" into plain markdown (.md) files
that are then compiled into HTML documents.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-brglm-r35-0.6.2-1 (Bias reduction in binomial-response)
Fit generalized linear models with binomial responses using either
an adjusted-score approach to bias reduction or maximum penalized
likelihood where penalization is by Jeffreys invariant prior.
These procedures return estimates with improved frequentist properties
(bias, mean squared error) that are always finite even in cases where
the maximum likelihood estimates are infinite (data separation).
Fitting takes place by fitting generalized linear models on iteratively
updated pseudo-data. The interface is essentially the same as 'glm'.
More flexibility is provided by the fact that custom pseudo-data
representations can be specified and used for model fitting. Functions
are provided for the construction of confidence intervals for the
reduced-bias estimates.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-jsonlite-r32-1.6-1 (JSON Parser and Generator for R)
A fast JSON parser and generator optimized for statistical data and the web.
Started out as a fork of RJSONIO, but has been completely rewritten in
recent versions. The package offers flexible, robust, high performance
tools for working with JSON in R and is particularly powerful for building
pipelines and interacting with web APIs. The implementation is based on the
mapping described in the vignette of the package (Ooms, 2014). In addition
to drop-in replacements for toJSON and fromJSON, jsonlite contains functions
to stream, validate, and prettify JSON data. The unit tests included with
the package verify that all edge cases are encoded and decoded consistently
for use with dynamic data in systems and applications.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-pcamethods-r35-1.66.0-1 (Collection of PCA methods)
Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear
PCA and the conventional SVD PCA. A cluster based method for missing
value estimationn is included for comparison. BPCA, PPCA and NipalsPCA
may be used to perform PCA on incomplete data as well as for accurate
missing value estimation. A set of methods for printing and plotting
the results is also provided. All PCA methods make use of the same
data structure (pcaRes) to provide a unique interface to the PCA
results. Developed at the Max-Planck Institute for Molecular Plant
Physiology, Golm, Germany.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-xlconnectjars-r31-0.2-15-1 (JAR dependencies for the XLConnect)
Provides external JAR dependencies for the XLConnect package.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-mass-r34-7.3-51.1-1 (GNU R data sets for "Modern App. Stat", 4ed)
Functions and datasets to support Venables and Ripley,
'Modern Applied Statistics with S' (4th edition, 2002).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-keggraph-r33-1.32.0-1 (Graph approach to KEGG PATHWAY in R)
KEGGGraph is an interface between KEGG pathway and graph object as well
as a collection of tools to analyze, dissect and visualize these graphs.
It parses the regularly updated KGML (KEGG XML) files into graph models
maintaining all essential pathway attributes. The package offers
functionalities including parsing, graph operation, visualization and etc.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-gower-r32-0.2.0-1 (Gower's Distance)
Compute Gower's distance (or similarity) coefficient between records.
Compute the top-n matches between records. Core algorithms are executed
in parallel on systems supporting OpenMP.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-labeling-r34-0.3-1 (Axis Labeling)
Provides a range of axis labeling algorithms
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-formatr-r33-1.5-1 (GNU R Tools for formatting R source code)
This package provides a function tidy.source() and optionally a GUI
(by gWidgets and preferably gWidgetsRGtk2) to format R source code.
Spaces and indent will be added to the code automatically, and comments
will be preserved under certain conditions, so that R code will be more
human-readable and tidy.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-sys-r34-3.1-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bma-r34-3.18.9-1 (Bayesian Model Averaging)
Package for Bayesian model averaging for linear models, generalizable
linear models and survival models (cox regression).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-waveslim-r35-1.7.5-3 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-curl-r33-3.3-1 (Connection Interface to Libcurl)
The curl() function provides a drop-in replacement for base url() with better
performance and support for http 2.0, ssl (https://, ftps://), gzip, deflate
and other libcurl goodies. This interface is implemented using the RConnection
API in order to support incremental processing of both binary and text streams.
If you are looking for a more-user-friendly http client, try the RCurl or httr
packages instead.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ade4-r34-1.7-13-1 (Analysis of Ecological Data)
Multivariate data analysis and graphical display.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-adimpro-r33-0.8.2-1 (Adaptive Smoothing of Digital Images)
s package implements tools for manipulation of digital images and the
Propagation Separation approach by Polzehl and Spokoiny (2006) for
smoothing digital images.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rcpproll-r33-0.3.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-curl-r35-3.3-1 (Connection Interface to Libcurl)
The curl() function provides a drop-in replacement for base url() with better
performance and support for http 2.0, ssl (https://, ftps://), gzip, deflate
and other libcurl goodies. This interface is implemented using the RConnection
API in order to support incremental processing of both binary and text streams.
If you are looking for a more-user-friendly http client, try the RCurl or httr
packages instead.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-pspline-r35-1.0-18-2 (Penalized Smoothing Splines)
Smoothing splines with penalties on order m derivatives.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-fansi-r32-0.4.0-1 (ANSI Control Sequence Aware Functions)
Counterparts to R string manipulation functions that account for the
effects of ANSI text formatting control sequences.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-openxlsx-r35-4.1.0-1 (Read, Write and Edit XLSX Files)
Simplifies the creation of Excel .xlsx files by providing a high level
interface to writing, styling and editing worksheets. Through the use
of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect'
packages with the added benefit of removing the dependency on Java.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rcpparmadillo-r35-0.9.300.2.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-kohonen-r31-3.0.8-1 (Supervised/unsupervised self-organising maps)
Supervised and unsupervised self-organising maps
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-xts-r34-0.11-2-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-curl-r31-3.3-1 (Connection Interface to Libcurl)
The curl() function provides a drop-in replacement for base url() with better
performance and support for http 2.0, ssl (https://, ftps://), gzip, deflate
and other libcurl goodies. This interface is implemented using the RConnection
API in order to support incremental processing of both binary and text streams.
If you are looking for a more-user-friendly http client, try the RCurl or httr
packages instead.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-qvcalc-r35-0.9-1-1 (Quasi Variances for Effects in Stat Models)
Functions to compute quasi variances and associated measures of
approximation error.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-qvcalc-r33-0.9-1-1 (Quasi Variances for Effects in Stat Models)
Functions to compute quasi variances and associated measures of
approximation error.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-clv-r33-0.3-2.1-1 (Cluster Validation Techniques)
Package contains most of the popular internal and external cluster validation
methods ready to use for the most of the outputs produced by functions coming
from package "cluster". Package contains also functions and examples of usage
for cluster stability approach that might be applied to algorithms implemented
in "cluster" package as well as user defined clustering algorithms.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-lattice-r35-0.20-38-1 (GNU R Tools for lattice graphics)
Lattice is a powerful and elegant high-level data visualization
system, with an emphasis on multivariate data, that is sufficient
for typical graphics needs, and is also flexible enough to handle
most nonstandard requirements.
See ?Lattice for an introduction.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bayesm-r32-3.0-2-1 (Various R programming tools)
bayesm covers many important models used in marketing and micro-
econometrics applications. The package includes: Bayes Regression
(univariate or multivariate dep var), Bayes Seemingly Unrelated
Regression (SUR), Binary and Ordinal Probit, Multinomial Logit
(MNL) and Multinomial Probit (MNP), Multivariate Probit, Negative
Binomial (Poisson) Regression, Multivariate Mixtures of Normals
(including clustering), Dirichlet Process Prior Density Estimation
with normal base, Hierarchical Linear Models with normal prior and
covariates, Hierarchical Linear Models with a mixture of normals
prior and covariates, Hierarchical Multinomial Logits with a
mixture of normals prior and covariates, Hierarchical Multinomial
Logits with a Dirichlet Process prior and covariates, Hierarchical
Negative Binomial Regression Models, Bayesian analysis of choice-
ased conjoint data, Bayesian treatment of linear instrumental
variables models, and Analysis of Multivariate Ordinal survey
data with scale usage heterogeneity (as in Rossi et al, JASA (01)).
For further reference, consult our book, Bayesian Statistics and
Marketing by Rossi, Allenby and McCulloch.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-mime-r32-0.6-1 (Map Filenames to MIME Types)
Guesses the MIME type from a filename extension using the data
derived from /etc/mime.types in UNIX-type systems.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-xlconnect-r31-0.2-15-1 (Excel Connector for R)
Manipulate Excel files from R
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-caret-r35-6.0-82-1 (Classification and Regression Training)
Misc functions for training and plotting classification and regression models
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: bioconductor-preprocesscore-r35-1.36.0-1 (Collection of pre-processing functions)
A library of core preprocessing routines
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-atelier-r33-0.24-1 (GTK GUI for statistical tools)
A collection of statistical simulation and computation tools with a
GTK GUI, to help teach statistical concepts and compute probabilities.
Two domains are covered: I. Understanding (Central-Limit Theorem and
the Normal Distribution, Distribution of a sample mean, Distribution
of a sample variance, Probability calculator for common distributions),
and II. Elementary Bayesian Statistics (bayesian inference on proportions,
contingency tables, means and variances, with informative and
oninformative priors).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-randomforest-r31-4.6-12-2 (GNU R Tools for random forest class/regress)
Classification and regression based on a forest of trees using random inputs.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-iterators-r33-1.0.8-1 (Iterator construct for R)
Support for iterators, which allow a programmer to traverse
through all the elements of a vector, list, or other collection of data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-magick-r34-2.0-1 (Advanced Graphics and Image-Processing in R)
Bindings to 'ImageMagick': the most comprehensive open-source image
processing library available. Supports many common formats (png, jpeg,
tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip,
blur, etc). All operations are vectorized via the Magick++ STL meaning
they operate either on a single frame or a series of frames for working
with layers, collages, or animation. In RStudio images are automatically
previewed when printed to the console, resulting in an interactive
editing environment. The latest version of the package includes a native
graphics device for creating in-memory graphics or drawing onto images
using pixel coordinates.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-gwidgets-r34-0.0-54-1 (R interfaces to gWidgets API)
gWidgets provides a toolkit-independent API for building interactive
GUIs. At least one of the 'gWidgetsXXX packages', such as gWidgetstcltk,
needs to be installed. Some icons are on loan from the scigraphica
project http://scigraphica.sourceforge.net.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-htmltable-r35-1.13.1-1 (Advanced Tables for Markdown/HTML)
Tables with state-of-the-art layout elements such as row spanners,
column spanners, table spanners, zebra striping, and more. While
allowing advanced layout, the underlying css-structure is simple
in order to maximize compatibility with word processors such as
'MS Word' or 'LibreOffice'. The package also contains a few text
formatting functions that help outputting text compatible
with HTML/'LaTeX'.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-arules-r31-1.1-6-1 (Mining Association Rules)
Provides the infrastructure for representing, manipulating and analyzing
transaction data and patterns (frequent itemsets and association rules).
Also provides interfaces to C implementations of the association mining
algorithms Apriori and Eclat by C. Borgelt.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-base64enc-r33-0.1-3-1 (Tools for base64 encoding)
This package provides tools for handling base64 encoding.
It is more flexible than the orphaned base64 package.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-chemospec-r35-5.0.229-1 (Exploratory Chemometrics for Spectroscopy)
A collection of functions for plotting spectra (NMR, IR etc) and carrying
out various forms of top-down exploratory data analysis, such as HCA, PCA
and model-based clustering. The design allows comparison of data from
samples which fall into groups such as treatment vs. control. Robust
methods appropriate for this type of high-dimensional data are available.
ChemoSpec is designed to be very user friendly and suitable for people
with limited background in R.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-rlang-r35-0.3.2-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-als-r35-0.0.6-1 (MCR-ALS)
Alternating least squares is often used to resolve components contributing
to data with a bilinear structure; the basic technique may be extended to
alternating constrained least squares. Commonly applied constraints include
unimodality, non-negativity, and normalization of components. Several data
matrices may be decomposed simultaneously by assuming that one of the two
matrices in the bilinear decomposition is shared between datasets.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-assertthat-r33-0.2.0-1 (Easy pre and post assertions)
assertthat is an extension to stopifnot() that makes it easy
to declare the pre and post conditions that you code should
satisfy, while also producing friendly error messages so that
your users know what they've done wrong.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-permute-r32-0.9-4-1 (Generating restricted permutations of data)
The 'permute' package implements a set of restricted permutation designs
for freely exchangeable, line transects (time series), and spatial grid
designs plus permutation of blocks (groups of samples). 'permute' also
allows split-plot designs, in which the whole-plots or split-plots or
both can be freely-exchangeable or one of the restricted designs. The
'permute' package is modelled after the permutation schemes of Canoco
3.1 (and later) by Cajo ter Braak.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-pbkrtest-r35-0.4-7-1 (Kenward-Roger-based methods)
Test in linear mixed effects models. Attention is on linear mixed
effects models as implemented in the lme4 package. The package
implements a parametric bootstrap test. The package implements a
Kenward-Roger modification of F-tests.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-xlconnect-r34-0.2-15-1 (Excel Connector for R)
Manipulate Excel files from R
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-acepack-r31-1.4.1-1 (ACE and AVAS methods)
ACE and AVAS methods for choosing regression transformations.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rgtk2-r32-2.20.31-3 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-assertthat-r31-0.2.0-1 (Easy pre and post assertions)
assertthat is an extension to stopifnot() that makes it easy
to declare the pre and post conditions that you code should
satisfy, while also producing friendly error messages so that
your users know what they've done wrong.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-biglm-r31-0.9-1-3 (Bounded memory linear/generalized models)
Regression for data too large to fit in memory
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-wccsom-r33-1.2.11-1 (SOM networks for patterns with peak shifts)
SOM networks for comparing patterns with peak shifts.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-caret-r34-6.0-76-1 (Classification and Regression Training)
Misc functions for training and plotting classification and regression models
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-inline-r31-0.3.15-1 (Inline C, C++, Fortran function calls)
Functionality to dynamically define R functions and S4 methods
with in-lined C, C++ or Fortran code supporting .C and .Call
calling conventions.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-pkgconfig-r35-2.0.2-1 (Private Configuration for R Packages)
Set configuration options on a per-package basis. Options set by
a given package only apply to that package, other packages are unaffected.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-xlconnectjars-r35-0.2-15-1 (JAR dependencies for the XLConnect)
Provides external JAR dependencies for the XLConnect package.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-arulesviz-r35-1.3-2-1 (Visualizing Association Rules)
Various visualization techniques for association rules and itemsets.
The packages also includes several interactive visualizations for
rule exploration. This package extends package arules.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-rcpparmadillo-r31-0.7.960.1.1-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-classint-r34-0.3-1-1 (Choose Univariate Class Intervals)
Selected commonly used methods for choosing univariate class intervals
for mapping or other graphics purposes.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-barcode-r33-1.1-1 (Barcode distribution plots)
This package includes the function \code{barcode()}, which produces a
histogram-like plot of a distribution that shows granularity in the data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-digest-r31-0.6.18-1 (GNU R Tools for string function wrappers)
The digest package provides a function 'digest()' for the creation of
hash digests of arbitrary R objects (using the md5, sha-1, sha-256 and
crc32 algorithms) permitting easy comparison of R language objects,
as well as a function 'hmac()' to create hash-based message
authentication code. The md5 algorithm by Ron Rivest is specified in
RFC 1321, the sha-1 and sha-256 algorithms are specified in FIPS-180-1
and FIPS-180-2, and the crc32 algorithm is described in
ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt.
For md5, sha-1, sha-256 and aes, this package uses a small standalone
implementations that were provided by Christophe Devine.
For crc32, code from the zlib library is used.
For sha-512, an implementation by Aaron D. Gifford is used.
Please note that this package is not meant to be deployed for
cryptographic purposes for which more comprehensive (and widely tested)
libraries such as OpenSSL should be used.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-permute-r34-0.9-4-1 (Generating restricted permutations of data)
The 'permute' package implements a set of restricted permutation designs
for freely exchangeable, line transects (time series), and spatial grid
designs plus permutation of blocks (groups of samples). 'permute' also
allows split-plot designs, in which the whole-plots or split-plots or
both can be freely-exchangeable or one of the restricted designs. The
'permute' package is modelled after the permutation schemes of Canoco
3.1 (and later) by Cajo ter Braak.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-qvalue-r34-2.6.0-1 (Q-value estimation)
This package takes a list of p-values resulting from the simultaneous
testing of many hypotheses and estimates their q-values and local FDR
values. The q-value of a test measures the proportion of false positives
incurred (called the false discovery rate) when that particular test is
called significant. The local FDR measures the posterior probability
the null hypothesis is true given the test's p-value. Various plots
are automatically generated, allowing one to make sensible significance
cut-offs. Several mathematical results have recently been shown on the
conservative accuracy of the estimated q-values from this software.
The software can be applied to problems in genomics, brain imaging,
astrophysics, and data mining.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-magrittr-r34-1.5-2 (Forward-pipe operator for R)
Provides a mechanism for chaining commands with a new
forward-pipe operator, %>%. This operator will forward
a value, or the result of an expression, into the next
function call/expression. There is flexible support
for the type of right-hand side expressions. For more
information, see package vignette. To quote Rene Magritte,
"Ceci n'est pas un pipe."
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-globalancova-r35-3.42.0-1 (Global test for differential gene expression)
We give the following arguments in support of the GlobalAncova approach: After
appropriate normalisation, gene-expression-data appear rather symmetrical and
outliers are no real problem, so least squares should be rather robust. ANCOVA
with interaction yields saturated data modelling e.g. different means per group
and gene. Covariate adjustment can help to correct for possible selection bias.
Variance homogeneity and uncorrelated residuals cannot be expected. Application
of ordinary least squares gives unbiased, but no longer optimal estimates
(Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate,
due to correlation. The test statistic however mirrors deviations from the null
hypothesis. In combination with a permutation approach, empirical significance
levels can be approximated. Alternatively, an approximation yields asymptotic
p-values. This work was supported by the NGFN grant 01 GR 0459, BMBF, Germany.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: 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.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rlang-r34-0.3.2-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-sparsem-r35-1.77-1 (Sparse Linear Algebra)
Basic linear algebra for sparse matrices
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-vim-r32-4.7.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-xlconnect-r33-0.2-15-1 (Excel Connector for R)
Manipulate Excel files from R
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-protgenerics-r32-1.6.0-1 (S4 generic functions for proteomics)
S4 generic functions for Bioconductor proteomics infrastructure.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-deoptimr-r33-1.0-8-1 (Differential Evolution Optimization)
An implementation of the jDE variant of the Differential Evolution stochastic
algorithm for global optimization of nonlinear programming problems.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rcolorbrewer-r33-1.1-2-1 (GNU R Tools for variable-dependent palettes)
The packages provides palettes for drawing nice maps shaded
according to a variable.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-rpart-r32-4.1-13-1 (GNU R Tools for recursive partitioning)
Recursive partitioning and regression trees
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-doby-r31-4.5-13-1 (Groupwise summary statistics)
doBy originally contained facilities to 'do something' to data where data
is partitioned 'by' some variables which define groupings of data - hence
the name doBy. doBy contains a variety of utilities including: 1) Facilities
for groupwise computations of summary statistics and other facilities for
working with grouped data. 2) LSmeans (least-squares means), general linear
contrasts. 3) Miscellaneous other utilities.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-base64enc-r34-0.1-3-1 (Tools for base64 encoding)
This package provides tools for handling base64 encoding.
It is more flexible than the orphaned base64 package.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-iterators-r31-1.0.8-1 (Iterator construct for R)
Support for iterators, which allow a programmer to traverse
through all the elements of a vector, list, or other collection of data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-deoptimr-r31-1.0-8-1 (Differential Evolution Optimization)
An implementation of the jDE variant of the Differential Evolution stochastic
algorithm for global optimization of nonlinear programming problems.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-chron-r31-2.3-53-1 (Chronological objects)
Chronological objects which can handle dates and times
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-abind-r31-1.4-5-1 (Combine multi-dimensional arrays)
Combine multi-dimensional arrays into a single array. This is a
generalization of cbind and rbind. Works with vectors, matrices,
and higher-dimensional arrays. Also provides functions adrop,
asub, and afill for manipulating, extracting and replacing data
in arrays.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-iterators-r34-1.0.8-1 (Iterator construct for R)
Support for iterators, which allow a programmer to traverse
through all the elements of a vector, list, or other collection of data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-base64enc-r31-0.1-3-1 (Tools for base64 encoding)
This package provides tools for handling base64 encoding.
It is more flexible than the orphaned base64 package.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-rgraphviz-r35-2.18.0-1 (Plotting capabilities for R graph objects)
nterfaces R with the AT and T graphviz library for plotting R graph
objects from the graph package. Users on all platforms must install
graphviz; see the README file, available in the source distribution
of this file, for details.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-latticeextra-r34-0.6-28-1 (Extra Graphical Utilities)
Extra graphical utilities based on lattice
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-brglm-r33-0.6.2-1 (Bias reduction in binomial-response)
Fit generalized linear models with binomial responses using either
an adjusted-score approach to bias reduction or maximum penalized
likelihood where penalization is by Jeffreys invariant prior.
These procedures return estimates with improved frequentist properties
(bias, mean squared error) that are always finite even in cases where
the maximum likelihood estimates are infinite (data separation).
Fitting takes place by fitting generalized linear models on iteratively
updated pseudo-data. The interface is essentially the same as 'glm'.
More flexibility is provided by the fact that custom pseudo-data
representations can be specified and used for model fitting. Functions
are provided for the construction of confidence intervals for the
reduced-bias estimates.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-bvpsolve-r32-1.3.3-1 (Solvers for boundary value problems)
Functions that solve boundary value problems (BVP) of systems
of ordinary differential equations (ODE). The functions provide
an interface to the FORTRAN functionS twpbvpC, colnew/colsys,
and an R-implementation of the shooting method.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-nloptr-r35-1.2.1-1 (R interface to NLopt)
nloptr is an R interface to NLopt. NLopt is a free/open-source library
for nonlinear optimization, providing a common interface for a number
of different free optimization routines available online as well as
original implementations of various other algorithms. See
http://ab-initio.mit.edu/wiki/index.php/NLopt_Introduction for more
information on the available algorithms. During installation on Unix
the NLopt code is downloaded and compiled from the NLopt website.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-xcms-r34-1.50.1-2 (Base functions for Bioconductor)
Framework for processing and visualization of chromatographically separated
and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML,
and mzData files. Preprocesses data for high-throughput, untargeted analyte
profiling.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-nlme-r34-3.1-137-1 (Linear and Nonlinear Mixed Effects Models)
Fit and compare Gaussian linear and nonlinear mixed-effects models.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bca-r33-0.9-3-1 (Business and Customer Analytics)
Underlying support functions for RcmdrPlugin.BCA and a companion to 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-nloptr-r33-1.2.1-1 (R interface to NLopt)
nloptr is an R interface to NLopt. NLopt is a free/open-source library
for nonlinear optimization, providing a common interface for a number
of different free optimization routines available online as well as
original implementations of various other algorithms. See
http://ab-initio.mit.edu/wiki/index.php/NLopt_Introduction for more
information on the available algorithms. During installation on Unix
the NLopt code is downloaded and compiled from the NLopt website.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-vim-r31-4.7.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-viridislite-r35-0.3.0-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-nlme-r33-3.1-128-1 (Linear and Nonlinear Mixed Effects Models)
Fit and compare Gaussian linear and nonlinear mixed-effects models.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ada-r34-2.0-5-1 (R package for stochastic boosting)
Performs discrete, real, and gentle boost under both exponential
and logistic loss on a given data set. The package ada provides
a straightforward, well-documented, and broad boosting routine
for classification, ideally suited for small to moderate-sized
data sets.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-chemometricswithr-r33-0.1.13-1 (Chemometrics with R)
The package provides functions and scripts used in the book
"Chemometrics with R - Multivariate Data Analysis in the
Natural Sciences and Life Sciences" by Ron Wehrens, Springer (2011).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-cairo-r32-1.5-9-2 (Graphics device using cairo graphics library)
This package provides a Cairo graphics device that can be use to
create high-quality vector (PDF, PostScript and SVG) and bitmap output
(PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32).
Since it uses the same back-end for all output, copying across formats
is WYSIWYG. Files are created without the dependence on X11 or other
external programs. This device supports alpha channel (semi-transparent
drawing) and resulting images can contain transparent and semi-transparent
regions. It is ideal for use in server environments (file output) and as
a replacement for other devices that don't have Cairo's capabilities
such as alpha support or anti-aliasing. Backends are modular such that
any subset of backends is supported.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-calibrate-r33-1.7.2-1 (Calibration of Scatterplot and Biplot Axes)
Package for drawing calibrated scales with tick marks on
(non-orthogonal) variable vectors in scatterplots and biplots.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-nlme-r35-3.1-137-1 (Linear and Nonlinear Mixed Effects Models)
Fit and compare Gaussian linear and nonlinear mixed-effects models.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-mzr-r34-2.8.1-2 (Parser for netCDF, mzXML, mzData and mzML)
mzR provides a unified API to the common file formats and parsers available
for mass spectrometry data. It comes with a wrapper for the ISB random access
parser for mass spectrometry mzXML, mzData and mzML files. The package contains
the original code written by the ISB, and a subset of the proteowizard library
for mzML. The netCDF reading code has previously been used in XCMS.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-pbkrtest-r32-0.4-7-1 (Kenward-Roger-based methods)
Test in linear mixed effects models. Attention is on linear mixed
effects models as implemented in the lme4 package. The package
implements a parametric bootstrap test. The package implements a
Kenward-Roger modification of F-tests.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-lattice-r33-0.20-38-1 (GNU R Tools for lattice graphics)
Lattice is a powerful and elegant high-level data visualization
system, with an emphasis on multivariate data, that is sufficient
for typical graphics needs, and is also flexible enough to handle
most nonstandard requirements.
See ?Lattice for an introduction.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-binda-r35-1.0.3-2 (Multi-Class Discriminant Analysis)
The "binda" package implements functions for multi-class discriminant
analysis using binary predictors, for corresponding variable selection,
and for dichotomizing continuous data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-class-r32-7.3-15-1 (GNU R Tools for classification)
Various functions for classification.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-acepack-r32-1.4.1-1 (ACE and AVAS methods)
ACE and AVAS methods for choosing regression transformations.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-nlme-r31-3.1-128-1 (Linear and Nonlinear Mixed Effects Models)
Fit and compare Gaussian linear and nonlinear mixed-effects models.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-matrixmodels-r34-0.4-1-1 (Modelling with Sparse And Dense Matrices)
Modelling with sparse and dense 'Matrix' matrices,
using modular prediction and response module classes.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-minqa-r31-1.2.4-3 (Derivative-free optimization by quadratic)
Derivative-free optimization by quadratic approximation based
on an interface to Fortran implementations by M. J. D. Powell.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-atelier-r35-0.24-1 (GTK GUI for statistical tools)
A collection of statistical simulation and computation tools with a
GTK GUI, to help teach statistical concepts and compute probabilities.
Two domains are covered: I. Understanding (Central-Limit Theorem and
the Normal Distribution, Distribution of a sample mean, Distribution
of a sample variance, Probability calculator for common distributions),
and II. Elementary Bayesian Statistics (bayesian inference on proportions,
contingency tables, means and variances, with informative and
oninformative priors).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-akima-r33-0.6-2-1 (Interpolation of irregularly spaced data)
Linear or cubic spline interpolation for irregular gridded data
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-gwidgetstcltk-r35-0.0-55-1 (Toolkit implementation of gWidgets for tcltk)
Port of the gWidgets API to the tcltk package. Requires TK 8.5 or
greater for the tile (ttk)widgets http://www.tcl.tk/software/tcltk/8.5.tml.
This is the default on Windows. Under linux, Tk must be installed.
Under Mac OS X (10.5) there are two options: native Tk or X11.
For the native one, Tk must be upgraded. See www.tcl.tk to download
source. Under the Mac it compiles and installs cleanly. For X11,
tcltk libraries can be downloaded to augment the R binary package.
See http://cran.r-project.org/bin/macosx/tools/. The gdf function
requires the add on Tk package TkTable (http://tktable.sourceforge.net/).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-adimpro-r35-0.8.2-1 (Adaptive Smoothing of Digital Images)
s package implements tools for manipulation of digital images and the
Propagation Separation approach by Polzehl and Spokoiny (2006) for
smoothing digital images.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-backports-r31-1.1.3-1 (Resolving the function names)
Implementations of functions which have been introduced in R
since version 3.0.0. The backports are conditionally exported
which results in R resolving the function names to the version
shipped with R (if available) and uses the implemented backports
as fallback. This way package developers can make use of the new
functions without worrying about the minimum required R version.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-pspline-r33-1.0-18-2 (Penalized Smoothing Splines)
Smoothing splines with penalties on order m derivatives.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-globaltest-r35-5.28.0-1 (Testing Association of Groups of Genes)
Testing whether sets of genes (e.g. KEGG pathways of GO terms) are
significantly associated with a clinical variable of interest.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-waveslim-r32-1.7.5-3 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-magick-r31-2.0-1 (Advanced Graphics and Image-Processing in R)
Bindings to 'ImageMagick': the most comprehensive open-source image
processing library available. Supports many common formats (png, jpeg,
tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip,
blur, etc). All operations are vectorized via the Magick++ STL meaning
they operate either on a single frame or a series of frames for working
with layers, collages, or animation. In RStudio images are automatically
previewed when printed to the console, resulting in an interactive
editing environment. The latest version of the package includes a native
graphics device for creating in-memory graphics or drawing onto images
using pixel coordinates.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: bioconductor-qvalue-r35-2.6.0-1 (Q-value estimation)
This package takes a list of p-values resulting from the simultaneous
testing of many hypotheses and estimates their q-values and local FDR
values. The q-value of a test measures the proportion of false positives
incurred (called the false discovery rate) when that particular test is
called significant. The local FDR measures the posterior probability
the null hypothesis is true given the test's p-value. Various plots
are automatically generated, allowing one to make sensible significance
cut-offs. Several mathematical results have recently been shown on the
conservative accuracy of the estimated q-values from this software.
The software can be applied to problems in genomics, brain imaging,
astrophysics, and data mining.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-chemometrics-r34-1.4.2-1 (Multivariate Statistical Analysis)
This package is the R companion to the book "Introduction to Multivariate
Statistical Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-clipr-r35-0.5.0-1 (Read and Write from the System Clipboard)
Simple utility functions to read from and write to the Windows, OS X,
and X11 clipboards.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-kohonen-r34-3.0.8-1 (Supervised/unsupervised self-organising maps)
Supervised and unsupervised self-organising maps
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-htmltable-r32-1.13.1-1 (Advanced Tables for Markdown/HTML)
Tables with state-of-the-art layout elements such as row spanners,
column spanners, table spanners, zebra striping, and more. While
allowing advanced layout, the underlying css-structure is simple
in order to maximize compatibility with word processors such as
'MS Word' or 'LibreOffice'. The package also contains a few text
formatting functions that help outputting text compatible
with HTML/'LaTeX'.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-chemospec-r32-5.0.229-1 (Exploratory Chemometrics for Spectroscopy)
A collection of functions for plotting spectra (NMR, IR etc) and carrying
out various forms of top-down exploratory data analysis, such as HCA, PCA
and model-based clustering. The design allows comparison of data from
samples which fall into groups such as treatment vs. control. Robust
methods appropriate for this type of high-dimensional data are available.
ChemoSpec is designed to be very user friendly and suitable for people
with limited background in R.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-gtable-r32-0.2.0-1 (Arrange grobs in tables)
Tools to make it easier to work with "tables" of grobs.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-randomforest-r33-4.6-12-2 (GNU R Tools for random forest class/regress)
Classification and regression based on a forest of trees using random inputs.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-openxlsx-r32-3.0.0-1 (Read, Write and Edit XLSX Files)
Simplifies the creation of Excel .xlsx files by providing a high level
interface to writing, styling and editing worksheets. Through the use
of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect'
packages with the added benefit of removing the dependency on Java.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-lmtest-r35-0.9-36-1 (Testing Linear Regression Models)
A collection of tests, data sets, and examples for diagnostic checking
in linear regression models. Furthermore, some generic tools for
inference in parametric models are provided
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-assertthat-r32-0.2.0-1 (Easy pre and post assertions)
assertthat is an extension to stopifnot() that makes it easy
to declare the pre and post conditions that you code should
satisfy, while also producing friendly error messages so that
your users know what they've done wrong.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-lmtest-r33-0.9-36-1 (Testing Linear Regression Models)
A collection of tests, data sets, and examples for diagnostic checking
in linear regression models. Furthermore, some generic tools for
inference in parametric models are provided
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-arules-r34-1.6-3-1 (Mining Association Rules)
Provides the infrastructure for representing, manipulating and analyzing
transaction data and patterns (frequent itemsets and association rules).
Also provides interfaces to C implementations of the association mining
algorithms Apriori and Eclat by C. Borgelt.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: bioconductor-siggenes-r35-1.48.0-1 (Multiple testing using SAM and EBAM)
Identification of differentially expressed genes and estimation of the
False Discovery Rate (FDR) using both the Significance Analysis of
Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-formatr-r35-1.5-1 (GNU R Tools for formatting R source code)
This package provides a function tidy.source() and optionally a GUI
(by gWidgets and preferably gWidgetsRGtk2) to format R source code.
Spaces and indent will be added to the code automatically, and comments
will be preserved under certain conditions, so that R code will be more
human-readable and tidy.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-bh-r34-1.69.0-1-1 (Boost C++ header files)
Boost provides free peer-reviewed portable C++ source libraries.
A large part of Boost is provided as C++ template code which is
resolved entirely at compile-time without linking. This package
aims to provide the most useful subset of Boost libraries for
template use among CRAN package. By placing these libraries in
this package, we offer a more efficient distribution system for
CRAN as replication of this code in the sources of other
packages is avoided.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-backports-r34-1.1.3-1 (Resolving the function names)
Implementations of functions which have been introduced in R
since version 3.0.0. The backports are conditionally exported
which results in R resolving the function names to the version
shipped with R (if available) and uses the implemented backports
as fallback. This way package developers can make use of the new
functions without worrying about the minimum required R version.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-recipes-r32-0.1.5-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-slam-r33-0.1-40-2 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-htmlwidgets-r35-1.3-1 (HTML Widgets for R)
A framework for creating HTML widgets that render in various
contexts including the R console, 'R Markdown' documents,
and 'Shiny' web applications.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-hms-r32-0.4.2-1 (Pretty Time of Day)
Implements an S3 class for storing and formatting time-of-day values,
based on the 'difftime' class.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clipr-r34-0.5.0-1 (Read and Write from the System Clipboard)
Simple utility functions to read from and write to the Windows, OS X,
and X11 clipboards.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-markdown-r31-0.9-1 (GNU R Tools for making web reports from text)
R Markdown is a format that enables easy authoring of reproducible
web reports from R. It combines the core syntax of Markdown
(an easy-to-write plain text format for web content) with embedded
R code chunks that are run so their output can be included in
the final document.
The concept of R Markdown is similar to Sweave (a system built-in
to R for combining R with LaTeX). In Sweave, Rnw files are "weaved"
into TeX files that are then compiled into PDFs. In R Markdown,
Rmd files are similarly "weaved" into plain markdown (.md) files
that are then compiled into HTML documents.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-kohonen-r32-3.0.8-1 (Supervised/unsupervised self-organising maps)
Supervised and unsupervised self-organising maps
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ape-r32-3.5-2 (Analyses of Phylogenetics and Evolution)
ape provides functions for reading, writing, plotting, and manipulating
phylogenetic trees, analyses of comparative data in a phylogenetic
framework, ancestral character analyses, analyses of diversification
and macroevolution, computing distances from allelic and nucleotide data,
reading and writing nucleotide sequences, and several tools such as
Mantel's test, generalized skyline plots, graphical exploration of
phylogenetic data (alex, trex, kronoviz), estimation of absolute
evolutionary rates and clock-like trees using mean path lengths and
penalized likelihood. Phylogeny estimation can be done with the NJ,
BIONJ, ME, MVR, SDM, and triangle methods, and several methods
handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the
corresponding triangle method). Some functions call external
applications (PhyML, Clustal, T-Coffee, Muscle) whose results are
returned into R.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-inline-r34-0.3.15-1 (Inline C, C++, Fortran function calls)
Functionality to dynamically define R functions and S4 methods
with in-lined C, C++ or Fortran code supporting .C and .Call
calling conventions.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-markdown-r33-0.9-1 (GNU R Tools for making web reports from text)
R Markdown is a format that enables easy authoring of reproducible
web reports from R. It combines the core syntax of Markdown
(an easy-to-write plain text format for web content) with embedded
R code chunks that are run so their output can be included in
the final document.
The concept of R Markdown is similar to Sweave (a system built-in
to R for combining R with LaTeX). In Sweave, Rnw files are "weaved"
into TeX files that are then compiled into PDFs. In R Markdown,
Rmd files are similarly "weaved" into plain markdown (.md) files
that are then compiled into HTML documents.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-matrix-r32-1.2-6-1 (Sparse and Dense Matrix Classes and Methods)
Classes and methods for dense and sparse matrices and operations
on them using LAPACK and SuiteSparse.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-calibrate-r34-1.7.2-1 (Calibration of Scatterplot and Biplot Axes)
Package for drawing calibrated scales with tick marks on
(non-orthogonal) variable vectors in scatterplots and biplots.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-bvpsolve-r35-1.3.3-1 (Solvers for boundary value problems)
Functions that solve boundary value problems (BVP) of systems
of ordinary differential equations (ODE). The functions provide
an interface to the FORTRAN functionS twpbvpC, colnew/colsys,
and an R-implementation of the shooting method.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-adaptivetau-r32-2.2-3-1 (Tau-leaping stochastic simulation)
Implements adaptive tau leaping to approximate the trajectory of a
continuous-time stochastic process as described by Cao et al. (2007)
The Journal of Chemical Physics. This package is based upon work
supported by NSF DBI-0906041 and NIH K99-GM104158 to Philip Johnson
and NIH R01-AI049334 to Rustom Antia.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-sparsem-r33-1.77-1 (Sparse Linear Algebra)
Basic linear algebra for sparse matrices
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-digest-r34-0.6.18-1 (GNU R Tools for string function wrappers)
The digest package provides a function 'digest()' for the creation of
hash digests of arbitrary R objects (using the md5, sha-1, sha-256 and
crc32 algorithms) permitting easy comparison of R language objects,
as well as a function 'hmac()' to create hash-based message
authentication code. The md5 algorithm by Ron Rivest is specified in
RFC 1321, the sha-1 and sha-256 algorithms are specified in FIPS-180-1
and FIPS-180-2, and the crc32 algorithm is described in
ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt.
For md5, sha-1, sha-256 and aes, this package uses a small standalone
implementations that were provided by Christophe Devine.
For crc32, code from the zlib library is used.
For sha-512, an implementation by Aaron D. Gifford is used.
Please note that this package is not meant to be deployed for
cryptographic purposes for which more comprehensive (and widely tested)
libraries such as OpenSSL should be used.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-calibrate-r31-1.7.2-1 (Calibration of Scatterplot and Biplot Axes)
Package for drawing calibrated scales with tick marks on
(non-orthogonal) variable vectors in scatterplots and biplots.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-recipes-r34-0.1.5-1 (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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-pkgconfig-r32-2.0.2-1 (Private Configuration for R Packages)
Set configuration options on a per-package basis. Options set by
a given package only apply to that package, other packages are unaffected.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-arulesviz-r32-1.3-2-1 (Visualizing Association Rules)
Various visualization techniques for association rules and itemsets.
The packages also includes several interactive visualizations for
rule exploration. This package extends package arules.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-ape-r31-3.5-2 (Analyses of Phylogenetics and Evolution)
ape provides functions for reading, writing, plotting, and manipulating
phylogenetic trees, analyses of comparative data in a phylogenetic
framework, ancestral character analyses, analyses of diversification
and macroevolution, computing distances from allelic and nucleotide data,
reading and writing nucleotide sequences, and several tools such as
Mantel's test, generalized skyline plots, graphical exploration of
phylogenetic data (alex, trex, kronoviz), estimation of absolute
evolutionary rates and clock-like trees using mean path lengths and
penalized likelihood. Phylogeny estimation can be done with the NJ,
BIONJ, ME, MVR, SDM, and triangle methods, and several methods
handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the
corresponding triangle method). Some functions call external
applications (PhyML, Clustal, T-Coffee, Muscle) whose results are
returned into R.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-pmml-r32-1.5.7-1 (Generate PMML for various models)
The Predictive Model Markup Language (PMML) is an XML-based language
which provides a way for applications to define statistical and data
mining models and to share models between PMML compliant applications.
More information about PMML and the Data Mining Group can be found at
http://www.dmg.org. The generated PMML can be imported into any PMML
consuming application, such as the Zementis ADAPA and UPPI scoring engines
which allow for predictive models built in R to be deployed and executed
on site, in the cloud (Amazon, IBM, and FICO), in-database (IBM Netezza,
Pivotal, Sybase IQ, Teradata and Teradata Aster) or Hadoop (Datameer and Hive).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-assertthat-r34-0.2.0-1 (Easy pre and post assertions)
assertthat is an extension to stopifnot() that makes it easy
to declare the pre and post conditions that you code should
satisfy, while also producing friendly error messages so that
your users know what they've done wrong.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-cairodevice-r35-2.24-1 (Cairo-based antialiased graphics driver)
Cairo/GTK graphics device driver with output to screen, file
(png, svg, pdf, and ps) or memory (arbitrary GdkDrawable or
Cairo context). The screen device may be embedded into RGtk2
interfaces. Supports all interactive features of other graphics
devices, including getGraphicsEvent().
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ca-r35-0.71-1 (Correspondence Analysis)
A package for computation and visualization of simple, multiple
and joint correspondence analysis.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-ash-r34-1.0-15-1 (David Scott's ASH routines)
David Scott's ASH routines
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-hms-r31-0.4.2-1 (Pretty Time of Day)
Implements an S3 class for storing and formatting time-of-day values,
based on the 'difftime' class.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-boot-r32-1.3-20-1 (GNU R Tools for bootstrap methods)
functions and datasets for bootstrapping from the book
"Bootstrap Methods and Their Applications"
by A. C. Davison and D. V. Hinkley (1997, CUP).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-plogr-r32-0.2.0-1 (Parametrized Active Bindings)
Provides a simple interface for creating active bindings where
the bound function accepts additional arguments.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clustercrit-r32-1.2.8-1 (Clustering Indices)
compute clustering validation indices
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-barcode-r35-1.1-1 (Barcode distribution plots)
This package includes the function \code{barcode()}, which produces a
histogram-like plot of a distribution that shows granularity in the data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-clustvarsel-r34-2.3.1-1 (Variable Selection for Model-Based Clustering)
A function which implements variable selection methodology for
model-based clustering which allows to find the (locally) optimal
subset of variables in a dataset that have group/cluster information.
A greedy or headlong search can be used, either in a forward-backward
or backward-forward direction, with or without sub-sampling at the
hierarchical clustering stage for starting Mclust models. By default
the algorithm uses a sequential search, but parallelization is also
available.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-backports-r33-1.1.3-1 (Resolving the function names)
Implementations of functions which have been introduced in R
since version 3.0.0. The backports are conditionally exported
which results in R resolving the function names to the version
shipped with R (if available) and uses the implemented backports
as fallback. This way package developers can make use of the new
functions without worrying about the minimum required R version.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-mass-r31-7.3-51.1-1 (GNU R data sets for "Modern App. Stat", 4ed)
Functions and datasets to support Venables and Ripley,
'Modern Applied Statistics with S' (4th edition, 2002).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ade4-r33-1.7-13-1 (Analysis of Ecological Data)
Multivariate data analysis and graphical display.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-crayon-r35-1.3.4-1 (Colored Terminal Output)
Colored terminal output on terminals that support 'ANSI'
color and highlight codes. It also works in 'Emacs' 'ESS'.
'ANSI' color support is automatically detected. Colors
and highlighting can be combined and nested. New styles
can also be created easily. This package was inspired by
the 'chalk' 'JavaScript' project.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-gwidgetstcltk-r31-0.0-55-1 (Toolkit implementation of gWidgets for tcltk)
Port of the gWidgets API to the tcltk package. Requires TK 8.5 or
greater for the tile (ttk)widgets http://www.tcl.tk/software/tcltk/8.5.tml.
This is the default on Windows. Under linux, Tk must be installed.
Under Mac OS X (10.5) there are two options: native Tk or X11.
For the native one, Tk must be upgraded. See www.tcl.tk to download
source. Under the Mac it compiles and installs cleanly. For X11,
tcltk libraries can be downloaded to augment the R binary package.
See http://cran.r-project.org/bin/macosx/tools/. The gdf function
requires the add on Tk package TkTable (http://tktable.sourceforge.net/).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-mass-r35-7.3-51.1-1 (GNU R data sets for "Modern App. Stat", 4ed)
Functions and datasets to support Venables and Ripley,
'Modern Applied Statistics with S' (4th edition, 2002).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-permute-r31-0.9-4-1 (Generating restricted permutations of data)
The 'permute' package implements a set of restricted permutation designs
for freely exchangeable, line transects (time series), and spatial grid
designs plus permutation of blocks (groups of samples). 'permute' also
allows split-plot designs, in which the whole-plots or split-plots or
both can be freely-exchangeable or one of the restricted designs. The
'permute' package is modelled after the permutation schemes of Canoco
3.1 (and later) by Cajo ter Braak.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-crayon-r33-1.3.4-1 (Colored Terminal Output)
Colored terminal output on terminals that support 'ANSI'
color and highlight codes. It also works in 'Emacs' 'ESS'.
'ANSI' color support is automatically detected. Colors
and highlighting can be combined and nested. New styles
can also be created easily. This package was inspired by
the 'chalk' 'JavaScript' project.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-analyzefmri-r35-1.1-17-1 (Functions for analysis of fMRI datasets)
Functions for I/O, visualisation and analysis of functional Magnetic
Resonance Imaging (fMRI) datasets stored in the ANALYZE or NIFTI format.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: bioconductor-zlibbioc-r35-1.20.0-1 (R packaged zlib-1.2.5)
An R packaged zlib-1.2.5
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-histdata-r33-0.8-4-1 (History of statistics data sets)
The HistData package provides a collection of small data sets that
are interesting and important in the history of statistics and data
visualization. The goal of the package is to make these available,
both for instructional use and for historical research. Some of
these present interesting challenges for graphics or analysis in R.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: 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 Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: bioconductor-siggenes-r31-1.48.0-1 (Multiple testing using SAM and EBAM)
Identification of differentially expressed genes and estimation of the
False Discovery Rate (FDR) using both the Significance Analysis of
Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
Add r35 for bioconductor packages2019-04-13: cran-clustergeneration-r32-1.3.4-1 (Random cluster generation)
The package contains functions for generating random clusters, generating
random covariance/correlation matrices, calculating a separation index
(data and population version) for pairs of clusters or cluster distributions,
and 1-D and 2-D projection plots to visualize clusters. The package also
contains a function to generate random clusters based on factorial designs
with factors such as degree of separation, number of clusters, number of
variables, number of noisy variables.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-mass-r33-7.3-51.1-1 (GNU R data sets for "Modern App. Stat", 4ed)
Functions and datasets to support Venables and Ripley,
'Modern Applied Statistics with S' (4th edition, 2002).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ade4-r31-1.7-13-1 (Analysis of Ecological Data)
Multivariate data analysis and graphical display.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-acepack-r34-1.4.1-1 (ACE and AVAS methods)
ACE and AVAS methods for choosing regression transformations.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-aer-r34-1.2-6-1 (Applied Econometrics with R)
Functions, data sets, examples, demos, and vignettes for the book
Christian Kleiber and Achim Zeileis (2008), Applied Econometrics
with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-curl-r34-3.3-1 (Connection Interface to Libcurl)
The curl() function provides a drop-in replacement for base url() with better
performance and support for http 2.0, ssl (https://, ftps://), gzip, deflate
and other libcurl goodies. This interface is implemented using the RConnection
API in order to support incremental processing of both binary and text streams.
If you are looking for a more-user-friendly http client, try the RCurl or httr
packages instead.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-histdata-r31-0.8-4-1 (History of statistics data sets)
The HistData package provides a collection of small data sets that
are interesting and important in the history of statistics and data
visualization. The goal of the package is to make these available,
both for instructional use and for historical research. Some of
these present interesting challenges for graphics or analysis in R.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-car-r34-3.0-2-1 (Companion to Applied Regression)
This package accompanies J. Fox and S. Weisberg, An R Companion to
Applied Regression, Second Edition, Sage, 2011.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
All CRAN based rmods use a custom mirror2019-04-13: cran-ade4-r35-1.7-13-1 (Analysis of Ecological Data)
Multivariate data analysis and graphical display.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-chemometricswithrdata-r33-0.1.3-1 (Data for package ChemometricsWithR)
The package provides data sets used in the book "Chemometrics with R
- Multivariate Data Analysis in the Natural Sciences and Life Sciences"
by Ron Wehrens, Springer (2011).
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates2019-04-13: cran-binda-r34-1.0.3-2 (Multi-Class Discriminant Analysis)
The "binda" package implements functions for multi-class discriminant
analysis using binary predictors, for corresponding variable selection,
and for dichotomizing continuous data.
commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):
R-3.5 updates
