# 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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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')

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)

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)

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)

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)

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')

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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')

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)

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)

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)

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)

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)

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)

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 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)

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)

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)

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 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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)