The ‘Changes on CRAN’ article from the 2010-1 issue.
Phylogenetics, especially comparative methods.
Packages: MCMCglmm, PHYLOGR, PhySim, TreeSim, ade4,
adephylo, apTreeshape, ape\(^*\), geiger, laser, maticce,
ouch, paleoTS, phangorn, phybase, phyclust, phylobase,
phyloclim, picante, scaleboot, vegan.
Maintainer: Brian O’Meara.
(* = core package)
GLMMarp, zic.
apcluster.
BayesPanel, VGAM, effects, fxregime, gam, gamlss, mgcv, micEconCES, micEconSNQP, truncreg.
FD.
DiceDesign, DiceKriging, FrF2.catlg128, dae.
SV.
Rdsm, batch, biglars, doMPI, doRedis.
PTAk, cudaBayesreg, dcemriS4\(^*\), oro.dicom\(^*\), oro.nifti\(^*\).
BradleyTerry2, CMC, caGUI, lavaan\(^*\), lordif, pscl.
Guerry, cshapes, rworldmap.
AIM, Cprob, DTDA, TraMineR, flexCrossHaz, ipw, mspath.
rtv.
parcor.
(* = core package)
AIM: adaptive index model. Authors: L. Tian and R. Tibshirani. In view: Survival.
Bayesian Two-Zone Model. Authors: João Vitor Dias Monteiro, Sudipto Barnejee and Gurumurthy Ramachandran.
This package fits a Brownian bridge movement model to observed locations in space and time. Authors: Ryan Nielson, Hall Sawyer and Trent McDonald.
Bayesian Linear Regression. Authors: Gustavo de los Campos and Paulino Pérez Rodríguez.
Bayesian Time-Stratified Population Analysis. Authors: Carl J Schwarz and Simon J Bonner.
Bayesian methods for panel data modeling and inference. Authors: Chunhua Wu and Siddhartha Chib. In view: Econometrics.
Bayesian multi-locus QTL analysis based on the BIC criterion. Author: Rod Ball.
Bayesian inference for exponential random graph models. Authors: Alberto Caimo and Nial Friel.
Connecting sequence information and biophysical models Authors: Franziska Hoffgaard, with contributions from Philipp Weil and Kay Hamacher.
Companion to the book “Exercices et problèmes de statistique avec le logiciel R”. Authors: Frederic Bertrand and Myriam Maumy-Bertrand.
Bayesian sampling for stick-breaking mixtures. Author: Matt Taddy. In view: Cluster.
A bunch of structure and sequence analysis. Author: Pierre Lefeuvre.
Bolstad functions. Author: James Curran.
Generation, reconstruction, simulation and analysis of synchronous, asynchronous, and probabilistic Boolean networks. Authors: Christoph Müssel, Martin Hopfensitz, Dao Zhou and Hans Kestler.
A tool for finding significant attributes in information systems. Authors: Algorithm by Witold R. Rudnicki, R implementation by Miron B. Kursa.
Bradley-Terry models. Authors: Heather Turner and David Firth. In view: Psychometrics.
Cambial Activity and wood formation data processing, VIsualisation and Analysis using R. Author: Cyrille Rathgeber.
Clustering through “Correlation Clustering Model” (CCM) and cluster analysis tools. Author: Mathieu Vrac.
Significance tests for Canonical Correlation Analysis (CCA). Author: Uwe Menzel.
Cronbach-Mesbah Curve. Authors: Michela Cameletti and Valeria Caviezel. In view: Psychometrics.
Conway-Maxwell Poisson (COM-Poisson) Regression. Author: Kimberly Sellers.
Estimation of causal effects with Generalized Additive Models. Authors: Adam Glynn and Kevin Quinn.
Graphical modelling by CG regressions. Author: Jens Henrik Badsberg.
Interactive and dynamic graphs for the CoCo objects. Author: Jens Henrik Badsberg.
Collocation inference for dynamic systems. Authors: Giles Hooker, Luo Xiao and James Ramsay.
Nonparametrics with clustered binary data. Author: Aniko Szabo.
Conditional probability function of a competing event. Author: Arthur Allignol. In view: Survival.
Dave Armstrong’s miscellaneous functions. Author: Dave Armstrong.
Calculation of Gst and D values characterizing the genetic differentiation between populations. Authors: Alexander Jueterbock, Philipp Kraemer, Gabriele Gerlach and Jana Deppermann.
Computation of functional similarities between DO terms and gene products; DO enrichment analysis; Disease Ontology annotation. Author: Jiang Li.
File-based access to large matrices stored on HDD in binary format. Authors: Yurii Aulchenko and Stepan Yakovenko.
Deducer plug-in example. Author: Ian Fellows.
Design patterns in R to build reusable object-oriented software. Authors: Jitao David Zhang, supported by Stefan Wiemann and Wolfgang Huber.
Designs of computer experiments. Authors: Jessica Franco, Delphine Dupuy and Olivier Roustant. In view: ExperimentalDesign.
Construction and evaluation of metamodels. Authors: D. Dupuy and C. Helbert.
Kriging methods for computer experiments. Authors: O. Roustant, D. Ginsbourger and Y. Deville. In view: ExperimentalDesign.
Kriging-based optimization for computer experiments. Authors: D. Ginsbourger and O. Roustant.
Distribution utilities. Author: David Scott.
Planning and analyzing dose finding experiments. Authors: Bornkamp, José Pinheiro and Frank Bretz.
Exact Multinomial Test: Goodness-of-fit test for discrete multivariate data. Author: Uwe Menzel.
Factor Analysis for Multiple Testing (FAMT): Simultaneous tests under dependence in high-dimensional data. Authors: David Causeur, Chloé Friguet, Magalie Houée-Bigot and Maela Kloareg.
Fast Nearest Neighbor search algorithms and applications. Author: Shengqiao Li.
Complete catalogues of resolution IV 128 run 2-level fractional factorials up to 24 factors. Author: Ulrike In view: ExperimentalDesign.
SNP annotation data methods and species specific database builder. Authors: S. J. Goodswen with contributions from N. S. Watson-Haigh, H. N. Kadarmideen and C. Gondro.
Applies GAMbag, GAMrsm and GAMens ensemble classifiers for binary classification. Authors: Koen W. De Bock, Kristof Coussement and Dirk Van den Poel.
GEV conditonal density estimation network. Author: Alex J. Cannon.
Extension to ggplot2. Authors: Barret Schloerke, Di Cook, Heike Hofmann and Hadley Wickham.
A package for fitting Generalized Waring Regression Models. Authors: A.J. Saez-Castillo, J. Rodríguez-Avi, A. Conde-Sánchez, M.J. Olmo-Jiménez and A.M. Martinez-Rodriguez.
The generalized hyperbolic distribution. Author: David Scott.
Grassmann Manifold Optimization. Authors: Kofi Placid Adragni and Seongho Wu.
Guerry: maps, data and methods related to Guerry (1833) “Moral Statistics of France”. Authors: Michael Friendly and Stephane Dray. In view: Spatial.
Statistical analysis tools for High Dimension Molecular Data (HDMD). Author: Lisa McFerrin.
Hierarchical Generalized Linear Models. Author: Marek Molas.
Hidden Markov Models. Authors: Scientific Software Development — Dr. Lin Himmelmann.
Data sets from the history of statistics and data visualization. Authors: Michael Friendly, with contributions by Stephane Dray and Hadley Wickham.
Identifying functional polymorphisms in genetic association studies. Author: Leeyoung Park.
Interactive Mapping. Author: John R. Wallace.
Calculates polychorical correlations for several copula families. Authors: Jeroen Ooms and Joakim
Joint Optimization Plot. Authors: Sonja Kuhnt and Nikolaus Rudak.
Link function and distribution diagnostic test for social science researchers. Author: Yongmei Ni.
Locally stationary two-dimensional wavelet process estimation scheme. Authors: Idris Eckley and Guy Nason.
Linear predictive models based on the Liblinear C/C++ Library. Author: Thibault Helleputte.
Infer network based on binary arrays using regularized logistic regression. Authors: Pei Wang, Dennis Chao and Li Hsu.
This package provides some basic methods for meta-analysis. Author: Karl Kugler.
Meta-Analysis of MicroArray. Author: Ivana Ihnatova.
Meta-analysis with correlations. Author: AC Del Re and William T. Hoyt.
Meta-analysis with mean differences. Author: AC Del Re and William T. Hoyt.
Modeling Functional Data in Finance. Author: Wei Dou.
Mixture summary method for multiple imputation. Authors: Russell Steele, Naisyin Wang and Adrian Raftery.
Multivariate Nonparametric Methods. An approach based on spatial signs and ranks. Authors: Klaus Nordhausen, Jyrki Mottonen and Hannu Oja.
Multivariate two-sample tests based on K-Nearest-Neighbors. Authors: Lisha Chen, Peng Dai and Wei Dou.
Give power for a given effect size using multivariate classification methods. Authors: Raji Balasubramanian and Yu Guo.
Exact max-type Cochran-Armitage trend test (CATT). Authors: Jianan Tian and Chenliang Xu.
Validation of prediction models. Author: Thomas A. Gerds.
Smoothing Poisson counts with P-splines. Author: Carlo G. Camarda.
Automating Mplus model estimation and interpretation. Author: Michael Hallquist.
Multi-model inference. Author: Kamil Bartoń.
Algorithms and framework for Nonnegative Matrix Factorization (NMF). Author: Renaud Gaujoux.
Non-Negative Matrix Factorization. Authors: Suhai (Timothy) Liu
based on multiplicative updates (Lee and Sung 2001) and alternating
least squares algorithm; Lars Kai Hansen’s nnmf_als Matlab
implementation; Torsten Hothorn’s Moore-Penrose inverse function.
Oligo Specificity System. Authors: Rory Michelland and Laurent Cauquil.
PBS ADMB. Authors: Jon T. Schnute and Rowan Haigh.
Model diagnostics for pharmacokinetic models. Author: Xiaoyong Sun.
Software for Pharmacokinetic model. Authors: Eun-Kyung Lee, Gyujeong Noh and Hyeong-Seok Lim.
Significance testing of transcriptome profiling for RNA-sequencing data. Authors: Taeheon Lee, Bo-Young Lee, Hee-Seok Oh, Heebal Kim.
Power and sample size based on two-one-sided-t-tests (TOST) for BE studies. Author: Detlew Labes.
Product Density Estimation for ICA using tilted Gaussian density estimates. Authors: Trevor Hastie and Rob Tibshirani.
Computes confidence intervals for proportions, differences in proportions, an odds-ratio and the relative risk in a \(2 \times 2\) table. Author: Ralph Scherer.
QT Knowledge Management System. Author: Christoffer W. Tornoe.
Interactive software package for QTL visualization. Author: Zheng Wenjun.
Multidimensional numerical integration. Authors: The Cuba library has been written by Thomas Hahn; Interface to R was written by Annie Bouvier and Kiên Kiêu.
Simple R Interface to Microsoft PowerPoint using rcom. Author: Wayne Jones.
Fast Nearest Neighbour Search. Authors: Samuel E. Kemp and Gregory Jefferis.
Tools to analyse RFLP data. Authors: Fabienne Flessa, Alexandra Kehl, Matthias Kohl.
Japanese stock market from Yahoo!-finance-Japan Authors: Yohei Sato and Nobuaki Oshiro.
Improved data frame editor for RGtk2. Authors: Tom Taverner, with contributions from John Verzani.
DBI/RJDBC interface to H2 Database. Author: G. Grothendieck. Author of H2 is Thomas Mueller.
R interface to Oracle Data Mining. Authors: Pablo Tamayo and Ari Mozes.
Convenient Tools for Working with Oracle Databases. Author: Arni Magnusson.
Reads, annotates, and normalizes reverse phase protein array data. Author: Heiko Mannsperger with contributions from Stephan Gade.
R interface to the Protocol Buffers API. Authors: Romain François and Dirk Eddelbuettel.
Math and String Extension Functions for RSQLite. Author: Seth Falcon.
Conjugate gradient minimization of nonlinear functions with box constraints. Author: John C. Nash.
Meta-analysis with correlations (MAc) Rcmdr Plug-in. Author: AC Del Re.
Meta-analysis with mean differences (MAd) Rcmdr Plug-in. Author: AC Del Re.
Some discrete exponential dispersion models: Poisson-Tweedie. Authors: David Pechel Cactcha, Laure Pauline Fotso and Célestin C Kokonendji.
SLC Rcmdr plug-in. Authors: Antonio Solanas and Rumen Manolov.
Rcmdr plugin for Stat 4309 course. Author: Erin Hodgess.
Efficiently search R Help pages. Author: Liviu Andronic.
Steepness Rcmdr plug-in. Author: David Leiva and Han de Vries.
Rcpp/Armadillo bridge. Authors: Romain François, Dirk Eddelbuettel and Doug Bates.
Examples using Rcpp to interface R and C++. Authors: Dirk Eddelbuettel and Romain François, based on code written during 2005 and 2006 by Dominick Samperi.
Threads-Like Environment for R. Author: Norm Matloff. In view: HighPerformanceComputing.
Record linkage in R. Authors: Andreas Borg and Murat Sariyar.
Calculating multilocus heterozygosity and heterozygosity-heterozygosity correlation. Authors: Jussi Alho and Kaisa Välimäki.
Infinitesimally robust estimators for preprocessing omics data. Author: Matthias Kohl.
DBI/RJDBC interface to PostgreSQL database. Author: G. Grothendieck.
General non-linear optimization. Authors: Alexios Ghalanos and Stefan Theussl.
Variable metric nonlinear function minimization with bounds constraints. Author: John C. Nash.
Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises. Authors: Jeremy VanDerWal, Luke Shoo and Stephanie Januchowski. This package was made possible in part by support from Lorena Falconi and Collin Storlie, and financial support from the Australian Research Council & ARC Research Network for Earth System Science.
Integrated methodology for the identification of homogeneous profiles in data distribution. Author: Fabrice Colas.
SHrinkage covariance Incorporating Prior knowledge. Authors: Monika Jelizarow and Vincent Guillemot.
Slope and level change. Authors: Antonio Solanas, Rumen Manolov and Patrick Onghena.
Memory management in R by delayed assignments. Authors: Bill Venables, based on original code by David Brahm.
A program to estimate animal aabundance and density using Spatially-Explicit Capture-Recapture. Authors: Pallavi Singh, Arjun M. Gopalaswamy, Andrew J. Royle, N. Samba Kumar and K. Ullas Karanth with contributions from Sumanta Mukherjee, Vatsaraj and Dipti Bharadwaj.
Subset quantile normalization. Author: Zhijin(Jean) Wu.
Indirect inference in non-Gaussian stochastic volatility models. Author: Øivind Skare. In view: Finance.
Sample size calculations for normal means. Authors: Lawrence Joseph and Patrick Belisle.
Calculating sample size requirements when estimating the difference between two binomial proportions. Authors: Lawrence Joseph, Roxane du Berger and Patrick Belisle.
The Skew Hyperbolic Student t-distribution. Authors: David Scott and Fiona Grimson.
Data sets from Ramsey and Schafer’s “Statistical Sleuth (2nd ed)”. Authors: Original by F.L. Ramsey and D.W. Schafer, modifications by Daniel W Schafer, Jeannie Sifneos and Berwin A Turlach.
Performs various spatial epidemiological analyses. Author: Albert Y. Kim.
Simulate QQ-Norm and TA-Plot. Author: Matthias Salvisberg.
Time Course Analysis of Variance for Microarray. Authors: Baiyu Zhou and Weihong Xu.
Teaching GUI — Core functionality. Authors: Matthias Templ, Gerlinde Dinges, Alexander Kowarik and Bernhard Meindl.
Teaching GUI — prototype. Authors: Matthias Templ, Gerlinde Dinges, Alexander Kowarik and Bernhard Meindl.
Incorporating ecological data and associated uncertainty in bioaccumulation modeling. Authors: Frederik De Laender and Karline Soetaert.
Implementation of the TreeRank methodology for building tree-based ranking rules for bipartite ranking through ROC curve optimization. Author: Nicolas Baskiotis.
Simulating trees under the birth-death model. Author: Tanja Stadler. In view: Phylogenetics.
US Census 2000 suite of R Packages. Author: Zack W. Almquist. In view: Spatial.
US Census 2000 suite of R Packages: Demographic add. Author: Zack W. Almquist.
US Census 2000 block group shapefiles and additional Demographic Data. Author: Zack W. Almquist.
US Census 2000 designated places shapefiles and additional demographic data. Author: Zack W. Almquist.
US Census 2000 tract level shapefiles and additional demographic Data. Author: Zack W. Almquist.
Unicode data and utilities. Author: Kurt Hornik.
Discrimination/Classification in very high dimension with linear and quadratic rules. Author: Robin Girard.
Variable Penalty Dynamic Time Warping. Authors: David Clifford and Glenn Stone.
Vhayu R interface. Author: The Brookhaven Group. In view: TimeSeries.
Visualisation of Computer Models. Author: Neil Diamond.
William and Mary Parser for Bruker-Ultraflex mass spectrometry data. Authors: William Cooke, Maureen Tracy and Dariya Malyarenko.
Wavelet change point detection for array CGH data. Author: M. Shahidul Islam.
Exploratory analyses for the phylogenetic comparative method. Authors: Thibaut Jombart and Stephane Dray. In view: Phylogenetics.
Extracting and preprocessing Agilent express arrays. Author: Benny Chain.
Additive Models for Business Applications. Author: Charlotte Maia.
ANES Raking Implementation. Author: Josh Pasek.
Affinity Propagation Clustering. Authors: Ulrich Bodenhofer and Andreas Kothmeier. In view: Cluster.
Algorithms for Quantitative Pedology. Author: Dylan Beaudette.
Copy-number analysis of large microarray data sets. Authors: Henrik Bengtsson and Pierre Neuvial.
Light-weight methods for normalization and visualization of microarray data using only basic R data types. Author: Henrik Bengtsson.
A collection of statistical tools for biologists. Authors: Ken Aho; many thanks to V. Winston and D. Roberts.
Simulations for adaptive seamless designs. Author: Nick parsons.
Base 64 encoder/decoder. Authors: Romain François, based on code by Bob Trower available at http://base64.sourceforge.net/.
Batching routines in parallel and passing command-line arguments to R. Author: Thomas Hoffmann. In view: HighPerformanceComputing.
BFAST: Breaks For Additive Seasonal and Trend. Authors: Jan Verbesselt, with contributions from Rob Hyndman.
BibTeX parser. Author: Romain François.
A library of utilities for "big.matrix" objects of package
bigmemory. Authors: John W. Emerson and Michael J. Kane.
Scalable Least-Angle Regression and Lasso. Authors: Mark Seligman, Chris Fraley and Tim Hesterberg. In view: HighPerformanceComputing.
table-, tapply-, and split-like functionality for "matrix"
and "big.matrix" objects. Authors: Michael J. Kane and John W.
Emerson.
Haar-Fisz functions for binomial data. Author: Matt Nunes.
Cryptographic Boolean functions. Author: F. Lafitte.
A bootstrap test for the probability of ruin in the classical risk process. Authors: Benjamin Baumgartner, Riccardo Gatto.
Categorical Bayesian network inference. Authors: Nikolay Balov and Peter Salzman.
Calculate the consensus clustering result from re-sampled clustering experiments with the option of using multiple algorithms and parameter. Authors: Dr. T. Ian Simpson.
Covariance Matrix Adapting Evolutionary Strategy. Authors: Heike Trautmann, Olaf Mersmann and David Arnu.
A collection of functions to help with analysis of coarse infectious disease data. Author: Nicholas G. Reich.
Multiscale codependence analysis. Authors: Guillaume Guenard, with contributions from Bertrand Pages.
Gradient-Based Coenospace Vegetation Simulator. Author: David W. Roberts.
Compute Effect Sizes. Author: AC Del Re.
Visualization of a correlation matrix. Author: Taiyun Wei.
CCMN and other noRMalizatioN methods for metabolomics data. Author: Henning Redestig.
Complex wavelet denoising software. Author: Stuart Barber.
Adaptive multivariate integration over hypercubes. Authors: C code by Steven G. Johnson, R by Balasubramanian Narasimhan.
Cusp Catastrophe Model Fitting Using Maximum Likelihood. Author: Raoul P. P. P. Grasman.
Functions useful in the design and ANOVA of experiments. Author: Chris Brien. In view: ExperimentalDesign.
R functions for directed acyclic graphs. Author: Lutz P Breitling.
A system for mapping foreign objects to R variables and environments. Author: Jeffrey Horner.
A Package for Medical Image Analysis (S4 implementation). Authors: Brandon Whitcher and Volker Schmid, with contributions from Andrew Thornton. In view: MedicalImaging.
Data Cloning and MCMC Tools for Maximum Likelihood Methods. Author: Peter Solymos.
Deconvolution Estimation in Measurement Error Models. Authors: Xiao-Feng Wang and Bin Wang.
Detection of differentially expressed genes. Author: Klaus Jung.
A plot digitizer in R. Author: Timothee Poisot.
S4 classes for elliptically contoured distributions. Author: Peter Ruckdeschel.
Foreach parallel adaptor for the Rmpi package. Author: Steve Weston. In view: HighPerformanceComputing.
Foreach parallel adapter for the rredis package. Author: B. W. Lewis. In view: HighPerformanceComputing.
Dirichlet Process Mixture model simulation for clustering and image segmentation. Author: Adelino Ferreira da Silva.
Discrete variations of a fractional Brownian motion. Author: Jean-Francois Coeurjolly.
Dynamic trees for learning and design. Authors: Robert B. Gramacy and Matt A. Taddy.
Empirical Bayes Estimation of Dynamic Bayesian Networks. Author: Andrea Rau.
Provide tools for dimension reduction methods. Authors: Benoit Liquet and Jerome Saracco.
Integrating R’s debug() with Your Text Editor. Author: Norm
Matloff.
Tool for ego-centric measures in Social Network Analysis. Authors: A. Sciandra, F. Gioachin and L. Finos.
Evolutionary Multiobjective Optimization Algorithms. Author: Olaf Mersmann.
Envelope normality test. Author: Felipe Acosta.
A collection of epidemic/network-related tools. Authors: Chris Groendyke, David Welch and David R. Hunter.
Statistical methods for test score equating. Author: Anthony Albano.
Functions for post-processing and gridding empirical-statistical downscaled climate scenarios. Author: Rasmus E. Benestad.
Exact p-values and matching confidence intervals for simple discrete parametric cases. Author: M. P. Fay.
Expectile regression. Authors: Fabian Sobotka, Thomas Kneib, Sabine Schnabel and Paul Eilers.
Graphic axtensions for categorical data. Author: Alexander
Univariate outlier detection. Author: Mark van der Loo.
Basics of certificates and structured products valuation. Author: Stefan Wilhelm.
Formatted actuarial vignettes in R. Author: Benedict Escoto.
Frequency Distribution Tables, Histograms and Poligons. Author: Jose Claudio Faria and Enio Jelihovschi.
Fast FFT and DCT based on FFTW. Author: Sebastian Krey, Uwe Ligges and Olaf Mersmann.
Fisheye and hyperbolic-space-alike interactive visualization tools in R. Author: Eduardo San Miguel Martin.
Flexible crossing hazards in the Cox model. Authors: Vito M.R. Muggeo and Miriam Tagliavia. In view: Survival.
Statistical tools for the interpretation of forensic DNA mixtures. Author: Hinda Haned.
Format R code automatically. Author: Yihui Xie.
Tools for working with formulas, expressions, calls and other R objects. Author: Christopher Brown.
Approximation of first-passage-time densities for diffusion processes. Authors: Patricia Román-Román, Juan J. Serrano-Pérez and Francisco Torres-Ruiz.
Futile library to provide some polymorphism. Author: Brian Lee Yung Rowe.
Futile logger subsystem. Author: Brian Lee Yung Rowe.
Futile matrix utilities. Author: Brian Lee Yung Rowe.
Futile options management. Author: Brian Lee Yung Rowe.
GAMLSS additive. Authors: Mikis Stasinopoulos and Bob Rigby.
Demos for GAMLSS. Authors: Mikis Stasinopoulos, Bob Rigby, Paul Eilers and Brian Marx with contributions from Larisa Kosidou.
GAMLSS utilities. Authors: Mikis Stasinopoulos, Bob Rigby, Paul Eilers.
Provides an inequation algorithm function and a solution to import DIMACS files. Authors: Jeffrey L. Duffany, Ph.D. and Euripides Rivera Negron.
Relevant functions for gene expression analysis, especially in breast cancer. Authors: Benjamin Haibe-Kains, Gianluca Bontempi and Christos Sotiriou.
Plot publication-grade gene and genome maps. Author: Lionel Guy.
Manages microsatellite projects. Creates 96-well maps, genotyping submission forms, rerun management, and import into statistical software. Author: Brian J. Knaus.
Geophysics, continuum mechanics, Mogi model. Author: Jonathan M. Lees.
Spherical trigonometry. Authors: Robert J. Hijmans, Ed Williams and Chris Vennes.
The package was developed to fit many growth curves obtained under different conditions. Authors: Matthias Kahm and Maik Kschischo.
Software to perform Haar Fisz transforms. Author: Piotr Fryzlewicz.
Show certain type of comments from function bodies as “live-help”. Author: Daniel Haase.
Heteroscedastic Discriminant Analysis. Author: Gero Szepannek.
Estimation in the linear mixed model using heavy-tailed distributions. Author: Felipe Osorio.
Hierarchical Exponential-family Random Graph Models. Author: Michael Schweinberger.
High-dimensional Additive Modelling. Authors: The students of the “Advanced R Programming Course” Hannah Frick, Ivan Kondofersky, Oliver S. Kuehnle, Christian Lindenlaub, Georg Pfundstein, Matthias Speidel, Martin Spindler, Ariane Straub, Florian Wickler and Katharina Zink, under the supervision of Manuel Eugster and Torsten Hothorn.
Hierarchical Generalized Linear Models. Authors: Moudud Alam, Lars Ronnegard, Xia Shen.
Syntax highlighter. Author: Romain François.
Construction of regular and irregular histograms with different options for automatic choice of bins. Authors: Thoralf Mildenberger, Yves Rozenholc and David Zasada.
Hierarchical time series. Authors: Rob J Hyndman, Roman A Ahmed, and Han Lin Shang.
Interface for hyperspectral data sets, i.e., spectra + meta information (spatial, time, concentration, …). Author: Claudia Beleites.
An interface to R2WinBUGS by gWidgets. Author: Yihui Xie.
Integrative clustering of multiple genomic data types. Author: Ronglai Shen.
Iterative Bias Reduction. Authors: Pierre-Andre Cornillon, Nicolas Hengartner and Eric Matzner-Lober.
Estimate inverse probability weights. Author: Willem M. van der Wal. In view: Survival.
Isopam (hierarchical clustering). Author: Sebastian Schmidtlein.
Iterator tools. Authors: Steve Weston and Hadley Wickham.
Routines for fitting kinetic models to chemical degradation data. Author: Johannes Ranke.
K-means for joint longitudinal data. Author: Christophe Genolini.
Latent Variable Analysis. Author: Yves Rosseel. In view: Psychometrics.
Estimation of latent class mixed models. Authors: Cecile Proust-Lima and Benoit Liquet.
Bivariate linear errors-in-variables estimation. Author: David Leonard.
Jitter/Box Plot with Ordered Points Below the Limit of Detection. Author: Omar E. Olmedo.
Permutation tests for linear models. Author: Bob Wheeler.
Decimal log plotting in two and three dimensions. Author: Timothée Poisot.
A tentative logging package. Author: Mario Frasca.
Robust loss development using MCMC. Authors: Christopher W. Laws and Frank A. Schmid.
Penalized likelihood inference for GLMs. Author: Jan Ulbricht.
Simulate micro-magnets dynamics. Author: Hai Qian.
Model Based Multifactor Dimensionality Reduction. Authors: Victor Urrea, Malu Calle, Kristel Van Steen and Nuria Malats.
Mixed Conditional Logit. Author: Martin Elff.
Multivariate ECDF-Based Models. Author: Charlotte Maia. In view: Distributions.
Demand analysis with the Almost Ideal Demand System (AIDS). Author: Arne Henningsen. In view: Econometrics.
Analysis with the Constant Elasticity of Scale (CES) function. Authors: Arne Henningsen and Geraldine Henningsen. In view: Econometrics.
Symmetric Normalized Quadratic Profit Function. Author: Arne Henningsen. In view: Econometrics.
Graphical User Interface of the mi Package. Authors: Daniel Lee and Yu-Sung Su.
tktcl quick and simple function GUI. Author: Jorge Luis Ojeda Cabrera.
Derivative-free optimization algorithms by quadratic approximation. Authors: Douglas Bates, Katharine M. Mullen, John C. Nash and Ravi Varadhan.
Miscellanneous Tools and Utilities. Author: Arne Henningsen.
Handling missing values with/in multivariate data analysis (principal component methods). Authors: François Husson and Julie Josse.
Integrate omics data project. Authors: Sébastien Dejean, Ignacio González and Kim-Anh Lê Cao.
Routines for fitting kinetic models with one or more state variables to chemical degradation data. Author: Johannes Ranke.
Bayesian Model Averaging for multinomial logit models. Authors: Hana Ševčíková and Adrian Raftery.
Map pages of memory. Author: Jeffrey A. Ryan.
Monotone multi-layer perceptron neural network. Author: Alex J. Cannon.
Model-robust concentration-response analysis. Authors: Christian Ritz and Mads Jeppe Tarp-Johansen.
Modeling non-uniformity in short-read rates in RNA-Seq data. Author: Jun Li.
Multi-state Path-dependent models in discrete time. Authors: Ross
Boylan and Peter Bacchetti, building on the work of Christopher H.
Jackson. Thorsten Ottosen for the ptr_container library. Gennadiy
Rozental for the Boost Test Library. And the authors of other Boost
libraries used by the previous two. In view:
Survival.
Multivariate timeseries cluster-based models. Author: Charlotte Maia.
Mixture of Gaussian Bayesian network model. Author: Nikolay Balov.
Multivariate Sensitivity Analysis. Authors: Matieyendou Lamboni and Hervé Monod.
Metric Unfolding. Author: Martin Elff.
Mutable objects for R. Author: Hadley Wickham.
Statistical methods for analysing multivariate abundance data. Authors: Ulrike Naumann, Yi Wang, Stephen Wright and David Warton.
Software for moving grid adjustment in plant breeding field trials. Author: Frank Technow.
Tools for nanoparticle simulation and PDF calculation. Author: Katharine Mullen.
Interface to Unidata netCDF (version 4 or earlier) format data files. Author: David Pierce.
Regularization paths for SCAD- and MCP-penalized regression models. Author: Patrick Breheny.
R port of the Scilab neldermead module. Authors: Sebastien Bihorel and Michael Baudin (author of the original module).
NGA earthquake ground motion prediction equations. Authors: James Kaklamanos and Eric M. Thompson.
Regression in the Normal Linear ADG Model. Authors: Lutz F. Gruber
k-Nearest Neighbor diagnostic tools. Authors: Brian Walters, Andrew O. Finley and Zhen Zhang.
Nonparametric methods for measuring efficiency and productivity. Author: Dong-hyun Oh.
Stratification and matching by the propensity score. Author: Susanne Stampf.
Parallel nonparametric kernel smoothing methods for mixed data types. Authors: Tristen Hayfield and Jeffrey S. Racine.
Nonparametric Partially-Balanced Incomplete Block Design Analysis. Authors: David Allingham and D.J. Best.
Data for “R in a Nutshell”. Author: Joseph Adler.
Provides access to the NY Times API. Author: Shane Conway.
Object-Functional Programming. Author: Charlotte Maia.
Filter the molecular descriptors for QSAR. Author: Bin Ma.
Open Intro data sets and supplement functions. Authors: David M Diez and Christopher D Barr.
R port of the Scilab optimbase module. Authors: Sebastien Bihorel and Michael Baudin (author of the original module).
R port of the Scilab optimsimplex module. Authors: Sebastien Bihorel and Michael Baudin (author of the original module).
Command line option parser. Authors: Trevor Davis. getopt
function, some documentation and unit tests ported from Allen Day’s
getopt package. Based on the optparse Python library by the Python
Software Foundation.
Optimal partitioning of similarity relations. Author: David W. Roberts.
Regression models for ordinal data. Author: Rune Haubo B Christensen.
Rigorous — DICOM Input / Output. Author: Brandon Whitcher. In view: MedicalImaging.
Rigorous — NIfTI Input / Output. Authors: Brandon Whitcher, Volker Schmid and Andrew Thornton. In view: MedicalImaging.
Generalized Least Square in comparative Phylogenetics. Authors: Xianyun Mao and Timothy Ryan.
Display and analyze ROC curves. Authors: Xavier Robin, Natacha Turck, Alexandre Hainard, Natalia Tiberti, Frédérique Lisacek, Jean-Charles Sanchez and Markus Müller.
Paleoecological Analysis. Authors: Alexander Correa-Metrio, Dunia Urrego, Kenneth Cabrera, Mark Bush.
Principal Axes Methods for Contingency Tables with Partition Structures on Rows and Columns. Author: Campo Elías Pardo.
Compute a distance metric between two partitions of a set. Authors: David Weisman and Dan Simovici.
Parviol combines parallel coordinates and violin plot. Author: Jaroslav Myslivec.
Functions to facilitate power and sensitivity analyses for genetic studies of natrual popualtions. Author: Michael Morrissey.
Quality speedy graphics compilation with Sweave. Authors: Cameron Bracken and Charlie Sharpsteen.
Phylogenetic Clustering (Phyloclustering). Author: Wei-Chen Chen. In view: Phylogenetics.
Base package for phylogenetic structures and comparative data. Authors: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler, Peter Cowan, Damien de Vienne, Thibaut Jombart, Steve Kembel, François Michonneau, David Orme, Brian O’Meara, Emmanuel Paradis, Jim Regetz, Derrick Zwickl). In view: Phylogenetics.
Integrating phylogenetics and climatic niche modelling. Author: Christoph Heibl. In view: Phylogenetics.
Particle Learning of Gaussian Processes. Author: Robert B. Gramacy.
Degrees of freedom and confidence intervals for Partial Least Squares regression. Authors: Nicole Krämer and Mikio L. Braun.
Penalized Multinomial Logistic Regression. Authors: Sarah Colby, Sophia Lee, Juan Pablo Lewinger and Shelley Bull.
Read and write PNG images. Author: Simon Urbanek.
Poisson-Tweedie exponential family models. Authors: David Pechel Cactcha, Laure Pauline Fotso and Célestin C Kokonendji.
Simulate and test marker dosage for dominant markers in autopolyploids. Author: Peter Baker.
Bayesian mixture models for marker dosage in autopolyploids. Author: Peter Baker.
Summary of population pharmacokinetic analysis. Author: Christoffer W. Tornoe and Fang Li.
Power/sample size calculation for mediation analysis. Author: Weiliang Qiu.
Point pattern distances and prototypes. Authors: David M Diez, Katherine E Tranbarger Freier, and Frederic P Schoenberg.
Profile Dirichlet Process Mixtures. Author: Matt Shotwell.
Recursive partitioning based on psychometric models. Authors: Achim Zeileis, Carolin Strobl and Florian Wickelmaier. In view: Psychometrics.
Parametric Time Warping. Authors: Jan Gerretzen, Paul Eilers, Hans Wouters, Tom Bloemberg and Ron Wehrens. In view: TimeSeries.
Functions to draw population pyramid. Author: Minato Nakazawa.
Quantile regression neural network. Author: Alex J. Cannon.
Arithmetics and linear algebra with Quaternions. Author: K. Gerald van den Boogaart.
2dRue: 2d Rain Use Efficience model. Authors: Gabriel del Barrio, Juan Puigdefabregas, Maria E. Sanjuan and Alberto Ruiz.
R to LaTeX and HTML. Authors: Christophe Genolini, Bernard Desgraupes, Lionel Riou Franca.
R code for Stock Synthesis. Authors: Ian Taylor, Ian Stewart, Tommy Garrison, Andre Punt, John Wallace, and other contributors.
Extensible Markov Model (EMM) for data stream clustering in R. Authors: Michael Hahsler and Margaret H. Dunham.
A parallel analysis with polychoric correlation matrices. Author: Fabio Presaghi and Marta Desimoni.
A package for easy generation of biodiversity (species richness) or life-history traits maps using species geographical ranges. Authors: Mihai Valcu and James Dale.
Geographic analysis and modeling with raster data. Author: Robert J. Hijmans and Jacob van Etten.
Lab for testing and developing recommender algorithms for binary data. Author: Michael Hahsler.
Remix your data. Author: David Hajage.
R genetic programming framework. Authors: Oliver Flasch, Olaf Mersmann, Thomas Bartz-Beielstein and Joerg Stork.
RIS package for bibliographic analysis. Author: Stephanie Kovalchik.
toolbox for WELL random number generators. Authors: C code by F. Panneton, P. L’Ecuyer and M. Matsumoto; R port by Christophe Dutang and Petr Savicky.
ROC based classification. Author: Martin Lauss.
Statistics for psychiatric research. Author: Yasuyuki Okumura.
Redis client for R. Author: B. W. Lewis.
Generic rule engine for R. Authors: Oliver Flasch, Olaf Mersmann, Thomas Bartz-Beielstein.
For mapping global data: rworldmap. Authors: Andy South, with contributions from Barry Rowlingson, Roger Bivand, Matthew Staines and Pru Foster. In view: Spatial.
A collection of sample size functions. Author: Ralph Scherer.
Survey sampling procedures. Authors: Juliane Manitz, contributions by Mark Hempelmann, Kauermann, Helmut Küchenhoff, Cornelia Oberhauser, Nina Westerheide, Manuel Wiesenfarth.
Small-Sample Adjustments for Wald tests Using Sandwich Estimators. Author: Michael Fay.
Optimization toolkit for pharmacokinetic-pharmacodynamic models. Author: Sebastien Bihorel.
Tools for scraping data from HTML and XML documents. Author: Ryan M. Acton.
Spatially explicit capture-recapture. Author: Murray Efford.
Structural Equation Modeling using Partial Least Squares. Author: Armin Monecke.
Principal stratification sensitivity analysis functions. Author: Charles Dupont.
Swedish inflation forecast data set. Author: Michael Lundholm.
Simulation of synthetic populations for surveys based on sample data. Authors: Stefan Kraft and Andreas Alfons.
SISUS: Stable Isotope Sourcing using Sampling. Author: Erik Barry Erhardt.
t-test with Graph of Standardized Mean Difference, and More. Authors: David W. Gerbing, School of Business Administration, Portland State University.
Solar photovoltaic aystems. Author: Oscar Perpiñán Lamigueiro.
Controlling the Generalized Familywise Error Rate. Authors: L. Finos and A. Farcomeni.
Species Association Analysis. Author: Jinlong Zhang Qiong Ding Jihong Huang.
Sparse PArtial Correlation Estimation. Authors: Jie Peng , Pei Wang, Nengfeng Zhou and Ji Zhu.
Perform sparse hierarchical clustering and sparse k-means clustering. Authors: Daniela M. Witten and Robert Tibshirani.
Sparklines and graphical tables for TeXand HTML. Authors: Alexander Kowarik, Bernhard Meindl and Stefan Zechner.
The sparr package: SPAtial Relative Risk. Authors: T.M. Davies, M.L. Hazelton and J.C. Marshall.
Semiparametric estimating functions. Authors: Xiaojing Wang and Jun Yan.
Spatial models with heteroskedastic innovations. Author: Gianfranco Piras.
Prediction and variable selection using spike and slab regression. Author: Hemant Ishwaran.
Spatio-Temporal Analysis and Modelling. Author: Zhijie Zhang.
Testing steepness of dominance hierarchies. Author: David Leiva and Han de Vries.
Build stock models and analyze stock portfolios. Authors: David Diez and Nicolas Christou. In view: Finance.
R functions for solving stoichiometric equations. Author: Peter Reichert.
Univariate stratification of survey populations. Authors: Sophie Baillargeon and Louis-Paul Rivest.
Toolkit for the plotting and analysis of stratigraphic and palaeontological data. Author: Walton A. Green.
Make it easier to work with strings. Author: Hadley Wickham.
Presmoothed estimation in survival analysis. Authors: Ignacio Lopez-de-Ullibarri and Maria Amalia Jacome.
Symbol plots. Author: Jaroslav Myslivec.
Symbolic central moments of the multivariate normal distribution. Author: Kem Phillips.
Robust trimmed clustering. Authors: Agustín Mayo Iscar, Luis Angel García Escudero and Heinrich Fritz.
Testthat code. Tools to make testing fun :). Author: Hadley Wickham.
Functions to compute and plot tracheidograms. Authors: Marcelino de la Cruz and Lucia DeSoto.
Topic models. Authors: Bettina Grün and Kurt Hornik.
Implement tour methods in pure R code. Authors: Dianne Cook and Hadley Wickham.
A Tour GUI using gWidgets. Authors: Bei, Dianne Cook, and Hadley Wickham.
An interface for creating GUIs modeled in part after traits UI module for Python. Author: John Verzani.
Truncated exact test for two-stage case-control design for studying rare genetic variants. Authors: Schaid DJ and Sinnwell JP.
Detection of disease-associated SNP interactions in case-parent trio data. Authors: Qing Li and Holger Schwender.
T-distributed Stochastic Neighbor Embedding for R (t-SNE). Author: Justin Donaldson.
Translate neurodevelopmental event timing across species. Author: Radhakrishnan Nagarajan.
Interactive manipulation of R expressions. Authors: Oliver Flasch and Olaf Mersmann.
QTL Mapping for Point-mass Mixtures. Author: Sandra L. Taylor.
Open Source Development with UML and R. Author: Charlotte Maia.
Models for Data from Unmarked Animals. Authors: Ian Fiske and Richard Chandler.
vcd additions. Authors: Michael Friendly with Heather Turner, David Firth, Achim Zeileis and Duncan Murdoch.
Functions to use vegetation databases (Turboveg) for vegetation analyses in R. Author: Florian Jansen.
Venn and Euler Diagrams. Author: Lee Wilkinson.
Visualization of Missing Values. Author: Waqas Ahmed Malik.
Waterfall Charts in R. Authors: James P. Howard, II.
Computes credible intervals for Bayesian wavelet shrinkage. Author: Stuart Barber.
Create graphics for the web from R. Author: Shane Conway.
Exploring water quality monitoring data. Authors: Alan D. Jassby and James E. Cloern.
Read, write, format Excel 2007 (xlsx) files. Author: Adrian A.
Dragulescu.
Package required jars for the xlsx package. Author: Adrian A. Dragulescu.
Bayesian Inference for Zero-Inflated Count Models. Author: Markus Jochmann. In view: Bayesian.
The following packages were moved to the Archive: CTFS, ComPairWise, DICOM, GFMaps, HFWutils, IQCC, JointGLM, MIfuns, RGrace, RII, SimHap, SoPhy, adapt, agce, agsemisc, assist, cir, connectedness, dirichlet, empiricalBayes, gcl, gtm, latentnetHRT, markerSelectionPower, mcgibbsit, networksis, nlts, popgen, poplab, qdg, r2lUniv, rankreg, spatclus, staRt, sublogo, tdist, tutoR, vabayelMix, and varmixt.
The following packages were resurrected from the Archive: ProbForecastGOP, SciViews, apTreeshape, far, norm, vardiag and xlsReadWrite.
Package atm was renamed to amba.
This article is converted from a Legacy LaTeX article using the texor package. The pdf version is the official version. To report a problem with the html, refer to CONTRIBUTE on the R Journal homepage.
Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".
For attribution, please cite this work as
Hornik & Zeileis, "Changes on CRAN", The R Journal, 2010
BibTeX citation
@article{RJ-2010-1-cran,
author = {Hornik, Kurt and Zeileis, Achim},
title = {Changes on CRAN},
journal = {The R Journal},
year = {2010},
note = {https://rjournal.github.io/},
volume = {2},
issue = {1},
issn = {2073-4859},
pages = {72-84}
}