NCEAS

These pages present technical documentation selected by the NCEAS Scientific Computing staff for use by NCEAS associates learning and using The R Programming Language in their research activities.

The current page contains links to tutorials covering R Language essentials and recommended by NCEAS Scientific Computing personnel.

*** New ***An excellent set of R programming and analysis tutorials R Ecology and Epidemiology produced by the American Phytopathology Society (APS). Five chapters containing in-depth examples of widely used statistical and spatial analysis methods implemented using R.

The R Spatial Data Processing Workshop (February 2009) This page contains links to lecture notes and R scripts that demonstrate common spatial analysis tasks

The R Language Short Course page contains links to course materials from an introductory R programming seminar presented at NCEAS in Spring, 2005

The R Language Special Topics page contains links to reports describing specific R Language add-on packages and advanced geospatial and geostatistical analysis methods that incorporate the R Language.

Scientific Computing Services encourages contributions to this page. Please send your suggestions: email Scientific Computing Services

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Comprehensive R Archive Network (CRAN) Documentation Portals:

The R Contributed Packages page contains a comprehensive list of available packages, with links to the 'home page' for each available package.

To search for and access R package user manuals, click here.

The R FAQ page contains links to Frequently Asked Question and HOWTO lists.

The Rseek.org search portal is a great starting point for your R technique / package / resource search.

Tutorials and introductory materials:

The R Reference Card: Concise R Language reference

The major features of the R language, in a 4-page desktop reference format

University of Bristol (UK) Statistics Group: R: A Self-Learn Tutorial (160 kb PDF)

The basics of the R session: command lines, R objects, and simple statistical and graphics operations.

The R Development Core Team: An Introduction to R (640 kb PDF)

A comprehensive Introduction to all aspects of the R programming environment, derived from the development team's notes. Strongly Recommended.

Universite Montpellier (FR): R For Beginners (440 kb PDF)

An in-depth R introduction designed for life scientists. A good starting point, strong on R concepts.

Paul Johnson's R Tips page

Many good R scripting and data handling techniques, gathered from the RHelp list

Peter Adler's R Cheat Sheet (16 kb PDF)

Concise summary of useful R functions compiled by a former NCEAS Postoc and R 'Power User'

R Documentation: Software Installation, Package Development, Systems Administration, and Data Management

R Installation and Administration (427 kb PDF)

A guide to installation and administration for R.

R Data Import and Export (132 kb PDF)

A guide to importing and exporting data to an from the R programming environment.

Writing R Extensions (733 kb PDF)

Techniques for extending R: Creating R add-on packages, writing R documentation, R external interfaces.

R Internals (323 kb PDF)

The internal structures of the R programming environment: information for programmers working on R language core.

R Language Definition (397 kb PDF)

A formal introduction to the R language: syntax parsing, evaluation, object-oriented programming, and other topics

R Reference Manuals - NOTE: These are LARGE PDF files - 'Download With Care'

R Language and Environment Reference (Base Pkg) (8 Megabytes)

R Language and Environment Reference (Base Pkg & Support) (14 Megabytes)

R Special Application ('Add-On' ) Package Documentation Download Center

Select (single-click) an R package title from this list: View / download the latest PDF-format user manual for that package.

ADaCGH - Analysis of data from aCGH experiments AER - Applied Econometrics with R AIS - Tools to look at the data ("Ad Inidicia Spectata") ALS - multivariate curve resolution alternating least squares (MCR-ALS) AMORE - A MORE flexible neural network package ARES - Allelic richness estimation, with extrapolation beyond the sample size AcceptanceSampling - Creation of Acceptance Sampling Plans :AdMit - Adaptive Mixture of Student-t distributions AdaptFit - Adaptive Semiparametic Regression AlgDesign - AlgDesign Amelia - Amelia II: A Program for Missing Data AnalyzeFMRI - Functions for analysis of fMRI datasets ArDec - Time series autoregressive-based decomposition aaMI - Mutual information for protein sequence alignments abind - Combine multi-dimensional arrays accuracy - Tools: testing/improving accuracy of statistical results acepack - ace() and avas() for selecting regression transformations actuar - Actuarial functions ada - Performs boosting algorithms for a binary response adabag - Applies Adaboost.M1 and Bagging adapt - adapt -- multidimensional numerical integration ade4 - Ecological Data Analysis : Explor and Euclidean methods in Env sciences ade4TkGUI - ade4 Tcl/Tk Graphical User Interface adegenet - R package for the multivariate analysis of genetic markers adehabitat - Analysis of habitat selection by animals adimpro - Adaptive Smoothing of Digital Images adk - Anderson-Darling K-Sample Test and Combinations of Such Tests adlift - An adaptive lifting scheme algorithm ads - Spatial point patterns analysis agce - analysis of growth curve experiments agricolae - Statistical Procedures for Agricultural Research agsemisc - Miscellaneous plotting and utility functions akima - Interpolation of irregularly spaced data allelic - A fast, unbiased and exact allelic exact test alr3 - Methods and data to accompany Applied Linear Regression 3rd edition amap - Another Multidimensional Analysis Package anacor - Simple and Canonical Correspondence Analysis analogue - Analogue and weighted averaging methods for palaeoecology anapuce - Tools for microarray data analysis animation - Demonstrate Animations in Statistics anm - Analog model for downscaling aod - Analysis of Overdispersed Data apTreeshape - Analyses of Phylogenetic Treeshape ape - Analyses of Phylogenetics and Evolution aplpack - Another Plot PACKage: stem.leaf, bagplot, faces, spin3R, .. apsrtable - apsrtable model-output formatter for social science argosfilter - Argos locations filter arm - Data Analysis Using Regression and Multilevel/Hierarchical Models arrayImpute - Missing imputation for microarray data arrayMissPattern - Explor analysis of Missing microarray patterns ars - Adaptive Rejection Sampling arules - Mining Association Rules and Frequent Itemsets arulesSequences - Mining frequent sequences ash - David Scott's ASH routines aspace - Ffunctions for estimating centrographic statistcs spatial point patterns assist - A Suite of S-Plus Functions Implementing Smoothing Splines aster - Aster Models asuR - Advanced statistics using R asypow - Calculate Power Utilizing Asymptotic Likelihood Ratio Methods audio - Audio Interface for R aws - Adaptive Weights Smoothing BACCO - Bayesian Analysis of Computer Code Output BARD - Better Automated ReDistricting BAYSTAR - On Bayesian analysis of Threshold autoregressive model (BAYSTAR) BB - Solving and optimizing large-scale nonlinear systems BCE - Bayesian composition estimator: estimating sample (taxonomic) composition BHH2 - Useful Functions for Box, Hunter and Hunter II BLCOP - Black-Litterman and copula-opinion pooling frameworks BMA - Bayesian Model Averaging BPHO - Bayesian Prediction with High-order Interactions BSDA - Basic Statistics and Data Analysis BaM - Functions and datasets for books by Jeff Gill BayHaz - R Functions for Bayesian Hazard Rate Estimation BayesTree - Bayesian Methods for Tree Based Models BayesValidate - BayesValidate Package Bchron - Create chronologies based on radiocarbon and non-radiocarbon dated depths Bhat - General likelihood exploration BiasedUrn - Biased Urn model distributions BioIDMapper - Mapping between BioIDs Biodem - Biodemography functions BiodiversityR - GUI for biodiversity and community ecology analysis BiplotGUI - Interactive Biplots in R Bolstad - Bolstad functions BootCL - Bootstrapping test for chromosomal localization BootPR - Bootstrap Prediction Intervals and Bias-Corrected Forecasting BradleyTerry - Bradley-Terry models Brobdingnag - Very large numbers in R BsMD - Bayes Screening and Model Discrimination backfitRichards - Backfitted independent values of Richards curves backtest - Exploring portfolio-based conjectures about financial instruments bark - Bayesian Additive Regresssion Kernels bayesGARCH - Bayesian Estimation of the GARCH(1,1) Model with Student's t Innovations bayesSurv - Bayesian Survival Regression w/Flexible Error and Random Effects Distributions bayescount - Bayesian analysis of count distributions with JAGS bayesm - Bayesian Inference for Marketing/Micro-econometrics bayesmix - Bayesian Mixture Models with JAGS bbmle - Tools for general maximum likelihood estimation bcp - A Package for Performing a Bayesian Analysis of Change Point Problems bear - Average bioequivalence and bioavailability data analysis tool benchden - 28 benchmark densities from Berlinet/Devroye (1994) bentcableAR - Bent-Cable Regression for Independent Data or Autoregressive Time Series betaper - Distance decay of similarity among biological inventories in taxonomic uncertainty betareg - Beta Regression biOps - Image processing and analysis biOpsGUI - GUI for Basic image operations biclust - BiCluster Algorithms bicreduc - Reduction algorithm for NPMLE for the distribution function of bivariate data bifactorial - Inferences for bi- and trifactorial trial designs biglm - bounded memory linear and generalized linear models bigmemory - Manage massive matrices in R using C++, with UNIX support for shared memory bim - Bayesian Interval Mapping Diagnostics binGroup - Evaluation and experimental design for binomial group testing binMto - Asymptotic simultaneous confdence intervals for many-to-one comparisons of proportions bindata - Generation of Artificial Binary Data binom - Binomial Confidence Intervals For Several Parameterizations bio.infer - Compute biological inferences biopara - Self-contained parallel system for R bipartite - Visualises bipartite networks and calculates some ecological indices birch - Dealing with very large datasets using BIRCH bise - Auxiliary functions for phenological data analysis bit - A class for vectors of 1-bit booleans bitops - Functions for Bitwise operations bivpois - Bivariate Poisson Models Using The EM Algorithm blighty - United Kingdom coastlines blockTools - Block/assign/diagnose potential interference in randomized experiments blockrand - Randomization for block random clinical trials bmd - Benchmark dose analysis for dose-response data bnlearn - Bayesian network structure learning boa - Bayesian Output Analysis Program (BOA) for MCMC boolean - Boolean Binary Response Models boost - Boosting Methods for Real and Simulated Data boot - Bootstrap R (S-Plus) Functions (Canty) bootStepAIC - Bootstrap stepAIC bootstrap - Functions for the Book "An Introduction to the Bootstrap" bpca - Biplot of Multivariate Data Based on Principal Components Analysis bqtl - Bayesian QTL mapping toolkit brainwaver - Basic wavelet analysis of multivar time series using graph theory brew - Templating Framework for Report Generation brglm - Bias-reduction in binomial-response GLMs bs - Package for the Birnbaum-Saunders distribution bspec - Bayesian spectral inference bvls - The Stark-Parker algorithm for bounded-variable least squares CADStat - Provides a GUI to several statistical methods useful for causal assessment CCA - Canonical correlation analysis CDNmoney - Components of Canadian Monetary and Credit Aggregates CGIwithR - CGI Programming in R CHsharp - Choi and Hall Clustering in 3d CORREP - Multivariate Correlation Estimator and Statistical Inference Procedures COZIGAM - Constrained Zero-Inflated Generalized Additive Model CPE - Concordance Probability Estimates in Survival Analysis CTFS - The CTFS Large Plot Forest Dynamics Analyses CTT - Classical Test Theory Functions CVThresh - Level-Dependent Cross-Validation Thresholding Cairo - R graphics device using cairo graphics library CarbonEL - Carbon Event Loop CellularAutomaton - One-Dimensional Cellular Automata ChainLadder - Mack- and Munich-chain-ladder methods for insurance claims reserving CircStats - Circular Statistics, from "Topics in circular Statistics" (2001) CoCo - Graphical modelling by CoCo ComPairWise - Compare phylogenetic or population genetic data alignments CombMSC - Combined Model Selection Criteria CompetingRiskFrailty - Risk Model with Frailties for Survival Data Containers - Object-Oriented Data Structures for R ConvergenceConcepts - Seeing convergence concepts in action CoxBoost - Cox survival models by likelihood based boosting CreditMetrics - Functions for calculating the CreditMetrics risk model CvM2SL1Test - L1-version of Cramer-von Mises Two Sample Tests CvM2SL2Test - Cramer-von Mises Two Sample Tests ca - Simple, Multiple and Joint Correspondence Analysis caMassClass - Processing/Classif of Protein Mass Spectra (SELDI) Data caTools - Tools: moving window statistics, GIF, Base64, ROC AUC, etc cacheSweave - Tools for caching Sweave computations cacher - Tools for caching and distributing statistical analyses cairoDevice - Cairo-based cross-platform antialiased graphics device driver calib - Statistical tool for calibration of plate based bioassays calibrate - Calibration of Biplot Axes candisc - Generalized Canonical Discriminant Analysis car - Companion to Applied Regression caret - Classification and Regression Training caretLSF - Classification and Regression Training LSF Style caretNWS - Classification and Regression Training in Parallel Using NetworkSpaces cat - Analysis of categorical-variable datasets with missing values catmap - Case-control And Tdt Meta-Analysis Package catspec - Special models for categorical variables cba - Clustering for Business Analytics ccgarch - Conditional Correlation GARCH models cclust - Convex Clustering Methods and Clustering Indexes celsius - Retrieve Affymetrix microarray meas and metadata from Celsius cem - CEM: Software for Coarsened Exact Matching cfa - Analysis of configuration frequencies (CFA) cggd - Continuous Generalized Gradient Descent cgh - Microarray CGH analysis using the Smith-Waterman algorithm cghFLasso - Detecting hot spot on CGH array data with fused lasso regression changeLOS - Change in LOS cheb - Discrete Linear Chebyshev Approximation chemCal - Calibration functions for analytical chemistry chemometrics - Multivariate Statistical Analysis in Chemometrics choplump - Choplump tests chplot - Augmented Convex Hull Plots chron - Chronological objects which can handle dates and times cir - Nonparam est of monotone functions via isotonic and centered isotonic regression circular - Circular Statistics clValid - Validation of Clustering Results clac - Clust Along Chromosomes, a method to call gains/losses in CGH array data classGraph - Construct Graphs of S4 Class Hierarchies classInt - Choose univariate class intervals classPP - Projection Pursuit for supervised classification classifly - Explore classification models in high dimensions clim.pact - Climate analysis and empirical-statistical downscaling (ESD) package climatol - Some Tools for Climatology clinfun - Clinical Trial Design and Data Analysis Functions clue - Cluster ensembles clustTool - GUI for clustering data with spatial information cluster - Cluster Analysis Extended Rousseeuw et al clusterGeneration - random cluster gen (w/specified degree of separation) clusterRepro - Reproducibility of gene expression clusters clusterSim - Searching for optimal clustering procedure for a data set clusterfly - Explore clustering interactively using R and GGobi clustvarsel - Variable Selection for Model-Based Clustering clv - Cluster Validation Techniques cmprsk - Subdistribution Analysis of Competing Risks cobs - COBS -- Constrained B-splines (Sparse matrix based) cobs99 - Constrained B-splines -- outdated 1999 version cocorresp - Co-correspondence analysis methods coda - Output analysis and diagnostics for MCMC codetools - Code Analysis Tools for R coin - Conditional Inference Procedures in a Permutation Test Framework colorRamps - Builds color tables colorspace - Colorspace Manipulation combinat - combinatorics utilities compHclust - Complementary hierarchical clustering compOverlapCorr - Comparing overlapping correlation coefficients compare - Comparing Objects for Differences compoisson - Conway-Maxwell-Poisson Distribution compositions - Compositional Data Analysis concor - Concordance concord - Concordance and reliability conf.design - Construction of factorial designs connectedness - Find disconnected subsets for a two-way classification contfrac - Continued fractions contrast - A collection of contrast methods convexHaz - Nonparametric MLE/LSE of convex hazard copas - Statistical methods to model and adjust for bias in meta-analysis copula - Multivariate dependence with copulas corpcor - Efficient Estimation of Covariance and (Partial) Correlation corpora - Statistics for corpus linguists corrgram - Plot a correlogram corrperm - Permutation Tests of Correlation with Repeated Measurements covRobust - Robust Covariance Estimation via Nearest Neighbor Cleaning coxphf - Cox regression with Firth's penalized likelihood coxphw - Weighted Cox regression coxrobust - Robust Estimation in Cox Model cramer - Multivariate nonparametric Cramer-Test for the two-sample-problem crank - Completing ranks crossdes - Design and Randomization in Crossover Studies crosshybDetector - Detection of cross-hybridization events crq - Censored Quantile Regression cslogistic - Conditionally Specified Logistic Regression cts - Continuous Time Autoregressive Models ctv - CRAN Task Views curvetest - Test the equality of two curves, or one curve with 0 cwhmisc - cwh's useful functions cyclones - Cyclone identification DAAG - Data Analysis And Graphics DAAGbio - Data Sets and Functions, for demonstrations with expression arrays DAAGxtras - Data Sets and Functions, supplementary to DAAG DBI - R Database Interface DCluster - Functions for the detection of spatial clusters of diseases DDHFm - Variance Stabilization by Data-Driven Haar-Fisz (for Microarrays) DEA - Data Envelopment Analysis DEoptim - Differential Evolution Optimization DICOM - Import medical imaging data using the DICOM Standard DPpackage - Bayesian Nonparametric and Semiparametric Analysis Davies - The Davies quantile function Defaults - Create Global Function Defaults DescribeDisplay - R interface to DescribeDisplay (GGobi plugin) Design - Design Package Devore5 - Data sets from Devore's "Prob and Stat for Eng (5th ed)" Devore6 - Data sets from Devore's "Prob and Stat for Eng (6th ed)" Devore7 - Data sets from Devore's "Prob and Stat for Eng (7th ed)" DiagnosisMed - Diagnostic test accuracy evaluation for medical professionals DierckxSpline - R companion to "Curve and Surface Fitting with Splines" data.table - Extension of data.frame. i and j expressions, keys and binary search dataframes2xls - dataframes2xls writes data frames to xls files date - Functions for handling dates dblcens - Compute the NPMLE of distribution from doubly censored data ddesolve - Solver for Delay Differential Equations ddst - Data driven smooth test deSolve - General solvers for (ODE) and (DAE) deal - Learning Bayesian Networks with Mixed Variables debug - MVB's debugger for R degreenet - Models for Skewed Count Distributions Relevant to Networks deldir - Delaunay Triangulation and Dirichlet (Voronoi) Tessellation delt - Estimation of multivariate densities with adaptive histograms demogR - Analysis of age-structured demographic models denpro - Visualization of multivariate, functions, sets, and data denstrip - Density strips and other methods for compactly illustrating distributions depmix - Dependent Mixture Models depmixS4 - Dependent Mixture Models desirability - Desirabiliy Function Optimization and Ranking dfcrm - Dose-finding by the continual reassessment method dglm - Double generalized linear models diagram - Functions for visualising simple graphs (networks), plotting flow diagrams diamonds - Analysis and sampling grids from diamond partitions dice - Calculate probabilities of various dice-rolling events dichromat - Color schemes for dichromats diffractometry - Baseline id/peak decomposition for x-ray diffractograms digest - Create cryptographic hash digests of R objects diptest - Hartigan's dip test statistic for unimodality - corrected code dirichlet - Dirichlet model of consumer buying behavior for marketing research dispmod - Dispersion models distr - Object orientated implementation of distributions distrDoc - Documentation for packages distr, distrEx, distrSim, distrTEst distrEx - Extensions of package distr distrMod - Object orientated implementation of probability models distrSim - Simulation classes based on package distr distrTEst - Estimation and Testing classes based on package distr distrTeach - Package distr ext for teaching Stochastics/Statistics distributions - Probability distributions based on TI-83 Plus divagis - Provides tools for quality checks of georeferenced plant species accessions diveMove - Dive analysis and calibration dlm - Bayesian and Likelihood Analysis of Dynamic Linear Models doBy - Groupwise computations of summary statistics and other utilities dplR - Dendrochronology Program Library in R dprep - Data preprocessing and visualization functions for classification dr - Methods for dimension reduction for regression drc - Analysis of dose-response curves drfit - Dose-response data evaluation drm - Regression and association models for repeated categorical data dse - Bundle of dse1, dse2 dti - DTI Analysis dtt - Discrete Trigonometric Transforms dtw - Dynamic Time Warping algorithms dyn - Time Series Regression dynamicGraph - dynamicGraph dynamicTreeCut - Methods for heierarchical cluster detection dynamo - Dynamic Models dynlm - Dynamic Linear Regression EDR - Estimation of the effective dimension reduction (EDR) space EMC - Evolutionary Monte Carlo (EMC) algorithm EMCC - Evolutionary Monte Carlo (EMC) methods for clustering EMD - Empirical Mode Decomposition and Hilbert Spectral Analysis EMV - Estimation of Missing Values for a Data Matrix ETC - Tests and simultaneous confidence intervals for equivalence to control EVER - Estimation of Variance by Efficient Replication EbayesThresh - Empirical Bayes thresholding and related methods Ecdat - Data sets for econometrics EffectiveDose - Effective Dose estimation inc Bootstrap conf intervals ElemStatLearn - Data sets, functions and examples from book: Hastie, et.al Epi - A package for statistical analysis in epidemiology e1071 - Misc Functions of the Department of Statistics (e1071), TU Wien eRm - Extended Rasch Modeling earth - Multivariate Adaptive Regression Spline Models eba - Elimination-By-Aspects (EBA) Models ecespa - Functions for spatial point pattern analysis eco - R Package for Ecological Inference in 2x2 Tables ecodist - Dissimilarity-based functions for ecological analysis ecolMod - "A practical guide to ecological modelling - using R as a simulation platform" effects - Effect Displays for Linear and Generalized Linear Models eha - Event History Analysis eiPack - eiPack: Ecological Inference and Higher-Dimension Data Management eigenmodel - Semiparametric factor and regression models for symmetric relational data elasticnet - Elastic-Net for Sparse Estimation and Sparse PCA ellipse - Functions for drawing ellipses and ellipse-like confidence regions elliptic - elliptic functions elrm - Exact Logistic Regression via MCMC emdbook - Ecological models and data (book support) emme2 - Read and Write to an EMME/2 databank empiricalBayes - Bundle of HighProbability, localFDR emplik - Empirical likelihood ratio for censored/truncated data emu - Interface to the Emu Speech Database System energy - E-statistics (energy statistics) ensembleBMA - Probabilistic Forecasting using Ensembles and Bayesian Model Averaging entropy - Entropy and Mutual Information Estimation epiR - Functions for analysing epidemiological data epibasix - Elementary Epidemiological Functions for a Graduate Epidemiology\Biostatistics Course epicalc - Epidemiological calculator epitools - Epidemiology Tools eqtl - Tools for analyzing eQTL experiments: A complementary to Karl Broman's 'qtl' package equivalence - Provides tests and graphics for assessing tests of equivalence ergm - Fit, Simulate and Diagnose Exponential-Family Models for Networks etm - Empirical Transition Matrix evd - Functions for extreme value distributions evdbayes - Bayesian Analysis in Extreme Value Theory evir - Extreme Values in R exactLoglinTest - Monte Carlo Exact Tests for Log-linear models exactRankTests - Exact Distributions for Rank and Permutation Tests exactmaxsel - Maximally selected statistics for binary response variables experiment - experiment: R package for designing and analyzing randomized experiments expert - Modeling without data using expert opinion extRemes - Extreme value toolkit FAiR - Factor Analysis in R FGN - Fractional Gaussian Noise Model Fitting FITSio - FITS (Flexible Image Transport System) utilities FKBL - fuzzy knowledge base learning FTICRMS - Programs for Analyzing Fourier Transform-Ion Cyclotron Data FactoMineR - Factor Analysis and Data Mining with R Fahrmeir - Data from the Ludwig Fahrmeir book FieldSim - Random fields simulations FinTS - Companion to Tsay (2005) Analysis of Financial Time Series FitAR - Subset AR Model Fitting Flury - Data Sets from Flury, 1997 FrF2 - Package for analysing Fractional Factorial designs with 2-level factors FracSim - Simulation of Lévy motions FunCluster - Functional Profiling of Microarray Expression Data FunNet - Integrative Functional Analysis of Transcriptional Networks fArma - Rmetrics - ARMA Time Series Modelling fAsianOptions - Rmetrics - EBM and Asian Option Valuation fAssets - Rmetrics - Assets Selection and Modelling fBasics - Rmetrics - Markets and Basic Statistics fBonds - Rmetrics - Bonds and Interest Rate Models fCalendar - Rmetrics - Chronological and Calendarical Objects fCopulae - Rmetrics - Dependence Structures with Copulas fEcofin - Rmetrics - Economic and Financial Data Sets fExoticOptions - Rmetrics - Exotic Option Valuation fExtremes - Rmetrics - Extreme Financial Market Data fGarch - Rmetrics - Autoregressive Conditional Heteroskedastic Modelling fImport - Rmetrics - Economic and Financial Data Import fMultivar - Rmetrics - Multivariate Market Analysis fNonlinear - Rmetrics - Nonlinear and Chaotic Time Series Modelling fOptions - Rmetrics - Basics of Option Valuation fPortfolio - Rmetrics - Portfolio Selection and Optimization fRegression - Rmetrics - Regression Based Decision and Prediction fSeries - Rmetrics - Financial Time Series Objects fTrading - Rmetrics - Technical Trading Analysis fUnitRoots - Rmetrics - Trends and Unit Roots fUtilities - Rmetrics - Rmetrics Function Utilities fame - Interface for FAME time series database far - Modelization for Functional AutoRegressive processes faraway - Functions and datasets for books by Julian Faraway fastICA - FastICA Algorithms to perform ICA and Projection Pursuit fbati - Gene by Environment Interaction Tests fda - Functional Data Analysis fdim - Functions for calculating fractal dimension fdrtool - Estimation and Control of (Local) False Discovery Rates feature - Feature significance for multivariate kernel density estimation femmeR - Output analysis of FEMME model results ff - memory-efficient storage of large atomic vectors and arrays ffmanova - Fifty-fifty MANOVA fgac - Generalized Archimedean Copula fgui - Function GUI fields - Tools for spatial data filehash - Simple key-value database filehashSQLite - Simple key-value database using SQLite financial - Solving financial problems in R fingerprint - Functions to operate on binary fingerprint data flexclust - Flexible Cluster Algorithms flexmix - Flexible Mixture Modeling fmri - Analysis of fMRI experiments forecasting - Bundle of forecast, fma, Mcomp, expsmooth foreign - Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, .. forensic - Statistical Methods in Forensic Genetics fork - R functions for handling multiple processes fortunes - R Fortunes forward - Forward search fossil - Palaeoecological and Palaeogeographical Analysis Tools fpc - Fixed point clusters, clusterwise regression and discriminant plots fpca - Restricted MLE for Functional Principal Components Analysis fracdiff - Fractionally differenced ARIMA aka ARFIMA(p,d,q) models fractal - Insightful Fractal Time Series Modeling and Analysis frailtypack - Frailty models using maximum penalized likelihood estimation fso - Fuzzy Set Ordination ftnonpar - Features and Strings for Nonparametric Regression fts - R interface to tslib (a time series library in c++) fuzzyFDR - Exact calculation of fuzzy decision rules for multiple testing fuzzyOP - Fuzzy numbers and the main mathematical operations fuzzyRankTests - Fuzzy Rank Tests and Confidence Intervals fxregime - Exchange Rate Regime Analysis G1DBN - A package performing Dynamic Bayesian Network inference GAMBoost - Generalized additive models by likelihood based boosting GDD - GD device for creating bitmap graphics as jpeg, png or gif files using gd library GEOmap - Topographic and Geologic Mapping GExMap - R functions for analysis genomic distribution of genes lists GLDEX - Fitting Single and Mixture of Generalised Lambda Distributions (RS and FMKL) GOSim - Computation of functional similarities between GO terms and gene products GPArotation - GPA Factor Rotation GRASS - Interface between GRASS 5.0 geographical information system and R GSA - Gene set analysis GSM - Gamma Shape Mixture GenABEL - genome-wide SNP association analysis GenKern - Functions for generating and manipulating kernel density estimates GeneCycle - Identification of Periodically Expressed Genes GeneF - Package for Generalized F-statistics GeneNT - Relevance or Dependency network and signaling pathway discovery GeneNet - Modeling and Inferring Gene Networks GeneTS - Microarray Time Series and Network Analysis Geneland - Simulation and MCMC inference of structure from genetic data GeoXp - Interactive exploratory spatial data analysis GillespieSSA - Gillespie's Stochastic Simulation Algorithm (SSA) GroupSeq - Performing computations related to group sequential designs g.data - Delayed-Data Packages gRain - Graphical Independence Networks gRbase - A package for graphical modelling in R gRc - Inference in Graphical Gaussian Models with Edge and Vertex Symmetries gWidgets - gWidgets API for building toolkit-independent, interactive GUIs gWidgetsRGtk2 - Toolkit implementation of gWidgets for RGtk2 gWidgetsWWW - Toolkit implementation of gWidgets for www gWidgetsrJava - Toolkit implementation of gWidgets for rJava gWidgetstcltk - Toolkit implementation of gWidgets for tcltk package gafit - Genetic Algorithm for Curve Fitting gam - Generalized Additive Models gamair - Data for "GAMs: An Introduction with R" gamlss - Generalized Additive Models for Location Scale and Shape gamlss.cens - Fitting an interval response variable using gamlss.family distributions gamlss.dist - Extra distributions to be used for GAMLSS modelling gamlss.mx - A GAMLSS add on package for fitting mixture distributions gamlss.nl - Fitting non linear parametric GAMLSS models gamlss.tr - Generating and fitting truncated (gamlss.family) distributions gap - Genetic analysis package gbev - Gradient Boosted Regression Trees with Errors-in-Variables gbm - Generalized Boosted Regression Models gbs - Package for Generalized Birnbaum-Saunders Distributions gcl - Compute a fuzzy rules or tree classifier from data gclus - Clustering Graphics gcmrec - General class of models for recurrent event data gdata - Various R programming tools for data manipulation gee - Generalized Estimation Equation solver geepack - Generalized Estimating Equation Package geiger - Analysis of evolutionary diversification genalg - R Based Genetic Algorithm gene2pathway - Prediction of KEGG pathway membership for individual genes genetics - Population Genetics geoR - Analysis of geostatistical data geoRglm - geoRglm - a package for generalised linear spatial models geomapdata - Data for topographic and Geologic Mapping geometry - Mesh generation and surface tesselation geozoo - Zoo of Geometric Objects getopt - C-like getopt behavior ggm - Graphical Gaussian Models ggplot2 - An implementation of the Grammar of Graphics ghyp - A package on the generalized hyperbolic distribution and its special cases giRaph - The giRaph package for graph representation in R gibbs.met - Naive Gibbs Sampling with Metropolis Steps glasso - Graphical lasso- estimation of Gaussian graphical models gld - Estimation and use of the generalised (Tukey) lambda distribution gllm - Generalised log-linear model glmc - Fitting Generalized Linear Models Subject to Constraints glmmAK - Generalized Linear Mixed Models glmmBUGS - Generalised Linear Mixed Models with WinBUGS glmmML - Generalized linear models with clustering glmnet - Lasso and elastic-net regularized generalized linear models glmpath - L1 Regularization Path for Ge. Linear Models and Cox Hazards Model glpk - GNU Linear Programming Kit gmaps - Wrapper and auxilliary functions for maps package to work with grid graphics system gmodels - Various R programming tools for model fitting gmp - Multiple Precision Arithmetic gmt - Interface between GMT map-making software and R gmvalid - Validation of graphical models gnm - Generalized Nonlinear Models gnomeGUI - GNOME Console for R goalprog - Weighted and lexicographical goal programming and optimization gpclib - General Polygon Clipping Library for R gplots - Various R programming tools for plotting data gpls - Classification using generalized partial least squares grImport - Importing Vector Graphics grade - Grade granova - Graphical Analysis of Variance graph - graph: A package to handle graph data structures grasp - Generalized Regression Analysis and Spatial Prediction for R gregmisc - Greg's Miscellaneous Functions gridBase - Integration of base and grid graphics grnnR - A Generalized Regression Neural Network grouped - Regression Analysis of Grouped and Coarse Data grplasso - Fitting user specified models with Group Lasso penalty gsarima - Two functions for Generalized SARIMA time series simulation gsl - wrapper for the Gnu Scientific Library gss - General Smoothing Splines gstat - geostatistical modelling, prediction and simulation gsubfn - Utilities for strings and function arguments gtm - Generative topographic mapping gtools - Various R programming tools gumbel - Gumbel copula gvlma - Global Validation of Linear Models Assumptions HAPim - HapIM HFWutils - csv import, csv export, garbage collection, string matching and pass by ref HH - Statistical Analysis and Data Display: Heiberger and Holland HI - Simulation from distributions supported by nested hyperplanes HSAUR - A Handbook of Statistical Analyses Using R HTMLapplets - Dynamic visualisation in HTML documents HardyWeinberg - Graphical tests for Hardy-Weinberg equilibrium HiddenMarkov - Hidden Markov Models Hmisc - Harrell Miscellaneous HydroMe - Estimation of Soil Hydraulic Parameters from Experimental Data HyperbolicDist - The hyperbolic distribution hapassoc - Inference of trait associations with SNP haplotypes and other attributes haplo.ccs - Estimate Haplotype Relative Risks in Case-Control Data haplo.stats - Statistical Analysis of Haplotypes with Traits and Covariates hapsim - Haplotype Data Simulation hbim - Hill/Bliss Independence Model for Combination Vaccines hddplot - Use known groups in high-dimensional data to derive scores for plots hdeco - Hierarchical DECOmposition of Entropy for Categorical Map Comparisons hdf5 - HDF5 hdrcde - Highest density regions and conditional density estimation heatmap.plus - Heatmap with more sensible behavior helloJavaWorld - Hello Java World heplots - Visualizing Tests in Multivariate Linear Models hett - Heteroscedastic t regression hexView - Viewing Binary Files hier.part - Hierarchical Partitioning hierfstat - Estimation and tests of hierarchical F-statistics hints - Provide hints on what to do next hlr - Hidden Logistic Regression hmm.discnp - Hidden Markov models with discrete non-parametric observation dist hoa - Bundle of cond, marg, nlreg, csampling homals - Homogeneity Analysis homtest - Homogeneity tests for Regional Frequency Analysis hopach - Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) hot - Computation on micro-arrays howmany - A lower bound for the number of correct rejections hsmm - Hidden Semi Markov Models httpRequest - Basic HTTP Request hwde - Models and tests for departure from Hardy-Weinberg equilibrium and loci independence hwriter - HTML Writer - Outputs R objects in HTML format hybridHclust - Hybrid hierarchical clustering hydrogeo - Groundwater data presentation and interpretation hydrosanity - Graphical user interface for exploring hydrological time series hypergeo - The hypergeometric function IBrokers - R API to Interactive Brokers Trader Workstation ICE - Iterated Conditional Expectation ICEinfer - Incremental Cost-Effectiveness (ICE) Inference (from Two Unbiased Samples) ICS - Tools for Exploring Multivariate Data via ICS/ICA ICSNP - Tools for Multivariate Nonparametrics IDPmisc - Utilities of Institute of Data Analyses and Process Design (www.idp.zhaw.ch) ISA - INTRODUZIONE ALLA STATISTICA APPLICATA con esempi in R ISOcodes - Selected ISO codes ISwR - Introductory Statistics with R Icens - NPMLE for Censored and Truncated Data Iso - Functions to perform isotonic regression ibdreg - Regression Methods for IBD Linkage With Covariates ic.infer - Inequality constrained inference in linear normal situations ic50 - Standardized high-throughput evaluation of compound screens icomp - ICOMP criterion identity - Jacquard Condensed Coefficients of Identity ifa - Independent Factor Analysis ifs - Iterated Function Systems ifultools - Insightful Research Tools ig - Package for a General Class of Inverse Gaussian Distributions igraph - Routines for simple graphs, network analysis iid.test - iid-test impute - impute: Imputation for microarray data imputeMDR - The Multifactor Dimensionality Reduction (MDR) Analysis for Imcomplete Data ineq - Measuring inequality, concentration and poverty inetwork - Network Analysis and Plotting inline - Inline C, C++, Fortran function calls from R intcox - Iterated Convex Minorant Algorithm for interval censored event data intervals - Tools for working with points and intervals iplots - iPlots - interactive graphics for R ipred - Improved Predictors irr - Various Coefficients of Interrater Reliability and Agreement irtoys - Simple interface to the estimation and plotting of IRT models ismev - An Introduction to Statistical Modeling of Extreme Values its - Irregular Time Series ivivc - in vitro-in vivo correlation (IVIVC) modeling JADE - JADE and ICA performance criteria JGR - JGR - Java Gui for R JM - Joint Modelling of Longitudinal and Survival Data JavaGD - Java Graphics Device JointGLM - Joint Modelling of Mean and Dispersion (outdated, see JointModeling) JointModeling - Joint Modelling of Mean and Dispersion JudgeIt - JudgeIt jit - Just-in-time compiler for the R language KMsurv - Data sets from Klein and Moeschberger (1997), Survival Analysis Kendall - Kendall rank correlation and Mann-Kendall trend test KernSmooth - Functions for kernel smoothing for Wand & Jones (1995) kappalab - Non-additive measure and integral manipulation functions kerfdr - semi-parametric kernel-based approach to local fdr estimations kernelPop - Spatially explicit population genetic simulations kernlab - Kernel-based Machine Learning Lab kin.cohort - Analysis of kin-cohort studies kinship - mixed-effects Cox models/sparse matrices/modeling data from large pedigrees kknn - Weighted k-Nearest Neighbors klaR - Classification and visualization klin - Linear equations with Kronecker structure kml - K-Means for Longitudinal data knnFinder - Fast Near Neighbour Search knnTree - k-nn classification with variable selection inside leaves of a tree knncat - Nearest-neighbor classification with categorical variables knnflex - A more flexible KNN knorm - Microarray Data From Multiple Biologically Interrelated Experiments kohonen - Supervised and unsupervised self-organising maps ks - Kernel smoothing kza - Kolmogorov-Zurbenko Adaptive Filters kzft - Kolmogorov-Zurbenko Fourier Transform and Applications kzs - Kolmogorov-Zurbenko Spline Smoothing and Applications LDheatmap - Graphical display of pairwise linkage disequilibria between SNPs LDtests - Exact tests for Linkage Disequilibrium and Hardy-Weinberg Equilibrium LIStest - Longest Increasing Subsequence Independence Test LLAhclust - Hierarchical clustering of variables/objects:likelihood linkage analysis LLN - Learning with latent networks LMGene - LMGene Software for Date Transformation and Identification of Diff Expressed Genes LearnBayes - Functions for Learning Bayesian Inference Lmoments - L-moments and quantile mixtures LogConcDEAD - Maximum likelihood estimation of a log-concave density LogicReg - Logic Regression LoopAnalyst - A collection of tools to conduct Levins' Loop Analysis LowRankQP - Low Rank Quadratic Programming labdsv - Ordination and Multivariate Analysis for Ecology labstatR - Libreria del Laboratorio di Statistica con R laercio - Duncan test, Tukey test and Scott-Knott test lago - An efficient kernel algorithm for rare target detection and unbalanced classification lancet.iraqmortality - Surveys of Iraq Mortality Published in The Lancet languageR - Data sets and functions with "Analyzing Linguistic Data:" lars - Least Angle Regression, Lasso and Forward Stagewise laser - Likelihood Analysis of Speciation/Extinction Rates from Phylogenies lasso2 - L1 constrained estimation aka 'lasso' latentnet - Latent position and cluster models for statistical networks latentnetHRT - Latent position and cluster models for statistical networks lattice - Lattice Graphics latticeExtra - Extra Graphical Utilities Based on Lattice lawstat - A R package for biostatistics, public policy and law lazy - Lazy Learning for Local Regression ldDesign - Design of experiments for detection of linkage disequilibrium lda.cv - Cross-validation for linear discriminate analysis ldbounds - Lan-DeMets Method for Group Sequential Boundaries leaps - regression subset selection lga - Tools for linear grouping analysis (LGA) lgtdl - A set of methods for longitudinal data objects lhs - Latin Hypercube Samples limSolve - Solving linear inverse models linprog - Linear Programming / Optimization ljr - Logistic Joinpoint Regression lme4 - Linear mixed-effects models using S4 classes lmeSplines - lmeSplines lmm - Linear mixed models lmom - L-moments lmomco - L-moments, Trimmed L-moments, L-comoments, and Many Distributions lmtest - Testing Linear Regression Models lnMLE - Logistic-Normal Model for Clustered Binary (Binomial) Data locfdr - Computes local false discovery rates locfit - Local Regression, Likelihood and Density Estimation locpol - Kernel local polinomial regression lodplot - Plot a genome scan logcondens - Estimate a Log-Concave Probability Density from iid Observations logilasso - Analysis of sparse contingency tables with penalization approaches logistf - Firth's bias reduced logistic regression loglognorm - Double log normal distribution functions logregperm - Inference in Logistic Regression logspline - Logspline density estimation routines lokern - Kernel Regression Smoothing with Local or Global Plug-in Bandwidth longitudinal - Analysis of Multiple Time Course Data longmemo - Statistics for Long-Memory Processes (Jan Beran) -- Data and Functions lpSolve - Interface to Lp_solve v. 5.5 to solve linear/integer programs lpSolveAPI - Interface to lp_solve 5.5.0.13 lpc - Lassoed principal components for testing significance of features lpridge - Local Polynomial (Ridge) Regression lsa - Latent Semantic Analysis lspls - LS-PLS Models lss - accel failure time model to right censored data based on least-squares principle ltm - Latent Trait Models under IRT ltsa - Linear time series analysis luca - Likelihood inference from case-control data Under Covariate Assumptions (LUCA) lvplot - Level value plots for R MAclinical - Class prediction based on microarray data and clinical parameters MBA - Multilevel B-spline Approximation MBESS - Methods for the Behavioral, Educational, and Social Sciences MCAPS - MCAPS data and results MCMCpack - Markov chain Monte Carlo (MCMC) Package MCPAN - Multiple comparisons using normal approximation MCPMod - Design and Analysis of Dose-Finding Studies MChtest - Monte Carlo hypothesis tests with Sequential Stopping MDD - Minimum Detectable Difference Calculations MEMSS - Data sets from Mixed-effects Models in S MFDA - Model Based Functional Data Analysis MIfuns - Pharmacometric tools for data preparation, analysis, simulation, and reporting MKLE - Maximum kernel likelihood estimation MKmisc - Miscellaneous Functions from M. Kohl MLDA - Methylation Linear Discriminant Analysis (MLDA) MLDS - Maximum Likelihood Difference Scaling MLEcens - Computation of the MLE for bivariate (interval) censored data MMG - Mixture Model on Graphs MNP - R Package for Fitting the Multinomial Probit Model MPV - Data Sets from Montgomery, Peck and Vining's Book MSBVAR - Markov-Switching Bayesian Vector Autoregression Models MSVAR - Markov Switching VAR MarkedPointProcess - Analysis of Marks of Marked Point Processes MasterBayes - ML and MCMC Methods for Pedigree Reconstruction and Analysis MatchIt - MatchIt Matching - Multivariate and Propensity Score Matching with Balance Optimization Matrix - Sparse and Dense Matrix Classes and Methods Metabonomic - GUI for Metabonomic Analysis MiscPsycho - Miscellaneous Psychometrics MultEq - Equivalence tests and simultaneous confidence intervals for multiple endpoints mAr - Multivariate AutoRegressive analysis mFilter - Miscellaneous time series filters maanova - Tools for analyzing Micro Array experiments magic - create and investigate magic squares mapLD - Linkage Disequilibrium Mapping mapdata - Extra Map Databases mapproj - Map Projections maps - Draw Geographical Maps maptools - Tools for reading and handling spatial objects maptree - Mapping, pruning, and graphing tree models marginTree - marginTree: margin trees for high-dimensional classification marginalmodelplots - Marginal Model Plots mathgraph - Directed and undirected graphs matlab - MATLAB emulation package matrixcalc - Collection of functions for matrix differential calculus maxLik - Maximum Likelihood Estimation maxstat - Maximally Selected Rank Statistics mblm - Median-Based Linear Models mboost - Model-Based Boosting mcgibbsit - Warnes and Raftery's MCGibbsit MCMC diagnostic mclust - Model-Based Clustering / Normal Mixture Modeling mclust02 - Model-based cluster analysis (older version) mcmc - Markov Chain Monte Carlo mco - Multi criteria optimization algorithms mda - Mixture and flexible discriminant analysis meboot - Maximum Entropy Bootstrap for Time Series mefa - Multivariate Count Data Handling in Ecology and Biogeography meifly - Interactive model exploration using GGobi memisc - Tools for Mgmt of Survey Data/Graphics/Programming/Statistics/Simulation merror - Accuracy and Precision of Measurements meta - Meta-Analysis mfp - Multivariable Fractional Polynomials mgcv - GAMs with GCV smoothness estimation and GAMMs by REML/PQL mi - Missing Data Imputation and Model Checking micEcon - Microeconomics mice - Multivariate Imputation by Chained Equations mimR - A package for graphical modelling in R minet - Mutual Information Network Inference minpack.lm - R interface to the Levenberg-Marquardt algorithm mirf - MULT IMPUT AND RANDOM FORESTS FOR UNOBSERV PHASE, HIGH-DIMEN DATA misc3d - Miscellaneous 3D Plots mitools - Tools for multiple imputation of missing data mix - Estimation/multiple Imputation for Mixed Categorical and Continuous Data mixPHM - Mixtures of proportional hazard models mixdist - Finite Mixture Distribution Models mixlow - mixlow method for assessing drug synergism mixnet - random graph clustering mixreg - Functions to fit mixtures of regressions mixstock - functions for mixed stock analysis mixtools - Tools for analyzing finite mixture models mlCopulaSelection - Copula selection and fitting using maxlikelihood mlbench - Machine Learning Benchmark Problems mlegp - Maximum Likelihood Estimates of Gaussian Processes mlica - Independent Component Analysis using Maximum Likelihood mlmRev - Examples from Multilevel Modelling Software Review mlmmm - ML estimation under multivariate linear mixed models with missing values mlogit - multinomial logit model mmlcr - Mixed-Mode Latent Class Regression mnormt - The multivariate normal and t distributions moc - GENERAL NONLINEAR MIXTURES OF CURVES modeest - Mode Estimation -- Chernoff Distribution modehunt - Multiscale Analysis for Density Functions modeltools - Tools and Classes for Statistical Models moduleColor - Basic module functions mokken - Mokken Scale Analysis in R mombf - Moment and Inverse Moment Bayes factors moments - Moments, cumulants, skewness, kurtosis and related tests monoProc - strictly monotone smoothing procedure monomvn - Estimation for multivariate normal data with monotone missingness monreg - Nonparametric monotone regression moonsun - Basic astronomical calculations with R mota - Mean Optimal Transformation Approach mpm - Multivariate Projection Methods mprobit - Multivariate probit model for binary/ordinal response mra - Analysis of Mark-Recapture data mratios - Inferences for ratios of coefficients in the general linear model mrdrc - Model-robust concentration-response analysis msBreast - Protein Mass Spectra Dataset from a Breast Cancer Study msDilution - Protein Mass Spectra Dataset from a Dilution Experiment msProcess - Protein Mass Spectra Processing msProstate - Protein Mass Spectra Dataset from a Prostate Cancer Study msm - Multi-state Markov and hidden Markov models in continuous time muS2RC - Splus to R Compatibility for package muStat muStat - Prentice Rank Sum Test and McNemar Test muUtil - muStat Utility Functions muhaz - Hazard Function Estimation in Survival Analysis multcomp - Simultaneous Inference in General Parametric Models multcompView - Visualizations of Paired Comparisons multic - Quantitative linkage analysis tools using the variance components multilevel - Multilevel Functions multinomRob - Robust Estimation of Overdispersed Multinomial Regression Models multipol - multivariate polynomials multtest - Resampling-based multiple hypothesis testing mvbutils - MVB's utilities for R mvna - Nelson-Aalen estimator of the cumulative hazard in multistate models mvnmle - ML estimation for multivariate normal data with missing values mvnormtest - Normality test for multivariate variables mvoutlier - Multivariate outlier detection based on robust methods mvpart - Multivariate partitioning mvtnorm - Multivariate Normal and t Distributions mvtnormpcs - Multivariate Normal and T Distribution functions of (Dunnett, 1989) NADA - Nondetects And Data Analysis for environmental data NISTnls - Nonlinear least squares examples from NIST NMMAPSlite - NMMAPS Data Lite NORMT3 - Evaluates complex erf, erfc and density of sum of Gaussian and Student's t NRAIA - Data sets from "Nonlinear Regression Analysis and Its Applications" NestedCohort - Survival Analysis for Cohorts with Missing Covariate Information NetIndices - Estimates network indices, including trophic structure of foodwebs nFDR - Nonparametric Estimate of FDR Based on Bernstein Polynomials nFactors - Non Graphical Solution to the Cattell Scree Test ncdf - Interface to Unidata netCDF data files ncf - spatial nonparametric covariance functions ncomplete - ncomplete negenes - Estimating the number of essential genes in a genome netmodels - Tools for the study of scale free and small world networks network - Classes for Relational Data networksis - Simulate bipartite graphs with fixed marginals: sequential importance sampling neural - Neural Networks neuralnet - Training of neural networks nice - Get or Set UNIX Niceness nlme - Linear and Nonlinear Mixed Effects Models nlmeODE - Non-linear mixed-effects modelling in nlme using differential equations nlrwr - Non-linear regression with R nls2 - Non-linear regression with brute force nlstools - Tools for nonlinear regression diagnostics nlt - A nondecimated lifting transform for signal denoising nltm - Non-linear Transformation Models nlts - (non)linear time series analysis nnls - The Lawson-Hanson algorithm for non-negative least squares (NNLS) noia - Implementation of the Natural and Orthogonal InterAction (NOIA) model nonbinROC - ROC-type analysis for non-binary gold standards nor1mix - Normal (1-d) Mixture Models (S3 Classes and Methods) norm - Analysis of multivariate normal datasets with missing values normalp - Package for exponential power distributions (EPD) normwn.test - Normality and White Noise Testing nortest - Tests for Normality noverlap - ncomplete np - Nonparametric kernel smoothing methods for mixed data types nparcomp - nparcomp-package npde - Normalised prediction distribution errors for nonlinear mixed-effect models nplplot - Plotting non-parametric LOD scores from multiple input files npmc - Nonparametric Multiple Comparisons npmlreg - Nonparametric maximum likelihood estimation for random effect models nsRFA - Non-supervised Regional Frequency Analysis numDeriv - Accurate Numerical Derivatives nws - R functions for NetWorkSpaces and Sleigh OPE - Outer-product emulator ORMDR - ORMDR Oarray - Arrays with arbitrary offsets obsSens - Sensitivity analysis for Observational studies oc - OC Roll Call Analysis Software oce - Analysis of Oceanographic data odesolve - Solvers for Ordinary Differential Equations odfWeave - Sweave processing of Open Document Format (ODF) files ofw - Optimal Feature Weighting algorithm onemap - Software for constructing genetic maps in outcrossing species onion - octonions and quaternions openNLP - openNLP Interface openNLPmodels - (English and Spanish) openNLP models opentick - R API to opentick databases optmatch - Functions for optimal matching orientlib - Support for orientation data orloca - The package deals with Operations Research LOCational Analysis models orloca.es - Spanish version of orloca package orth - Multivariate Logistic Regressions Using Orthogonalized Residuals orthopolynom - Collection of functions:orthogonal and orthonormal polynomials ouch - Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses outliers - Tests for outliers oz - Plot the Australian coastline and states PARccs - Estimation of partial attributable risks (PAR) from case-control data PASWR - Probability and Statistics with R PBSddesolve - Solver for Delay Differential Equations PBSmapping - PBS Mapping 2.59 PBSmodelling - PBS Modelling PET - Simulation and Reconstruction of PET Images PHYLOGR - Functions for phylogenetically based statistical analyses PK - Basic Pharmacokinetics PKfit - A Data Analysis Tool for Pharmacokinetics PKtools - unified computational interfaces for population PK POT - Generalized Pareto Distribution and Peaks Over Threshold PSAgraphics - Propensity Score Analysis Graphics PSM - Non-Linear Mixed-Effects modelling using Stochastic Differential Equations PTAk - Principal Tensor Analysis on k modes Peaks - Peaks PearsonICA - Independent component analysis using score functions from the Pearson system PerformanceAnalytics - Econometric tools for performance and risk analysis PhySim - Phylogenetic Tree Simulation Package PolynomF - Polynomials in R Pomic - Pattern Oriented Modelling Information Criterion PredictiveRegression - Prediction Intervals for Three Statistical Models PresenceAbsence - Presence-Absence Model Evaluation ProbForecastGOP - Probabilistic Weather Field Forecast using the GOP method ProbeR - Reliability for gene expression from Affymetrix chip ProfessR - Grades Setting and Exam Maker PtProcess - Time Dependent Point Process Modelling PwrGSD - Power in a Group Sequential Design pARtial - pARtial package pack - Convert values to/from raw vectors packClassic - Toy Pack Classic pairwiseCI - Confidence intervals for two sample comparisons paleoTS - Modeling evolution in paleontological time-series paltran - WA, WA-PLS, MW and POM for paleolimnology pamr - Pam: prediction analysis for microarrays pan - Multiple imputation for multivariate panel or clustered data panel - Panel papply - Parallel apply function using MPI paran - Horn's Test of Principal Components/Factors partitions - Additive partitions of integers partsm - Periodic Autoregressive Time Series Models party - A Laboratory for Recursive Partytioning pastecs - Package for Analysis of Space-Time Ecological Series pbatR - P2BAT pcaPP - Robust PCA by Projection Pursuit pcalg - Estimating the skeleton and equivalence class of a DAG pcse - Panel-Corrected Standard Error Estimation in R pcurve - Principal Curve analysis pear - Package for Periodic Autoregression Analysis pec - Prediction Error Curves for Survival Models penalized - L1 (lasso) / L2 (ridge) penalized estimation in GLMs peperr - Parallelised Estimation of Prediction Error permax - permax permtest - Permutation test to compare variability within two groups perturb - Tools for evaluating collinearity pga - Ensemble method: variable selection by carrying out Darwinian evolution pgam - Poisson-Gamma Additive Models pgirmess - Data analysis in ecology phangorn - Phylogenetic analysis in R pheno - Auxiliary functions for phenological data analysis phpSerialize - Serialize R to PHP associative array picante - Tools for integrating phylogenies and ecology pinktoe - Graphically traverse a tree via GUI widgets or web based system pixmap - Bitmap Images ("Pixel Maps") plRasch - Log Linear by Linear Asscociation models playwith - A GUI for interactive plots using GTK+ plink - IRT Separate Calibration Linking Methods plm - Linear models for panel data plotSEMM - Graphing nonlinear latent variable interactions in SEMM plotrix - Various plotting functions pls - Partial Least Squares Regression (PLSR) and Principal Component Regression (PCR) plsgenomics - PLS analyses for genomics plugdensity - Plug-in Kernel Density Estimation plyr - Tools for splitting, applying and combining data pmg - Poor Man's GUI pmml - Generate PMML for various models poLCA - Polytomous variable Latent Class Analysis poilog - Poisson lognormal and bivariate Poisson lognormal distribution polspline - Polynomial spline routines polyapost - Simulating from the Polya posterior polycor - Polychoric and Polyserial Correlations polynom - A collection of functions: class for univariate polynomial manipulations pomp - Statistical inference for partially observed Markov processes popbio - Construction and analysis of matrix population models popgen - Statistical and Population Genetics poplab - Population Lab portfolio - Analysing equity portfolios portfolioSim - Framework for simulating equity portfolio strategies powell - Powell's UObyQA algorithm powerpkg - Power analyses for the affected sib pair and the TDT design ppc - Peak Probability Contrasts ppls - Penalized Partial Least Squares pps - Functions for PPS sampling prabclus - Functions for clustering of presence-absence and abundance data predbayescor - Classification rule based on Bayesian naive Bayes models predmixcor - Classification rule based on Bayesian mixture models prettyR - Pretty descriptive stats prim - Patient Rule Induction Method (PRIM) princurve - Fits a Principal Curve in Arbitrary Dimension prob - Elementary Probability on Finite Sample Spaces prodlim - Product Limit Estimation profileModel - Tools for profiling inference functions for various model classes profr - An alternative display for profiling information proftools - Profile Output Processing Tools for R proj4 - A simple interface to the PROJ.4 cartographic projections library proptest - Tests of the Proportional Hazards Assumption proto - Prototype object-based programming proxy - Distance and Similarity Measures pscl - Political Science Computational Laboratory, Stanford University pseudo - Pseudo - observations pspline - Penalized Smoothing Splines psy - Various procedures used in psychometry psych - Procedures for Personality, Psychometric, and Psychological Research psychometric - Applied Psychometric Theory psyphy - Functions for analyzing psychophysical data in R pvclust - Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling pwr - Basic functions for power analysis pwt - Penn World Table QCA - Qualitative Comparative Analysis QCAGUI - QCA Graphical User Interface QRMlib - Provides R-language code to examine Quantitative Risk Management concepts QuantPsyc - Quantitative Psychology Tools qAnalyst - Variables and Attributes Control Charts qcc - Quality Control Charts qdg - QTL directed graphs qgen - Quantitative Genetics using R qlspack - Quasi Least Square Package qp - q-order partial correlation graph search algorithm qpcR - Modelling and analysis of real-time PCR data qtl - Tools for analyzing QTL experiments qtlDesign - Design of QTL experiments qtlbim - QTL Bayesian Interval Mapping quadprog - Functions to solve Quadratic Programming Problems qualV - Qualitative Validation Methods quantchem - Quantitative chemical analysis: calibration and evaluation of results quantmod - Quantitative Financial Modelling Framework quantreg - Quantile Regression quantregForest - Quantile Regression Forests qvalue - Q-value estimation for false discovery rate control qvcalc - Quasi variances for factor effects in statistical models R.cache - Fast and light-weight caching of objects R.huge - Methods for accessing huge amounts of data R.matlab - Read and write of MAT files together with R-to-Matlab connectivity R.methodsS3 - Utility function for defining S3 methods R.oo - R object-oriented programming with or without references R.rsp - R Server Pages R.utils - Various programming utilities R2HTML - HTML exportation for R objects R2WinBUGS - Running WinBUGS and OpenBUGS from R / S-PLUS R2jags - R2jags: A Package for Running jags from R RArcInfo - Functions to import data from Arc/Info V7.x binary coverages RBGL - An interface to the BOOST graph library RBloomberg - R/Bloomberg RColorBrewer - ColorBrewer palettes RCurl - HTTP request interface RDieHarder - R interface to the dieharder RNG test suite RExcelInstaller - Integration of R and Excel, (use R in Excel) RFA - Regional Frequency Analysis RFOC - Graphics for Spherical Distributions and Earthquake Focal Mechanisms RFreak - R/FrEAK interface RGrace - RGrace RGraphics - Data and Functions from the book R Graphics RGtk2 - R bindings for Gtk 2.8.0 and above RHmm - Hidden Markov Models simulations and estimations RII - Relative index of inequality estimation RItools - Randomization inference tools RJDBC - Provides access to databases through the JDBC interface RJaCGH - Reversible Jump MCMC for the analysis of CGH arrays RKEA - R/KEA interface RLMM - A Genotype Calling Algorithm for Affymetrix SNP Arrays RLRsim - Exact (Restricted) Likelihood Ratio tests for mixed and additive models RLadyBug - Analysis of infectious diseases using stochastic epidemic models RM2 - Revenue Management and Pricing Package RMySQL - R interface to the MySQL database RNetCDF - R Interface to NetCDF Datasets ROCR - Visualizing the performance of scoring classifiers RODBC - ODBC Database Access ROptEst - Optimally robust estimation ROptRegTS - Optimally robust estimation for regression-type models ROracle - Oracle database interface for R RPMG - Graphical User Interface (GUI) for interactive R analysis sessions RPyGeo - ArcGIS Geoprocessing in R via Python RQuantLib - R interface to the QuantLib library RSAGA - SAGA Geoprocessing and Terrain Analysis in R RSEIS - Seismic Time Series Analysis Tools RSQLite - SQLite interface for R RSVGTipsDevice - An R SVG graphics device with dynamic tips/hyperlinks RScaLAPACK - Seamless interface to perform parallel computation on linear algebrs RSeqMeth - Package for analysis of Sequenom EpiTYPER Data RSvgDevice - An R SVG graphics device RTOMO - Visualization for seismic tomography RTisean - R interface to Tisean algorithms RUnit - R Unit test framework RWeka - R/Weka interface RWinEdt - R-WinEdt RXshrink - Maximum Likelihood Shrinkage via Ridge or Least Angle Regression RadioSonde - Tools for plotting skew-T diagrams and wind profiles RandVar - Implementation of random variables RandomFields - Simulation and Analysis of Random Fields RankAggreg - Weighted rank aggregation RaschSampler - Rasch Sampler Ratings - Model-based Ratings Figures Rcapture - Loglinear Models in Capture-Recapture Experiments Rcmdr - R Commander RcmdrPlugin.Export - Graphically export objects to LaTeX or HTML RcmdrPlugin.FactoMineR - Graphical User Interface for FactoMineR RcmdrPlugin.HH - Rcmdr support for the HH package RcmdrPlugin.IPSUR - Introduction to Probability and Statistics Using R RcmdrPlugin.TeachingDemos - Rcmdr Teaching Demos Plug-In RcmdrPlugin.epack - Rcmdr plugin for time series Rcplex - R interface to CPLEX Read.isi - Automated access to old World Fertility Survey data saved in fixed-width format Reliability - Functions for estimating parameters in software reliability models ResearchMethods - Using GUIs to help teach statistics to non-statistics students ResistorArray - electrical properties of resistor networks Rfwdmv - Forward Search for Multivariate Data Rglpk - R/GNU Linear Programming Kit Interface RiboSort - Classification and Analysis Package for Microbial Community Profiles Rigroup - Rigroup: Provides small integer group functions Rlab - Functions and Datasets Required for ST370 class Rlsf - Interface to the LSF Queuing System Rmdr - R-Multifactor Dimensionality Reduction Rmetrics - Rmetrics - Financial Engineering and Computational Finance Rmpi - Interface (Wrapper) to MPI (Message-Passing Interface) RobAStBase - Robust Asymptotic Statistics RobLox - Optimally robust influence curves for location and scale RobRex - Optimally robust influence curves for regression and scale Rpad - Workbook-style, web-based interface to R Rsac - Seismic analysis tools in R Rserve - Binary R server Rsge - Interface to the SGE Queuing System Rsundials - Suite of Nonlinear Differential Algebraic Equations Solvers in R Rsymphony - Symphony in R Runuran - R interface to the UNU.RAN random variate generators Rvelslant - Downhole Seismic Analysis in R Rwave - Time-Frequency analysis of 1-D signals Ryacas - R interface to the yacas computer algebra system r2lUniv - R to LaTeX Univariate rJava - Low-level R to Java interface rPorta - R/PORTA interface race - Racing methods for the selection of the best rake - Normalize sample weights using marginal total population weights ramps - Bayesian Geostatistical Modeling with RAMPS randaes - Random number generator based on AES cipher random - True random numbers using random.org randomForest - Breiman and Cutler's random forests for classification and regression randomLCA - Random Effects Latent Class Analysis randomSurvivalForest - Ishwaran and Kogalur's Random Survival Forest randtoolbox - toolbox for pseudo and quasi random number generation and RNG tests rankreg - Rank regression for censored data AFT model rateratio.test - Exact rate ratio test rattle - A graphical user interface for data mining in R using GTK rbounds - Perform Rosenbaum bounds sensitivity tests for matched data rbugs - Fusing R and OpenBugs rcdd - rcdd (Computational Geometry) rcdk - rcdk - Interface to the CDK Libraries rcom - R COM Client Interface and internal COM Server rcompgen - Completion generator for R rda - Shrunken Centroids Regularized Discriminant Analysis rdetools - Relevant Dimension Estimation (RDE) in Feature Spaces realized - Realized ref - References for R regress - Gaussian linear models with linear covariance structure regsubseq - Detect and Test Regular Sequences and Subsequences regtest - Regression testing relaimpo - Relative importance of regressors in linear models relations - Data Structures and Algorithms for Relations relax - relax -- R Editor for Literate Analysis and lateX relaxo - Relaxed Lasso reldist - Relative Distribution Methods relimp - Relative Contribution of Effects in a Regression Model relsurv - Relative survival regression repolr - Repeated measures proportional odds logistic regression reshape - Flexibly reshape data resper - Sampling from restricted permutations reweight - Adjustment of Survey Respondent Weights rgcvpack - R Interface for GCVPACK Fortran Package rgdal - Bindings for the Geospatial Data Abstraction Library rgenoud - R version of GENetic Optimization Using Derivatives rggm - Robustified methods for Gaussian Graphical Models rggobi - Interface between R and GGobi rgl - 3D visualization device system (OpenGL) rgr - The GSC Applied Geochemistry EDA Package rhosp - Side effect risks in hospital : simulation and estimation richards - Richards curves rimage - Image Processing Module for R rindex - Indexing for R risksetROC - Riskset ROC curve estimation from censored survival data rjacobi - rjacobi rjags - Bayesian graphical models using MCMC rjson - JSON for R rlecuyer - R interface to RNG with multiple streams rmeta - Meta-analysis rmetasim - An individual-based population genetic simulation environment robfilter - Robust Time Series Filters robust - Insightful Robust Library robustbase - Basic Robust Statistics rootSolve - Nonlinear root finding, equilibrium and steady-state analysis of ODE roxygen - Literate Programming in R rpanel - Simple interactive controls for R using the tcltk library rpart - Recursive Partitioning rpubchem - rpubchem - Interface to the PubChem Collection rpvm - R interface to PVM (Parallel Virtual Machine) rqmcmb2 - Markov Chain Marginal Bootstrap for Quantile Regression rrcov - Scalable Robust Estimators with High Breakdown Point rrp - Random Recursive Partitioning rscproxy - provides portable C-style interface to R (StatConnector) rsprng - R interface to SPRNG (Scalable Parallel Random Number Generators) rstream - Streams of random numbers rtiff - A tiff reader for R runjags - Run Bayesian MCMC Models in the BUGS syntax from Within R rv - Simulation-based random variable object class in R rwm - R Workspace Manager rwt - Rice Wavelet Toolbox wrapper SASPECT - Significant AnalysiS of PEptide CounTs SASmixed - Data sets from "SAS System for Mixed Models" SASxport - Read and Write SAS XPORT Files SDDA - Stepwise Diagonal Discriminant Analysis SIN - A SINful Approach to Selection of Gaussian Graphical Markov Models SLmisc - Miscellaneous Functions for analysis of gene expression data at SIRS-Lab GmbH SMC - Sequential Monte Carlo (SMC) Algorithm SMPracticals - Practicals for use with Davison (2003) Statistical Models SMVar - Structural Model for variances SNPMaP - SNP Microarrays and Pooling in R SNPMaP.cdm - Annotation for SNP Microarrays and Pooling in R SNPassoc - SNPs-based whole genome association studies SNPmaxsel - Maximally selected statistics for SNP data SQLiteDF - Stores data frames & matrices in SQLite tables SQLiteMap - package to manage vector graphical maps using SQLite SRPM - Shared Reproducibility Package Management STAR - Spike Train Analysis with R SciViews - Bundle of svMisc, svIO, svViews, svDialogs, svSocket, svGUI, svIDE, svWidgets SemiPar - Semiparametic Regression SenSrivastava - Datasets from Sen & Srivastava SensoMineR - Sensory data analysis with R SeqKnn - Sequential KNN imputation method SharedHT2 - Shared Hotelling T2 test for small sample microarray experiments SiZer - SiZer: Significant Zero Crossings SimHap - A comprehensive modeling framework for epidemiological outcomes SimpleTable - Bayesian Inference and Sensitivity Analysis for Causal Effects Snowball - Snowball Stemmers SoDA - Functions and Exampels for "Software for Data Analysis" SoPhy - Soil Physics Tools SparseLogReg - Sparse logistic regression SparseM - Sparse Linear Algebra SpatialNP - Multivariate nonparametric methods based on spatial signs and ranks SpherWave - Spherical Wavelets and SW-based Spatially Adaptive Methods StatDA - Statistical Analysis for Environmental Data StatDataML - implementation of the StatDataML proposal StatMatch - Statistical Matching StreamMetabolism-package for calculating single station metabolism SuppDists - Supplementary distributions SwissAir - Air Quality Data of Switzerland for one year in 30 min Resolution SyNet - Inference and Analysis of Sympatry Networks Synth - Synthetic Control Group Method for Comparative Case Studies s20x - Stats 20x sac - Semiparametric Analysis of Changepoint sampfling - Sampford sampling (w/o replacement and unequal probabilities) sampleSelection - Sample Selection Models sampling - Survey Sampling samr - SAM: Significance Analysis of Microarrays sandwich - Robust Covariance Matrix Estimators sapa - Insightful Spectral Analysis for Physical Applications sbgcop - Semiparametric Bayesian Gaussian copula estimation sca - Simple Component Analysis scagnostics - Compute scagnostics scaleboot - Approximately Unbiased P-values via Multiscale Bootstrap scape - Statistical catch-at-age plotting environment scapeMCMC - MCMC diagnostic plots scatterplot3d - 3D Scatter Plot schoolmath - Functions and datasets for math used in school sciplot - Scientific Graphing Functions for Factorial Designs scope - Data Manipulation Using Arbitrary Row and Column Criteria scrime - Analysis of High-Dimensional Categorical Data such as SNP Data scuba - Scuba diving calculations and decompression models sdcMicro - Statistical Disclosure Control methods: gen public- and scientific-use files sde - Simulation and Inference for Stochastic Differential Equations sdtalt - Signal detection theory measures and alternatives seacarb - Calculates parameters of the seawater carbonate system seas - Seasonal analysis and graphics, especially for climatology seewave - Time wave analysis and graphical representation segclust - SegClust : a package for Segmentation and Segmentation/Clustering segmented - Segmented relationships in regression models sem - Structural Equation Models sendplot - Tool for sending interactive plots with tool-tip content sensR - Thurstonian models for sensory discrimination sensitivity - Sensitivity Analysis seqinr - Biological Sequences Retrieval and Analysis seqmon - Sequential Monitoring of Clinical Trials seriation - Infrastructure for seriation session - Functions for interacting with, saving and restoring R sessions setRNG - Set (normal) random number generator and seed sets - Sets, Generalized Sets, and Customizable Sets sfsmisc - Utilities from Seminar fuer Statistik ETH Zurich sgeostat - An Object-oriented Framework for Geostatistical Modeling in S+ shape - Functions for plotting graphical shapes, colors shapefiles - Read and Write ESRI Shapefiles shapes - Statistical shape analysis siar - Stable Isotope Analysis in R sigma2tools - Test of hypothesis about sigma2 signal - Signal processing signalextraction - Real-Time Signal Extraction (Direct Filter Approach) simba - A Collection of functions for similarity calculation of binary data simco - A package to import Structure files and deduce similarity coefficients from them simecol - Simulation of ecological (and other) dynamic systems simex - SIMEX- and MCSIMEX-Algorithm for measurement error models similarityRichards - Similarity of Richards curves simpleboot - Simple Bootstrap Routines singlecase - statistical tests for single case studies in neuropsychology skewt - The Skewed Student-t Distribution sm - Smoothing methods for nonparametric regression and density estimation sma - Statistical Microarray Analysis smacof - smacof for Multidimensional Scaling smatr - (Standardised) Major Axis Estimation and Testing Routines smoothSurv - Survival Regression with Smoothed Error Distribution smoothtail - Smooth Estimation of GPD Shape Parameter sn - The skew-normal and skew-t distributions sna - Tools for Social Network Analysis snow - Simple Network of Workstations snowFT - Fault Tolerant Simple Network of Workstations snowfall - Easier cluster computing (based on snow) snp.plotter - snp.plotter snpXpert - Tools to analysis SNP data som - Self-Organizing Map sound - A Sound Interface for R sp - classes and methods for spatial data spBayes - Univariate and Multivariate Spatial Modeling space - Sparse PArtial Correlation Estimation spam - SPArse Matrix spatclus - Arbitrarily Shaped Multiple Spatial Cluster Detection for Case Event Data spatgraphs - Graphs for spatial point patterns spatialCovariance - Compue spatial covar matrices for data on rectangles spatialkernel - Nonparameteric est:spatial segregation in multivariate point proc spatstat - Spatial Point Pattern analysis, model-fitting, simulation, tests spc - Statistical Process Control spdep - Spatial dependence: weighting schemes, statistics and models spe - Stochastic Proximity Embedding spectralGP - Approximate Gaussian processes using the Fourier basis spectrino - Spectra organizer, visualization and data extraction spgrass6 - Interface between GRASS 6 geographical information system and R spgwr - Geographically weighted regression splancs - Spatial and Space-Time Point Pattern Analysis splus2R - Insightful package providing missing S-PLUS functionality in R spssDDI - Read SPSS System files and produce valid DDI Version 3.0 documents spsurvey - Spatial Survey Design and Analysis sqldf - Perform SQL Selects on R Data Frames ssanv - Sample Size Adjusted for Nonadherence or Variability of input parameters ssize.fdr - Sample Size Calculations for Microarray Experiments sspir - State Space Models in R sspline - Smoothing Splines on the Sphere st - Shrinkage t Statistic staRt - Inferenza classica con TI-83 Plus stab - data analysis of drug stability startupmsg - Utilities for start-up messages stashR - A Set of Tools for Administering SHared Repositories statmod - Statistical Modeling statnet - Software tools for the Statistical Modeling of Network Data stepPlr - L2 penalized logistic regression with a stepwise variable selection stepwise - Stepwise detection of recombination breakpoints stinepack - Stineman, a consistently well behaved method of interpolation stochasticGEM - R Package for Fitting Stochastic General Epidemic Models stochmod - Stochastic Modeling stream.net - Building and analyzing binary stream networks strucchange - Testing, Monitoring and Dating Structural Changes subplex - Subplex optimization algorithm subselect - Selecting variable subsets sudoku - Sudoku Puzzle Generator and Solver supclust - Supervised Clustering of Genes superpc - Supervised principal components surv2sample - Two-Sample Tests for Survival Analysis survBayes - Fits a proportional hazards model to time to event data by a Bayesian approach surveillance - Outbreak detection algorithms for surveillance data survey - analysis of complex survey samples surveyNG - experimental revision of survey package survival - Survival analysis, including penalised likelihood survivalROC - Time-dependent ROC curve estimation from survival data survrec - Survival analysis for recurrent event data svcR - svcR package svcm - 2d and 3d Space-Varying Coefficient Models svmpath - svmpath: the SVM Path algorithm systemfit - Estimating Systems of Simultaneous Equations TIMP - a problem solving env for fitting separable nonlinear models in physics and chemistry TRAMPR - TRFLP Analysis and Matching Package for R TSA - Time Series Analysis TSHRC - Two Stage Hazard Rate Comparison TSMySQL - Time Series Database Interface extensions for MySQL TSP - Traveling Salesperson Problem (TSP) TSSQLite - Time Series Database Interface extentions for SQLite TSdbi - Time Series Database Interface TSpadi - TSdbi Interface to PADI Time Series Server (for e.g. Fame) TTR - Technical Trading Rules TWIX - Trees WIth eXtra splits TeachingDemos - Demonstrations for teaching and learning TinnR - Resources of Tinn-R GUI/Editor for R Environment TraMineR - Sequences and trajectories mining for social scientists TwoWaySurvival - Additiv Two-Way Hazards Modelling of Right Censored Survival Data TwslmSpikeWeight - Systematic approaches using TW-SLM: conntrol spots / data qual info taskPR - Task-Parallel R Package tcltk2 - Tcl/Tk Additions tdist - Distribution of a linear combination of independent Student's t-variables tdm - A Tool for Therapeutic Drug Monitoring (TDM) tdthap - TDT tests for extended haplotypes tensor - Tensor product of arrays tensorA - Advanced tensors arithmetic with named indices termstrc - Zero-coupon Yield Curve Estimation tframe - Time Frame coding kernel tframePlus - Time Frame coding kernel extensions tgp - Bayesian treed Gaussian process models tileHMM - Hidden Markov Models for ChIP-on-Chip Analysis time - Time tracking for developers timereg - timereg package timsac - TIMe Series Analysis and Control package tis - Time Indexes and Time Indexed Series titan - Titration analysis for mass spectrometry data titecrm - Time-to-event continual reassessment method and calibration tools tkrgl - TK widget tools for rgl package tkrplot - TK Rplot tlnise - Two-level normal independent sampling estimation tm - Text Mining Package topmodel - topmodel implementation in R tossm - Testing of Spatial Structure Methods tpr - Temporal Process Regression trackObjs - Track Objects tradeCosts - Trade Cost Analysis tree - Classification and regression trees treelet - Treelet triangle - Provides standard distribution functions for triangle distribution trimcluster - Cluster analysis with trimming trip - Spatial analysis of animal track data tripEstimation - Metropolis sampler and supporting functions tripack - Triangulation of irregularly spaced data truncgof - GoF tests allowing for left truncated data trust - Trust Region Optimization tsDyn - Time series analysis based on dynamical systems theory tsModel - Time Series Modeling for Air Pollution and Health tseries - Time series analysis and computational finance tseriesChaos - Analysis of nonlinear time series tsfa - Time Series Factor Analysis tuneR - Analysis of music tutoR - Student-friendly package to mask common functions twang - Toolkit for Weighting and Analysis of Nonequivalent Groups tweedie - Tweedie exponential family models twslm - A two-way semilinear model: normalization and analysis of cDNA microarray data UNF - Tools for creating universal numeric fingerprints for data USPS - Unsupervised and Supervised methods of Propensity Score Adjustment for Bias Umacs - Universal Markov chain sampler UsingR - Data sets for the text "Using R for Introductory Statistics" udunits - interface to Unidata's routines to convert units ump - Uniformly Most Powerful Tests unbalhaar - Function estimation via Unbalanced Haar wavelets uncompress - Uncompress untb - ecological drift under the UNTB urca - Unit root and cointegration tests for time series data urn - Urn : Sampling Without Replacement uroot - Unit Root Tests and Graphics for Seasonal Time Series VDCutil - utilities supporting the VDC system VGAM - Vector Generalized Linear and Additive Models VIM - Visualization and Imputation of Missing Values VLMC - VLMC -- Variable Length Markov Chains VR - Bundle of MASS, class, nnet, spatial VaR - Value at Risk estimation VhayuR - Vhayu R Interface vabayelMix - Variational Bayesian Mixture Modelling varSelRF - Variable selection using random forests varmixt - Mixture model on Variance for analysis of gene expression data vars - VAR Modelling vbmp - Variational Bayesian Multinomial Probit Regression vcd - Visualizing Categorical Data vegan - Community Ecology Package verification - Forecast verification utilities verify - Construction of test suites using verify objects vioplot - Violin plot vrtest - Variance Ratio tests and spectral shape tests for Weak-form Market Efficiency WINRPACK - Read in WIN format data WWGbook - Functions and datasets for WWGbook WeedMap - Map of weed intensity WhatIf - WhatIf: Software for Evaluating Counterfactuals WilcoxCV - Wilcoxon-based variable selection in cross-validation waveclock - Time-frequency analysis of cycling cell luminescence data waved - Wavelet Deconvolution wavelets - Funtions for computing wavelet filters, transforms and multires analyses waveslim - Basic wavelet routines for one-, two- and three-dimsignal processing wavethresh - Software to perform wavelet statistics and transforms wccsom - SOM networks for comparing patterns with peak shifts wgaim - Whole Genome Average Interval Mapping for QTL detection w/mixed models wikibooks - Functions and datasets of the german WikiBook "GNU R" wle - Weighted Likelihood Estimation wmtsa - Insightful Wavelet Methods for Time Series Analysis wnominate - WNOMINATE Roll Call Analysis Software wombsoft - Wombling Computation wordnet - WordNet Interface write.snns - Function for exporting data to SNNS pattern files XML - Tools for parsing and generating XML within R and S-Plus XReg - Extreme Regression xgobi - Interface to the XGobi and XGvis programs for graphical data analysis xlsReadWrite - Natively read and write Excel files xtable - Export tables to LaTeX or HTML xts - Extensible Time Series YaleToolkit - Data exploration tools from Yale University yaImpute - yaImpute: An R Package for k-NN Imputation yaml - Methods to convert R to YAML and back yest - Gaussian Independence Models ZIGP - Zero Inflated Generalized Poisson (ZIGP) regression models Zelig - Everyone's Statistical Software zipfR - Statistical models for word frequency distributions zoeppritz - Zoeppritz Equations zoo - Z's ordered observations