R 軟體的套件與用途

統計軟體 R 簡介 安裝 操作方式 變數與運算 有序數列 向量 矩陣 多維陣列 複數 因子 串列 資料框 時間數列 流程控制 輸出入 呼叫 函數 2D 繪圖 3D 繪圖 互動介面 套件列表 其他語言呼叫 R 的應用 集合 邏輯推論 模糊邏輯 機率邏輯 檢定 搜尋 優化算法 線性代數 決策樹 人工智慧 分群分類 SVM 向量機 神經網路 遺傳演算法 資料採礦 訊號處理 影像處理 語音處理 自然語言 機器學習 機器人 生物統計 數位訊號處理 方程式求解 數值分析 微積分 微分方程 線性規劃 圖形理論 統計推論 字串處理 正規表示式 視窗程式 網頁程式 文件格式 貝氏網路 訊息 機率統計書 相關網站 參考文獻 最新修改 簡體版 English

文章 相關文章：引入套件 套件列表 套件 用途 boot bootstraping 方法與抽樣 class 分類方法 cluster 分群(聚類)方法 foreign 讀取外部格式 (S3, Stata, SAS, Minitab, SPSS) … KernSmooth 核密度擬合方法 lattice Grid 新一代圖形套件 MASS Venables & Ripley Venables&Ripley 的 Modern Applied Statistics with S 書籍之範例程式與函式庫 mgcv 廣義的可加模型 nlme 線性與非線性回合效應模型 nnet 類神經網路和多項對數線性模型 rpart 遞迴分割方法 spatial 空間分析 (Kriging) survival 生存分析 關注套件 jit Just-in-time compiler for the R language languageR Data sets and functions with "Analyzing Linguistic Data: A practical introduction to statistics" penalizedSVM Feature Selection SVM using penalty functions rminer Simpler use of data mining methods (e.g. NN and SVM) in classification and regression SVMMaj SVMMaj algorithm svDialogs SciViews GUI API - Dialog boxes svGUI SciViews GUI API - Functions to manage GUI client svIDE SciViews GUI API - IDE and code editor functions svMisc SciViews GUI API - Miscellaneous functions svSocket SciViews GUI API - R Socket Server svSweave SciViews GUI API - Sweave functions svTools SciViews GUI API - Tools (wrapper for packages tools and codetools) svUnit SciViews GUI API - Unit testing svWidgets SciViews GUI API - Widgets & Windows svmpath svmpath: the SVM Path algorithm wSVM Weighted SVM with boosting algorithm for improving accuracy ade4TkGUI ade4 Tcl/Tk Graphical User Interface BiplotGUI Interactive Biplots in R biOpsGUI GUI for Basic image operations CommonJavaJars Useful libraries for building a Java based GUI under R caGUI A Tcl/Tk GUI for the functions in the ca package detrendeR Start the detrendeR Graphical User Interface (GUI) fgui Function GUI GrapheR A multiplatform GUI for drawing customizable graphs in R TGUICore Teaching GUI - Core functionality TGUITeaching Teaching GUI - prototype TinnR Resources of Tinn-R GUI/Editor for R Environment traitr An interface for creating GUIs modeled in part after traits UI module for python gooJSON Google JSON Data Interpreter for R googleVis Interface between R and the Google Visualisation API googlebigquery R client library for communicating with the Google Bigquery service DBI R Database Interface dbConnect Provides a graphical user interface to connect with databases that use MySQL filehash Simple key-value database filehashSQLite Simple key-value database using SQLite RMySQL R interface to the MySQL database RODBC ODBC Database Access ROracle Oracle database interface for R ROracleUI Convenient Tools for Working with Oracle Databases RPostgreSQL R interface to the PostgreSQL database system RpgSQL DBI/RJDBC interface to PostgreSQL Database sas7bdat SAS Database Reader (experimental) hapassoc Inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm lemma Laplace approximated EM Microarray Analysis cplm Monte Carlo EM algorithms and Bayesian methods for fitting Tweedie compound Poisson linear models 更多 R 套件 http://cran.r-project.org/web/packages/available_packages_by_name.html (3258 筆) ACCLMA ACC & LMA Graph Plotting ADGofTest Anderson-Darling GoF test ADM3 An Interpretation of the ADM method - automated detection algorithm ADaCGH Analysis of data from aCGH experiments AER Applied Econometrics with R AGSDest Estimation in adaptive group sequential trials AICcmodavg Model selection and multimodel inference based on (Q)AIC(c) AIGIS Areal Interpolation for GIS data AIM AIM: adaptive index model ALS multivariate curve resolution alternating least squares (MCR-ALS) AMA Anderson-Moore Algorithm AMORE A MORE flexible neural network package APSIMBatch Analysis the output of Apsim software AUCRF Variable Selection with Random Forest and the Area Under the Curve AcceptanceSampling Creation and evaluation of Acceptance Sampling Plans AdMit Adaptive Mixture of Student-t distributions AdaptFit Adaptive Semiparametic Regression Agreement Statistical Tools for Measuring Agreement AlgDesign Algorithmic Experimental Design AllPossibleSpellings Computes all of a word's possible spellings Amelia Amelia II: A Program for Missing Data AnalyzeFMRI Functions for analysis of fMRI datasets stored in the ANALYZE or NIFTI format Animal Analyze time-coded animal behavior data AnnotLists Data extraction tool from annotations files AquaEnv AquaEnv - an integrated development toolbox for aquatic chemical model generation ArDec Time series autoregressive-based decomposition aCGH.Spline Robust spline interpolation for dual color array comparative genomic hybridisation data abc Tools for Approximate Bayesian Computation (ABC) abd The Analysis of Biological Data abind Combine multi-dimensional arrays abn Multidimensional Bayesian Regression accuracy Tools for testing and improving accuracy of statistical results acepack ace() and avas() for selecting regression transformations actuar Actuarial functions ada ada: an R package for stochastic boosting adabag Applies Adaboost.M1 and Bagging adaptTest Adaptive two-stage tests adaptivetau Tau-leaping stochastic simulation ade4 Analysis of Ecological Data : Exploratory and Euclidean methods in Environmental sciences ade4TkGUI ade4 Tcl/Tk Graphical User Interface adegenet adegenet: an R package for the exploratory analysis of genetic and genomic data adehabitat Analysis of habitat selection by animals adehabitatHR Home range Estimation adehabitatHS Analysis of habitat selection by animals adehabitatLT Analysis of animal movements adehabitatMA Tools to Deal with Raster Maps adephylo adephylo: exploratory analyses for the phylogenetic comparative method 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 afc Calculate afc afmtools Estimation, Diagnostic and Forecasting Functions for ARFIMA models agilp Extracting and preprocessing Agilent express arrays agricolae Statistical Procedures for Agricultural Research agridat Agricultural datasets agsemisc Miscellaneous plotting and utility functions ahaz Regularization for semiparametric additive hazards regression akima Interpolation of irregularly spaced data alabama Constrained nonlinear optimization allan Automated Large Linear Analysis Node allanvar Allan Variance Analysis allelic A fast, unbiased and exact allelic exact test alphahull Generalization of the convex hull of a sample of points in the plane alr3 Data to accompany Applied Linear Regression 3rd edition amap Another Multidimensional Analysis Package amba Additive Models for Business Applications amei Adaptive Management of Epidemiological Interventions amer Additive mixed models with lme4 anacor Simple and Canonical Correspondence Analysis anaglyph 3D Anaglyph Plots analogue Analogue and weighted averaging methods for palaeoecology anapuce Tools for microarray data analysis anchors Statistical analysis of surveys with anchoring vignettes andrews Andrews curves anesrake ANES Raking Implementation animation A Gallery of Animations in Statistics and Utilities to Create Animations anm Analog model for downscaling ant Version of ant specific to R aod Analysis of Overdispersed Data apTreeshape Analyses of Phylogenetic Treeshape apcluster Affinity Propagation Clustering ape Analyses of Phylogenetics and Evolution aplpack Another Plot PACKage: stem.leaf, bagplot, faces, spin3R, and some slider functions approximator Bayesian prediction of complex computer codes apsrtable apsrtable model-output formatter for social science apt Asymmetric Price Transmission (apt) aqfig Functions to help display air quality model output and monitoring data aqp Algorithms for Quantitative Pedology aratio Assessment ratio analysis archetypes Archetypal Analysis ares Environment air pollution epidemiology: a library for time series analysis arf3DS4 Activated Region Fitting, fMRI data analysis (3D) argosfilter Argos locations filter arm Data Analysis Using Regression and Multilevel/Hierarchical Models aroma.affymetrix Analysis of large Affymetrix microarray data sets aroma.apd A probe-level data file format used by aroma.affymetrix [DEPRECATED] aroma.cn Copy-number analysis of large microarray data sets aroma.core Core methods and classes used by aroma.* package part of The Aroma Project aroma.light Light-weight methods for normalization and visualization of microarray data using only basic R data types arrayImpute Missing imputation for microarray data arrayMissPattern Exploratory analysis of Missing patterns for microarray data arrayhelpers Convenience functions for arrays ars Adaptive Rejection Sampling arules Mining Association Rules and Frequent Itemsets arulesNBMiner Mining NB-Frequent Itemsets and NB-Precise Rules arulesSequences Mining frequent sequences arulesViz arulesViz - Visualizing Association Rules and Frequent Itemsets asbio A collection of statistical tools for biologists ascii Export R objects to several markup languages asd Simulations for adaptive seamless designs ash David Scott's ASH routines aspace A collection of functions for estimating centrographic statistics and computational geometries for spatial point patterns aspect Aspects of Multivariables assist A Suite of S-Plus Functions Implementing Smoothing Splines aster Aster Models aster2 Aster Models asympTest Asymptotic statistic asypow Calculate Power Utilizing Asymptotic Likelihood Ratio Methods atmi Analysis of technical market indicators audio Audio Interface for R audit Bounds for Accounting Populations auteur Bayesian sampler of the trait-evolutionary process automap Automatic interpolation package aws Adaptive Weights Smoothing aylmer A generalization of Fisher's exact test B2Z Bayesian Two-Zone Model BACCO Bayesian Analysis of Computer Code Output (BACCO) BAMD Bayesian Association Model for Genomic Data with Missing Covariates BARD Better Automated ReDistricting BAS Bayesian Model Averaging using Bayesian Adaptive Sampling BAYSTAR On Bayesian analysis of Threshold autoregressive model (BAYSTAR) BB Solving and Optimizing Large-Scale Nonlinear Systems BBMM Brownian bridge movement model for estimating the movement path of an animal using discrete location data BCA Business and Customer Analytics BCBCSF Bias-corrected Bayesian Classification with Selected Features BCE Bayesian composition estimator: estimating sample (taxonomic) composition from biomarker data BGSIMD Block Gibbs Sampler with Incomplete Multinomial Distribution BHH2 Useful Functions for Box, Hunter and Hunter II BLCOP Black-Litterman and copula-opinion pooling frameworks BLR Bayesian Linear Regression BMA Bayesian Model Averaging BMN The pseudo-likelihood method for pairwise binary markov networks BMS Bayesian Model Averaging Library BPHO Bayesian Prediction with High-order Interactions BSDA Basic Statistics and Data Analysis BSagri Statistical methods for safety assessment in agricultural field trials BTSPAS Bayesian Time-Strat. Population Analysis BaBooN Bayesian Bootstrap Predictive Mean Matching - Multiple and single imputation for discrete data BaM Functions and datasets for books by Jeff Gill Barnard Barnard's Unconditional Test BayHap Bayesian analysis of haplotype association using Markov Chain Monte Carlo BayHaz R Functions for Bayesian Hazard Rate Estimation BayesDA Functions and Datasets for the book "Bayesian Data Analysis" BayesQTLBIC Bayesian multi-locus QTL analysis based on the BIC criterion BayesTree Bayesian Methods for Tree Based Models BayesValidate BayesValidate Package BayesX R Utilities Accompanying the Software Package BayesX Bchron Bayesian chronologies via compound Poisson-Gamma processes Benchmarking Benchmark and frontier analysis using DEA and SFA Bergm Bayesian inference for exponential random graph models Bessel Bessel – Bessel Functions Computations and Approximations Bhat General likelihood exploration BiGGR Creates an interface to BiGG database, provides a framework for simulation and produces flux graphs BiasedUrn Biased Urn model distributions BioIDMapper Mapping between BioIDs BioMark Find biomarkers in two-class discrimination problems BioPhysConnectoR BioPhysConnectoR BioStatR Initiation à la Statistique avec R Biodem Biodemography functions BiodiversityR GUI for biodiversity and community ecology analysis Biograph Explore life histories BiomarkeR Paired (pBI) and Unpaired Biomarker Identifier (uBI) including a method to infer networks BiplotGUI Interactive Biplots in R BlakerCI Blaker's binomial confidence limits Bmix Bayesian Sampling for Stick-breaking Mixtures BoSSA a Bunch of Structure and Sequence Analysis Bolstad Bolstad functions Bolstad2 Bolstad functions BoolNet Generation, reconstruction, simulation and analysis of synchronous, asynchronous, and probabilistic Boolean networks BootPR Bootstrap Prediction Intervals and Bias-Corrected Forecasting Boruta Boruta – a tool for finding significant attributes in information systems BradleyTerry Bradley-Terry Models – this package is now deprecated in favour of 'BradleyTerry2' BradleyTerry2 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 bamdit Bayesian Meta-Analysis of diagnostic test data barcode Barcode distribution plots bark Bayesian Additive Regresssion Kernels base64 Base 64 encoder/decoder baseline Baseline Correction of Spectra basicspace A Package to Recover a Basic Space from Issue Scales batade HTML reports and so on batch Batching Routines in Parallel and Passing Command-Line Arguments to R bayesDem Graphical User Interface for bayesTFR and bayesLife bayesGARCH Bayesian Estimation of the GARCH(1,1) Model with Student-t Innovations bayesLife Bayesian Projection of Life Expectancy bayesQR Bayesian quantile regression bayesSurv Bayesian Survival Regression with Flexible Error and Random Effects Distributions bayesTFR Bayesian Fertility Projection bayesclust Tests/Searches for significant clusters in genetic data bayescount Power calculations and Bayesian analysis of count distributions and FECRT data using MCMC bayesm Bayesian Inference for Marketing/Micro-econometrics bayesmix Bayesian Mixture Models with JAGS bayespack Numerical Integration for Bayesian Inference bayespref Hierarchical Bayesian analysis of ecological count data bbemkr Bayesian bandwidth estimation for multivariate kernel regression with Gaussian error bbmle Tools for general maximum likelihood estimation bclust Bayesian clustering using spike-and-slab hierarchical model, suitable for clustering high-dimensional data bcool Bringing to light significant Columns correlated with Organism Labels bcp A Package for Performing a Bayesian Analysis of Change Point Problems bcv Cross-Validation for the SVD (Bi-Cross-Validation) bdpv Inference and design for predictive values in binary diagnostic tests bdsmatrix Routines for Block Diagonal Symmetric matrices beadarrayMSV Analysis of Illumina BeadArray SNP data including MSV markers beanplot Visualization via Beanplots (like Boxplot/Stripchart/Violin Plot) bear Average bioequivalence and bioavailability data analysis tool beeswarm The bee swarm plot, an alternative to stripchart belief Contains basic functions to manipulate belief functions and associated mass assignments benchden 28 benchmark densities from Berlinet/Devroye (1994) benchmark Benchmark Experiments Toolbox bentcableAR Bent-Cable Regression for Independent Data or Autoregressive Time Series ber Batch Effects Removal bestglm Best Subset GLM betaper Functions to incorporate taxonomic uncertainty on multivariate analyses of ecological data betareg Beta Regression bethel Bethel's algorithm bfast BFAST: Breaks For Additive Seasonal and Trend bfp Bayesian Fractional Polynomials bgmm Gaussian Mixture Modeling algorithms. Including the belief-based mixture modeling biGraph Analysis Toolbox For Bipartite Graphs biOps Image processing and analysis biOpsGUI GUI for Basic image operations bibtex bibtex parser biclust BiCluster Algorithms bifactorial Inferences for bi- and trifactorial trial designs biganalytics A library of utilities for big.matrix objects of package bigmemory biglars Scalable Least-Angle Regression and Lasso biglm bounded memory linear and generalized linear models bigmemory Manage massive matrices with shared memory and memory-mapped files bigtabulate table-, tapply-, and split-like functionality for matrix and big.matrix objects bild bild: a package for BInary Longitudinal Data bimetallic Power for SNP analyses using silver standard cases binGroup Evaluation and experimental design for binomial group testing binMto Asymptotic simultaneous confidence intervals for many-to-one comparisons of proportions binarySimCLF Simulates Correlated Binary Data bindata Generation of Artificial Binary Data binhf Haar-Fisz functions for binomial data binom Binomial Confidence Intervals For Several Parameterizations binomSamSize Confidence intervals and sample size determination for a binomial proportion under simple random sampling and pooled sampling binomTools Performing diagnostics on binomial regression models bio.infer Predict environmental conditions from biological observations biopara Self-contained parallel system for R bios2mds From BIOlogical Sequences to MultiDimensional Scaling bipartite Visualising bipartite networks and calculating some (ecological) indices bise Auxiliary functions for phenological data analysis biseVec Auxiliary functions for phenological data analysis bisoreg Bayesian Isotonic Regression with Bernstein Polynomials bit A class for vectors of 1-bit booleans bitops Functions for Bitwise operations bivarRIpower Sample size calculations for bivariate longitudinal data biwt Functions to compute the biweight mean vector and covariance & correlation matrices blender Analyze biotic homogenization of landscapes blighty United Kingdom coastlines blm Binomial linear and linear-expit regression blme Bayesian Linear Mixed-Effects models blockTools Block, assign, and diagnose potential interference in randomized experiments blockmodeling An R package for Generalized and classical blockmodeling of valued networks blockrand Randomization for block random clinical trials bmd Benchmark dose analysis for dose-response data bmem Mediation analysis with missing data using bootstrap bnlearn Bayesian network structure learning, parameter learning and inference boa Bayesian Output Analysis Program (BOA) for MCMC boolean Boolean Binary Response Models boolfun Cryptographic Boolean Functions boot Bootstrap Functions (originally by Angelo Canty for S) bootRes Bootstrapped Response and Correlation Functions bootStepAIC Bootstrap stepAIC bootruin A bootstrap test for the probability of ruin in the classical risk process bootspecdens Testing equality of spectral densities 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 multivariate time series with a visualisation and parametrisation using graph theory brew Templating Framework for Report Generation brglm Bias reduction in binomial-response GLMs bs Package for the Birnbaum-Saunders distribution bsml Basis Selection from Multiple Libraries bspec Bayesian spectral inference bst Gradient Boosting bujar Buckley-James Regression for Survival Data with High-Dimensional Covariates bvls The Stark-Parker algorithm for bounded-variable least squares bvpSolve Solvers for boundary value problems of ordinary differential equations CADFtest This package performs the CADF unit root test proposed in Hansen (1995) CADStat Provides a GUI to several statistical methods useful for causal assessment CAVIAR Cambial Activity and wood formation data processing, visualisation and analysis using R CCA Canonical correlation analysis CCM Correlation classification method (CCM) CCMtools Clustering through "Correlation Clustering Model" (CCM) and cluster analysis tools CDFt Statistical downscaling through CDF-transform CDNmoney Components of Canadian Monetary and Credit Aggregates CDVine Statistical inference of C- and D-vine copulas CFL Compensatory Fuzzy Logic CGIwithR CGI Programming in R CGene Causal Genetic Analysis CHCN Canadian Historical Climate Network CHNOSZ Chemical Thermodynamics and Activity Diagrams CHsharp Choi and Hall Clustering in 3d CITAN CITation ANalysis toolpack CLSOCP A smoothing Newton method SOCP solver CMC Cronbach-Mesbah Curve CNVassoc Association analysis of CNV data COMPoissonReg Conway-Maxwell Poisson (COM-Poisson) Regression COP Variables selection for index models via correlation pursuit CORElearn CORElearn - classification, regression, feature evaluation and ordinal evaluation CORREP Multivariate Correlation Estimator and Statistical Inference Procedures COSINE COndition SpecIfic sub-NEtwork COUNT Functions, data and code for count data COZIGAM Constrained and Unconstrained Zero-Inflated Generalized Additive Models with Model Selection Criterion CPE Concordance Probability Estimates in Survival Analysis CRTSize Sample Size Estimation Functions for Cluster Randomized Trials CTT Classical Test Theory Functions CVThresh Level-Dependent Cross-Validation Thresholding Cairo R graphics device using cairo graphics library for creating high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG, PostScript) and display (X11 and Win32) output CalciOMatic Automatic Calcium Imaging Analysis CarbonEL Carbon Event Loop CatDyn Fishery Stock Assessment by Catch Dynamic Models CausalGAM Estimation of Causal Effects with Generalized Additive Models CellularAutomaton One-Dimensional Cellular Automata ChainLadder Mack, Bootstrap, Munich, Multivariate-chain-ladder, Clark methods and generalized linear models for insurance claims reserving ChemoSpec Exploratory Chemometrics for Spectroscopy ChemometricsWithR Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences ChemometricsWithRData Data for package ChemometricsWithR CircNNTSR CircNNTSR: An R package for the statistical analysis of circular data using nonnegative trigonometric sums (NNTS) models CircStats Circular Statistics, from "Topics in circular Statistics" (2001) CityPlot Visualization of structure and contents of a database Ckmeans.1d.dp Optimal distance-based clustering for one-dimensional data ClinicalRobustPriors Robust Bayesian Priors in Clinical Trials: An R Package for Practitioners ClustOfVar Clustering of variables CoCo Graphical modelling by log-linear models (an interface from R to CoCo) CoCoCg Graphical modelling by CG regressions CoCoGraph Interactive and dynamic graphs for the CoCo objects CollocInfer Collocation Inference for Dynamic Systems CombMSC Combined Model Selection Criteria CommonJavaJars Useful libraries for building a Java based GUI under R CompQuadForm Distribution function of quadratic forms in normal variables CompRandFld Composite-likelihood based Analysis of Random Fields CompareTests Estimate diagnostic accuracy (sensitivity, specificity, etc) and agreement statistics when one test is conducted on only a subsample of specimens CompetingRiskFrailty Competing Risk Model with Frailties for Right Censored Survival Data ConvCalendar Converts dates between calendars ConvergenceConcepts Seeing convergence concepts in action CorrBin Nonparametrics with clustered binary data Covpath COVPATH Package CoxBoost Cox models by likelihood based boosting for a single survival endpoint or competing risks Cprob Conditional probability function of a competing event CreditMetrics Functions for calculating the CreditMetrics risk model Cubist Rule- and Instance-Based Regression Modeling CvM2SL1Test L1-version of Cramer-von Mises Two Sample Tests CvM2SL2Test Cramer-von Mises Two Sample Tests c3net Infering large-scale gene networks with C3NET cMonkey cMonkey intgrated biclustering algorithm ca Simple, Multiple and Joint Correspondence Analysis caGUI A Tcl/Tk GUI for the functions in the ca package caMassClass Processing & Classification 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 Scatterplot and Biplot Axes calibrator Bayesian calibration of complex computer codes candisc Generalized Canonical Discriminant Analysis canvas R graphics device targeting the HTML canvas element caper Comparative Analyses of Phylogenetics and Evolution in R car Companion to Applied Regression care High-Dimensional Regression and CAR Score Variable Selection caret Classification and Regression Training caroline A Collection of General Purpose Functions for R caschrono Séries temporelles avec R - Méthodes et cas caspar Clustered and sparse regression (CaSpaR) cat Analysis of categorical-variable datasets with missing values catR Procedures to generate IRT adaptive tests (CAT) catmap Case-control And Tdt Meta-Analysis Package catnet Categorical Bayesian Network Inference catspec Special models for categorical variables cba Clustering for Business Analytics cccd Class Cover Catch Digraphs ccems Combinatorially Complex Equilibrium Model Selection ccgarch Conditional Correlation GARCH models cclust Convex Clustering Methods and Clustering Indexes cda Coupled dipole approximation cellVolumeDist Functions to fit cell volume distributions and thereby estimate cell growth rates and division times cem CEM: Software for Coarsened Exact Matching cems Conditional expectatation manifolds censReg Censored Regression (Tobit) Models cfa Analysis of configuration frequencies (CFA) cg Comparison of groups cgdsr R-Based API for accessing the MSKCC Cancer Genomics Data Server (CGDS) 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 cghseg Segmentation methods for array CGH analysis changeLOS Change in LOS changepoint An R package for changepoint analysis charlson Converts listwise icd9 data into comorbidity count and Charlson Index cheb Discrete Linear Chebyshev Approximation chemCal Calibration functions for analytical chemistry chemometrics Multivariate Statistical Analysis in Chemometrics cherry Multiple testing methods for exploratory research choplump Choplump tests chplot Augmented Convex Hull Plots chron Chronological objects which can handle dates and times cimis R package for retrieving data from CIMIS circular Circular Statistics citbcmst Assigning tumor samples to CIT Breast Cancer Molecular Subtypes from gene expression data clValid Validation of Clustering Results clac Clust Along Chromosomes, a method to call gains/losses in CGH array data class Functions for Classification classGraph Construct Graphs of S4 Class Hierarchies classInt Choose univariate class intervals classifly Explore classification models in high dimensions clim.pact Climate analysis and empirical-statistical downscaling (ESD) package for monthly and daily data climatol Some Tools for Climatology: series homogenization, plus windrose and Walter&Lieth diagrams clime Constrained L1-minimization for Inverse (covariance) Matrix Estimation clinfun Clinical Trial Design and Data Analysis Functions clinsig Clinical significance functions clpAPI R Interface to C API of COIN-OR Clp clue Cluster ensembles clues Clustering Method Based on Local Shrinking clustTool GUI for clustering data with spatial information cluster Cluster Analysis Extended Rousseeuw et al clusterCons Calculate the consensus clustering result from re-sampled clustering experiments with the option of using multiple algorithms and parameter clusterGeneration random cluster generation (with specified degree of separation) clusterPower Power calculations for cluster-randomized crossover trials clusterRepro Reproducibility of gene expression clusters clusterSim Searching for optimal clustering procedure for a data set clusterfly Explore clustering interactively using R and GGobi clustsig Significant Cluster Analysis clustvarsel Variable Selection for Model-Based Clustering clv Cluster Validation Techniques cmaes Covariance Matrix Adapting Evolutionary Strategy cmm Categorical Marginal Models cmprsk Subdistribution Analysis of Competing Risks cmprskContin Continuous mark-specific relative risks for two groups cmrutils Misc Functions of the Center for the Mathematical Research cncaGUI Canonical Non-symmetrical Correspondence Analysis in R coarseDataTools A collection of functions to help with analysis of coarse infectious disease data 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 codep Multiscale Codependence Analysis codetools Code Analysis Tools for R coenoflex Gradient-Based Coenospace Vegetation Simulator coin Conditional Inference Procedures in a Permutation Test Framework colbycol Read big text files column by column, sometimes much bigger than available RAM, into R colcor Tests for column correlation in the presence of row correlation colorRamps Builds color tables colorspace Color Space Manipulation combinat combinatorics utilities compHclust Complementary Hierarchical Clustering compOverlapCorr Comparing overlapping correlation coefficients compare Comparing Objects for Differences compareGroups descriptives by groups compeir Event-specific incidence rates for competing risks data compoisson Conway-Maxwell-Poisson Distribution compositions Compositional Data Analysis compute.es Compute Effect Sizes concor Concordance concord Concordance and reliability concreg Concordance regression cond Approximate conditional inference for logistic and loglinear models condGEE Parameter estimation in conditional GEE for recurrent event gap times conf.design Construction of factorial designs confReg Confidence Estimators for Individual Regression Predictions constrainedKriging Constrained, covariance-matching constrained and universal point or block kriging contfrac Continued fractions contrast A collection of contrast methods convexHaz Nonparametric MLE/LSE of convex hazard copBasic Basic Copula Functions copas Statistical methods to model and adjust for bias in meta-analysis copula Multivariate dependence with copulas copulaedas Estimation of Distribution Algorithms Based on Copula Theory corcounts Generate correlated count random variables 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 corrplot visualization of a correlation matrix corrsieve CorrSieve cosso COSSO, adaptive COSSO, variable selection for nonparametric smoothing spline models costat Time series costationarity determination and tests of stationarity countrycode Create and manipulate data frames that contain country names or country coding schemes covRobust Robust Covariance Estimation via Nearest Neighbor Cleaning coxme Mixed Effects Cox Models coxphf Cox regression with Firth's penalized likelihood coxphw Weighted Cox regression coxrobust Robust Estimation in Cox Model cplexAPI R Interface to C API of IBM ILOG CPLEX cplm Monte Carlo EM algorithms and Bayesian methods for fitting Tweedie compound Poisson linear models cramer Multivariate nonparametric Cramer-Test for the two-sample-problem crank Completing ranks crantastic Various R tools for http://crantastic.org/ crawl Fit continuous-time correlated random walk models for animal movement data crimCV Group-Based Modelling of Longitudinal Data crmn CCMN and other noRMalizatioN methods for metabolomics data crossdes Design and Randomization in Crossover Studies crosshybDetector Detection of cross-hybridization events in microarray experiments crossmatch The cross-match test crrSC Competing risks regression for Stratified and Clustered data crs Categorical Regression Splines cshapes CShapes Dataset and Utilities cslogistic Conditionally Specified Logistic Regression ctarma Estimation and simulation if carma(p,q) cthresh Complex Wavelet Denoising software cts Continuous Time Autoregressive Models ctv CRAN Task Views cubature Adaptive multivariate integration over hypercubes cudaBayesreg CUDA Parallel Implementation of a Bayesian Multilevel Model for fMRI Data Analysis cudaBayesregData Data sets for the examples used in the package "cudaBayesreg" cumSeg Change point detection in genomic sequences curvHDR curvHDR filtering curvetest Test the equality of two curves, or one curve with 0 cusp Cusp Catastrophe Model Fitting Using Maximum Likelihood cwhmisc CWH's functions for maths, plotting, printing, statistics, strings, and tools cyclones Cyclone identification DAAG Data Analysis And Graphics data and functions DAAGbio Data Sets and Functions, for demonstrations with expression arrays and gene sequences DAAGxtras Data Sets and Functions, supplementary to DAAG DAGGER Consensus genetic maps DAKS Data Analysis and Knowledge Spaces DALY DALY Calculator - A GUI for stochastic DALY calculation in R DAMisc Dave Armstrong's Miscellaneous Functions DART Denoising Algorithm based on Relevance network Topology DATforDCEMRI Deconvolution Analysis Tool for Dynamic Contrast Enhanced MRI DBGSA methods of distance-based gene set functional enrichment analysis DBI R Database Interface DCGL Differential Coexpression Analysis of Gene Expression Microarray Data DCluster Functions for the detection of spatial clusters of diseases DDHFm Variance Stabilization by Data-Driven Haar-Fisz (for Microarrays) DECIDE DEComposition of Indirect and Direct Effects DEMEtics Evaluating the genetic differentiation between populations based on Gst and D values DEoptim Global optimization by differential evolution DIME DIME (Differential Identification using Mixture Ensemble) DMwR Functions and data for "Data Mining with R" DNAtools Tools for analysing forensic genetic DNA data DOBAD Analysis of Discretely Observed linear Birth-And-Death(-and-immigration) Markov Chains DOSim Disease Analysis toolkit for gene set; Computation of similarities between DO terms and disease similarity between gene products; Module detection among the gene set and multilayer annotation for each module DPpackage Bayesian Nonparametric and Semiparametric Analysis DRI DR-Integrator DSpat Spatial modelling for distance sampling data DTDA Doubly truncated data analysis DTK Dunnett-Tukey-Kramer Pairwise Multiple Comparison Test Adjusted for Unequal Variances and Unequal Sample Sizes Daim Diagnostic accuracy of classification models DatABEL file-based access to large matrices stored on HDD in binary format Davies The Davies quantile function Deducer Deducer DeducerExtras Additional dialogs and functions for Deducer DeducerMMR A Deducer plugin for moderated multiple regressions and simple slopes analysis DeducerPlugInExample Deducer Plug-in Example DeducerPlugInScaling Reliability and factor analysis plugin Defaults Create Global Function Defaults Depela Depela DescribeDisplay R interface to DescribeDisplay (GGobi plugin) Design Design Package DesignPatterns Design Patterns in R to build reusable object-oriented software 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)" DiagTest3Grp Diagnostic test summary measures for three ordinal groups DiagnosisMed Diagnostic test accuracy evaluation for medical professionals DiceDesign Designs of Computer Experiments DiceEval Construction and evaluation of metamodels DiceKriging Kriging methods for computer experiments DiceOptim Kriging-based optimization for computer experiments DiceView Plot methods for computer experiments design and surrogate DierckxSpline R companion to "Curve and Surface Fitting with Splines" DistributionUtils Distribution Utilities DiversitySampler Functions for re-sampling a community matrix to compute diversity indices at different sampling levels DoE.base Full factorials, orthogonal arrays and base utilities for DoE packages DoE.wrapper Wrapper package for design of experiments functionality DoseFinding Planning and Analyzing Dose Finding experiments dae Functions useful in the design and ANOVA of experiments dafs Data analysis for forensic scientists dagR R functions for directed acyclic graphs darts Statistical Tools to Analyze Your Darts Game data.table Extension of data.frame for fast indexing, fast ordered joins and fast grouping dataframes2xls dataframes2xls writes data frames to xls files datamap A system for mapping foreign objects to R variables and environments dataview Human readable data presentation date Functions for handling dates dbConnect Provides a graphical user interface to connect with databases that use MySQL dbEmpLikeGOF Goodness-of-fit and two sample comparison tests using sample entropy dblcens Compute the NPMLE of distribution from doubly censored data dbstats Distance-based statistics (dbstats) dcemriS4 A Package for Medical Image Analysis (S4 implementation) dcens Doubly censoring estimation dclone Data Cloning and MCMC Tools for Maximum Likelihood Methods dcv Conventional Cross-validation statistics for climate-growth model ddepn Dynamic Deterministic Effects Propagation Networks: Infer signalling networks for timecourse RPPA data ddesolve Solver for Delay Differential Equations ddst Data driven smooth test deSolve General solvers for initial value problems of ordinary differential equations (ODE), partial differential equations (PDE), differential algebraic equations (DAE), and delay differential equations (DDE) deal Learning Bayesian Networks with Mixed Variables debug MVB's debugger for R decon Deconvolution Estimation in Measurement Error Models deducorrect Deductive correction of simple rounding, typing and sign errors degenes Detection of differentially expressed genes degreenet Models for Skewed Count Distributions Relevant to Networks deldir Delaunay Triangulation and Dirichlet (Voronoi) Tessellation delftfews delftfews R extensions delt Estimation of multivariate densities with adaptive histograms demography Forecasting mortality, fertility, migration and population data 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 - Hidden Markov Models of GLMs and Other Distributions in S4 depth Depth functions tools for multivariate analysis depthTools Depth Tools Package descr Descriptive statistics desirability Desirabiliy Function Optimization and Ranking desire Desirability functions detrendeR Start the detrendeR Graphical User Interface (GUI) devEMF EMF graphics output device devtools Tools to make developing R code easier dfcrm Dose-finding by the continual reassessment method dfoptim Derivative-free Optimization dglm Double generalized linear models dgof Discrete Goodness-of-Fit Tests 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 dicionariosIBGE Dictionaries for reading survey microdata from IBGE dielectric Defines some physical constants and dielectric functions commonly used in optics, plasmonics difR Collection of methods to detect dichotomous differential item functioning (DIF) in psychometrics diff Statistics: What's the Difference? diffractometry Baseline identification and peak decomposition for x-ray diffractograms diffusionMap Diffusion map digeR GUI tool for analyzing 2D DIGE data digest Create cryptographic hash digests of R objects digitize digitize : a plot digitizer in R diptest Hartigan's dip test statistic for unimodality - corrected code directlabels Direct labels for multicolor plots in lattice or ggplot2 dirmult Estimation in Dirichlet-Multinomial distribution discretization Data preprocessing, discretization for classification diseasemapping Calculate observed and expected disease incidence counts from a case file and population data dismo Species distribution modeling dispmod Dispersion models distory Distance Between Phylogenetic Histories distr Object oriented implementation of distributions distrDoc Documentation for packages distr, distrEx, distrSim, distrTEst, distrTeach, distrMod, and distrEllipse distrEllipse S4 classes for elliptically contoured distributions distrEx Extensions of package distr distrMod Object oriented implementation of probability models distrSim Simulation classes based on package distr distrTEst Estimation and Testing classes based on package distr distrTeach Extensions of package distr for teaching Stochastics/Statistics in secondary school divagis Provides tools for quality checks of georeferenced plant species accessions diveMove Dive analysis and calibration diversitree diversitree: comparative phylogenetic tests of diversification divisors Find the divisors of a number dixon Nearest Neighbour Contingency Table Analysis dlm Bayesian and Likelihood Analysis of Dynamic Linear Models dlmap Detection Localization Mapping for QTL dlmodeler Generalized Dynamic Linear Modeler dlnm Distributed Lag Non-linear Models dmt Dependency Modeling Toolkit doBy Groupwise summary statistics, general linear contrasts, LSMEANS (least-squares-means), and other utilities doMC Foreach parallel adaptor for the multicore package doMPI Foreach parallel adaptor for the Rmpi package doRedis Foreach parallel adapter for the rredis package doSMP Foreach parallel adaptor for the revoIPC package doSNOW Foreach parallel adaptor for the snow package dpa Dynamic Path Approach dplR Dendrochronology Program Library in R dpmixsim Dirichlet Process Mixture model simulation for clustering and image segmentation dr Methods for dimension reduction for regression drawExpression Visualising R syntax through graphics drc Analysis of dose-response curves drfit Dose-response data evaluation drm Regression and association models for repeated categorical data dse Dynamic Systems Estimation (time series package) dse1 DSE (unbundled transition package) dse2 DSE (unbundled transition package) dti Analysis of diffusion weighted imaging (DWI) data dtt Discrete Trigonometric Transforms dtw Dynamic Time Warping algorithms dummies Create dummy/indicator variables flexibly and efficiently dvfBm Discrete variations of a fractional Brownian motion dyad Analysis of dyadic observational data dyn Time Series Regression dynCorr Dynamic Correlation Package dynGraph Interactive visualization of dataframes and factorial planes dynaTree Dynamic trees for learning and design dynamicGraph dynamicGraph dynamicTreeCut Methods for detection of clusters in hierarchical clustering dendrograms dynamo Dynamic Models dynlm Dynamic Linear Regression EDR Estimation of the effective dimension reduction (EDR) space EMA Easy Microarray data Analysis EMD Empirical Mode Decomposition and Hilbert Spectral Analysis EMJumpDiffusion EM-Algorithm for Jump Diffusion processes EMT Exact Multinomial Test: Goodness-of-Fit Test for Discrete Multivariate data ENmisc Neuwirth miscellaenous EQL Extended-Quasi-Likelihood-Function (EQL) ESPRESSO Power Analysis and Sample Size Calculation ETC Equivalence to control EVER Estimation of Variance by Efficient Replication EbayesThresh Empirical Bayes Thresholding and Related Methods Ecdat Data sets for econometrics EcoHydRology A community modeling foundation for Eco-Hydrology ElectroGraph Enhanced routines for plotting and analyzing valued relational data ElemStatLearn Data sets, functions and examples from the book: "The Elements of Statistical Learning, Data Mining, Inference, and Prediction" by Trevor Hastie, Robert Tibshirani and Jerome Friedman EnQuireR A package dedicated to questionnaires EngrExpt Data sets from "Introductory Statistics for Engineering Experimentation" Epi A package for statistical analysis in epidemiology EquiNorm Normalize expression data using equivalently expressed genes EstCRM Calibrating Parameters for the Samejima's Continuous IRT Model EuclideanMaps Displays Euclidean Maps EvalEst Dynamic Systems Estimation - extensions ExPD2D Exact Computation of Bivariate Projection Depth Based on Fortran Code ExomeCNV Detect CNV and LOH from Exome Sequecing Data e1071 Misc Functions of the Department of Statistics (e1071), TU Wien eRm Extended Rasch Modeling eVenn eVenn: A powerful tool to compare lists and draw Venn diagrams eaf Plots of the Empirical Attainment Function earth Multivariate Adaptive Regression Spline Models eba Elimination-by-Aspects (EBA) Models ebal Entropy reweighting to create balanced samples ebdbNet Empirical Bayes Estimation of Dynamic Bayesian Networks 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" ecoreg Ecological regression using aggregate and individual data edci Edge Detection and Clustering in Images editrules R package for parsing and manipulating edit rules edrGraphicalTools Provide tools for dimension reduction methods edtdbg Integrating R's debug() with Your Text Editor effects Effect Displays for Linear, Generalized Linear, Multinomial-Logit, Proportional-Odds Logit Models and mixed-effects models egarch EGARCH simulation and fitting egonet Tool for ego-centric measures in Social Network Analysis eha Event History Analysis eiPack eiPack: Ecological Inference and Higher-Dimension Data Management eigeninv Generates (dense) matrices that have a given set of eigenvalues eigenmodel Semiparametric factor and regression models for symmetric relational data el.convex empirical likelihood ratio tests for means elasticnet Elastic-Net for Sparse Estimation and Sparse PCA elec Collection of functions for statistical election audits elec.strat Functions for election audits using stratified random samples 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) emg Exponentially Modified Gaussian (EMG) Distribution emme2 Read and Write to an EMME/2 databank emoa Evolutionary Multiobjective Optimization Algorithms emplik Empirical likelihood ratio for censored/truncated data emplik2 Empirical-likelihood test (two-sample, censored data) emu Interface to the Emu Speech Database System emulator Bayesian emulation of computer programs endogMNP R Package for Fitting Multinomial Probit Models with Endogenous Selection energy E-statistics (energy statistics) english Translate integers into English enrichvs Enrichment assessment of virtual screening approaches ensembleBMA Probabilistic Forecasting using Ensembles and Bayesian Model Averaging entropy Entropy and Mutual Information Estimation envelope Envelope normality test epade Easy Plots epiR Functions for analysing epidemiological data epibasix Elementary Epidemiological Functions for a Graduate Epidemiology\Biostatistics Course epicalc Epidemiological calculator epinet A collection of epidemic/network-related tools epitools Epidemiology Tools epoc EPoC (Endogenous Perturbation analysis of Cancer) epsi Edge Preserving Smoothing for Images eqtl Tools for analyzing eQTL experiments: A complementary to Karl Broman's 'qtl' package for genome-wide analysis equate Statistical Methods for Test Score Equating equivalence Provides tests and graphics for assessing tests of equivalence erer Empirical Research in Economics with R ergm Fit, Simulate and Diagnose Exponential-Family Models for Networks ergm.userterms User-specified terms for the statnet suite of packages esd4all esd4all esotericR esotericR articles from lemnica.com estout Estimates Output etm Empirical Transition Matrix evaluate Parsing and evaluation tools that provide more details than the default evd Functions for extreme value distributions evdbayes Bayesian Analysis in Extreme Value Theory evir Extreme Values in R exact2x2 Exact Conditional Tests and Confidence Intervals for 2x2 tables exactLoglinTest Monte Carlo Exact Tests for Log-linear models exactRankTests Exact Distributions for Rank and Permutation Tests exactci Exact P-values and Matching Confidence Intervals for simple Discrete Parametric Cases exactmaxsel Maximally selected statistics for binary response variables - Exact methods exams Automatic Generation of Standardized Exams for Large-Lecture Courses expectreg Expectile and Quantile Regression experiment experiment: R package for designing and analyzing randomized experiments expert Modeling without data using expert opinion expm Matrix exponential expsmooth Data sets from "Forecasting with exponential smoothing" extRemes Extreme value toolkit extfunnel Additional Funnel Plot Augmentations extracat Graphic Extensions for Categorical Data extremevalues Univariate outlier detection eyetracking Eyetracking Helper Functions ez Easy analysis and visualization of factorial experiments FAMT Factor Analysis for Multiple Testing (FAMT) : simultaneous tests under dependence in high-dimensional data FAdist Distributions that are sometimes used in hydrology FAiR Factor Analysis in R FAmle Maximum Likelihood and Bayesian Estimation of Univariate Probability Distributions FAwR Functions and Datasets for "Forest Analytics with R" FBN FISH Based Normalization and Copy Number inference of SNP microarray data FD Measuring functional diversity (FD) from multiple traits, and other tools for functional ecology FEST Identification of Family Relations using linked markers FFD Freedom From Disease FGN Fractional Gaussian Noise, estimation and simulaton FITSio FITS (Flexible Image Transport System) utilities FKF Fast Kalman Filter FLLat Fused Lasso Latent Feature Model FME A Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability, Monte Carlo Analysis FNN Fast Nearest Neighbor Search Algorithms and Applications FRB Fast and Robust Bootstrap FRBData Download financial data from FRB's website FSelector Selecting attributes FTICRMS Programs for Analyzing Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry Data FactoClass Combination of Factorial Methods and Cluster Analysis FactoMineR Multivariate Exploratory Data Analysis and Data Mining with R Fahrmeir Data from the book "Multivariate Statistical Modelling Based on Generalized Linear Models", first edition, by Ludwig Fahrmeir and Gerhard Tutz FeaLect Scores features for Feature seLection FieldSim Random fields simulations FinTS Companion to Tsay (2005) Analysis of Financial Time Series FisherEM Model-Based Clustering in the Fisher Discriminative Subspace FitAR Subset AR Model Fitting FitARMA FitARMA: Fit ARMA or ARIMA using fast MLE algorithm Flury Data Sets from Flury, 1997 ForImp Imputation of missing values through a forward imputation algorithm Formula Extended Model Formulas FourierDescriptors Generate images using Fourier descriptors FrF2 Fractional Factorial designs with 2-level factors FrF2.catlg128 Complete catalogues of resolution IV 128 run 2-level fractional factorials up to 24 factors FracSim Simulation of Lévy motions FunCluster Functional Profiling of Microarray Expression Data FunNet Integrative Functional Analysis of Transcriptional Networks FuncMap Hive Plots of R Package Function Calls fANCOVA Nonparametric Analysis of Covariance fArma ARMA Time Series Modelling fAsianOptions EBM and Asian Option Valuation fAssets Rmetrics - Assets Selection and Modelling fBasics Rmetrics - Markets and Basic Statistics fBonds Bonds and Interest Rate Models fCalendar Chronological and Calendarical Objects fCertificates fCertificates - Basics of Certificates and Structured Products Valuation fCopulae Rmetrics - Dependence Structures with Copulas fEcofin Economic and Financial Data Sets fExoticOptions Exotic Option Valuation fExtremes Rmetrics - Extreme Financial Market Data fGarch Rmetrics - Autoregressive Conditional Heteroskedastic Modelling fImport Rmetrics - Economic and Financial Data Import fMultivar Multivariate Market Analysis fNonlinear Nonlinear and Chaotic Time Series Modelling fOptions Basics of Option Valuation fPortfolio Rmetrics - Portfolio Selection and Optimization - ebook available at www.rmetrics.org fRegression Regression Based Decision and Prediction fSeries Financial Time Series Objects fTrading Technical Trading Analysis fUnitRoots Trends and Unit Roots fUtilities Function Utilities factorQR Bayesian quantile regression factor models factualR thin wrapper for the Factual.com server API fairselect Feature Annealed Independence Rules (demo) fame Interface for FAME time series database far Modelization for Functional AutoRegressive processes faraway Functions and datasets for books by Julian Faraway farmR Mixed Integer model of Arable Farms fast Implementation of the Fourier Amplitute Sensitivity Test (FAST) fastICA FastICA Algorithms to perform ICA and Projection Pursuit fastR Data sets and utilities for Foundations and Applications of Statistics by R Pruim fastVAR fastVAR fastcluster Fast hierarchical clustering routines for R and Python fastmatch Fast match() function favir Formatted Actuarial Vignettes in R fbati Gene by Environment Interaction and Conditional Gene Tests for Nuclear Families fda Functional Data Analysis fda.usc Functional Data Analysis and Utilities for Statistical Computing (fda.usc) fdaMixed Functional data analysis in a mixed model framework fdim Functions for calculating fractal dimension fdrci Permutation-based FDR Point and Confidence Interval Estimation fdrtool Estimation and Control of (Local) False Discovery Rates fds Functional data sets fdth Frequency Distribution Tables, Histograms and Poligons feature Feature significance for multivariate kernel density estimation features Feature Extraction for Discretely-Sampled Functional Data fechner Fechnerian Scaling of Discrete Object Sets ff memory-efficient storage of large data on disk and fast access functions ffbase Basic statistical functions for package ff ffmanova Fifty-fifty MANOVA fftw Fast FFT and DCT based on FFTW 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 finebalance Approximate fine balance when exact fine balance is not achievable fingerprint Functions to operate on binary fingerprint data fisheyeR Fisheye and Hyperbolic-space-alike Interactive Visualization Tools in R fishmethods Fisheries Methods and Models in R fit4NM NONMEM platform fitDRC Fitting Density Ratio Classes fitdistrplus Help to fit of a parametric distribution to non-censored or censored data flashClust Implementation of optimal hierarchical clustering flexclust Flexible Cluster Algorithms flexmix Flexible Mixture Modeling flsa Path algorithm for the general Fused Lasso Signal Approximator flubase Baseline of mortality free of influenza epidemics flux Flux rate calculation from dynamic closed chamber measurements fma Data sets from "Forecasting: methods and applications" by Makridakis, Wheelwright & Hyndman (1998) fmri Analysis of fMRI experiments fmsb Functions for medical statistics book with some demographic data foba greedy variable selection forams Foraminifera and Community Ecology Analyses foreach Foreach looping construct for R forecast Forecasting functions for time series foreign Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, .. forensic Statistical Methods in Forensic Genetics forensim Statistical tools for the interpretation of forensic DNA mixtures fork R functions for handling multiple processes formatR Format R Code Automatically formula.tools Utilities for working with formulas, expressions, calls and other R objects fortunes R Fortunes forward Forward search fossil Palaeoecological and Palaeogeographical Analysis Tools fpc Flexible procedures for clustering fpca Restricted MLE for Functional Principal Components Analysis fpow Computing the noncentrality parameter of the noncentral F distribution fpp Data sets for the "Forecasting: principles and practice" workshop by Rob J Hyndman, June 2011 fptdApprox Approximation of first-passage-time densities for diffusion processes fracdiff Fractionally differenced ARIMA aka ARFIMA(p,d,q) models fractal Insightful Fractal Time Series Modeling and Analysis fractaldim Estimation of fractal dimensions fractalrock Generate fractal time series with non-normal returns distribution frailtyHL Frailty Models via H-likelihood frailtypack Frailty models using maximum penalized likelihood estimation frbf Implementation of the "Flexible kernels for RBF network" algorithm freqMAP Frequency Moving Average Plots (MAP) of Multinomial Data by a Continuous Covariate frontier Stochastic Frontier Analysis fso Fuzzy Set Ordination ftnonpar Features and Strings for Nonparametric Regression fts R interface to tslib (a time series library in c++) ftsa Functional time series analysis fun Use R for Fun functional Curry, Compose, and other higher-order functions futile Futile base package futile.any Futile library to provide some polymorphism futile.logger Futile logger subsystem futile.matrix Futile matrix utilities futile.options Futile options management futile.paradigm A framework for working in a functional programming paradigm in R 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 fwdmsa Forward search for Mokken scale analysis fxregime Exchange Rate Regime Analysis GA4Stratification A genetic algorithm approach to determine stratum boundaries and sample sizes of each stratum in stratified sampling GAD GAD: Analysis of variance from general principles GAMBoost Generalized linear and additive models by likelihood based boosting GAMens Applies GAMbag, GAMrsm and GAMens ensemble classifiers for binary classification GANPA Gene Association Network-based Pathway Analysis GANPAdata The GANPA Datasets Package GB2 Generalized Beta Distribution of the Second Kind: properties, likelihood, estimation GDD GD device for creating bitmap graphics as jpeg, png or gif files using gd library GEOmap Topographic and Geologic Mapping GEVcdn GEV conditonal density estimation network GExMap A visual, intuitive, easy to use software giving access to a new type of information buried into your microarray data GGEBiplotGUI GGE Biplots in R GGMselect Gaussian Graphs Models selection GGally Extension to ggplot2 GLDEX Fitting Single and Mixture of Generalised Lambda Distributions (RS and FMKL) using Various Methods GOFSN Goodness-of-fit tests for the family of skew-normal models GOSim Computation of functional similarities between GO terms and gene products; GO enrichement analysis GPArotation GPA Factor Rotation GPseq gpseq: Using the generalized Poisson distribution to model sequence read counts from high throughput sequencing experiments GRRGI Gauge R and R Confidence Intervals GSA Gene set analysis GSM Gamma Shape Mixture GUTS GUTS: Fast Calculation of the Likelihood of a Stochastic Survival Model GWAF Genome-Wide Association analyses with Family data GWASExactHW Exact Hardy-Weinburg testing for Genome Wide Association Studies GWAtoolbox GWAS Quality Control GWRM GWRM GenABEL genome-wide SNP association analysis GenKern Functions for generating and manipulating binned kernel density estimates GenSA R functions for Generalized Simulated Annealing GeneCycle Identification of Periodically Expressed Genes GeneF Package for Generalized F-statistics GeneNet Modeling and Inferring Gene Networks GeneReg Construct time delay gene regulatory network Geneclust Simulation and analysis of spatial structure of population genetics data Geneland Detection of structure from multilocus genetic data GeneralizedHyperbolic The generalized hyperbolic distribution GeoXp Interactive exploratory spatial data analysis GhcnDaily Downloads and processes GHCN daily GillespieSSA Gillespie's Stochastic Simulation Algorithm (SSA) GrapheR A multiplatform GUI for drawing customizable graphs in R GrassmannOptim Grassmann Manifold Optimization GridR Executes functions on remote hosts, clusters or grids GriegSmith Uses Grieg-Smith method on 2 dimentional spatial data GroupSeq Performing computations related to group sequential designs Guerry Guerry: maps, data and methods related to Guerry (1833) "Moral Statistics of France" g.data Delayed-Data Packages gMCP Graph Based Multiple Comparison Procedures gPdtest Bootstrap goodness-of-fit test for the generalized Pareto distribution gRain Graphical Independence Networks gRapHD Efficient selection of undirected graphical models for high-dimensional datasets gRbase A package for graphical modelling in R gRc Inference in Graphical Gaussian Models with Edge and Vertex Symmetries gRim Graphical Interaction Models gWidgets gWidgets API for building toolkit-independent, interactive GUIs gWidgetsRGtk2 Toolkit implementation of gWidgets for RGtk2 gWidgetsWWW Toolkit implementation of the gWidgets API for use with web pages gWidgetstcltk Toolkit implementation of gWidgets for tcltk package gafit Genetic Algorithm for Curve Fitting galts Genetic algorithms and C-steps based LTS (Least Trimmed Squares) estimation gam Generalized Additive Models gamair Data for "GAMs: An Introduction with R" gamboostLSS Boosting Methods for GAMLSS Models games Statistical Estimation of Game-Theoretic Models gamesNws Playing games using a NWS Server gamlss Generalized Additive Models for Location Scale and Shape gamlss.add GAMLSS Additive gamlss.cens Fitting an interval response variable using gamlss.family distributions gamlss.data GAMLSS Data gamlss.demo Demos for GAMLSS gamlss.dist 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 gamlss.util GAMLSS Utilities gamm4 Generalized additive mixed models using mgcv and lme4 gap Genetic analysis package gaussDiff Difference measures for multivariate Gaussian probability density functions gaussquad Collection of functions for Gaussian quadrature gbRd Utilities for processing Rd objects and files gbev Gradient Boosted Regression Trees with Errors-in-Variables gbm Generalized Boosted Regression Models gbs Package for Generalized Birnbaum-Saunders Distributions gcExplorer Graphical Cluster Explorer gcbd GPU/CPU Benchmarking in Debian-based systems gclus Clustering Graphics gcmr Gaussian Copula Marginal Regression gcmrec General class of models for recurrent event data gcolor Provides an Inequation Algorithm Function and a solution to import DIMACS files gdata Various R programming tools for data manipulation gdistance distances and routes on geographical grids gdsfmt CoreArray Genomic Data Structure (GDS) R Interface gee Generalized Estimation Equation solver geepack Generalized Estimating Equation Package geiger Analysis of evolutionary diversification genalg R Based Genetic Algorithm geneARMA Simulate, model, and display data from a time-course microarray experiment with periodic gene expression geneListPie Profiling a gene list into GOslim or KEGG function pie genepi Genetic Epidemiology Design and Inference genetics Population Genetics genoPlotR Plot publication-grade gene and genome maps genomatic Manages microsatellite projects. Creates 96-well maps, genotyping submission forms, rerun management, and import into statistical software genridge Generalized ridge trace plots for ridge regression geoPlot Performs Address Comparison geoR Analysis of geostatistical data geoRglm geoRglm - a package for generalised linear spatial models geofd Spatial prediction for function value data geomapdata Data for topographic and Geologic Mapping geometry Mesh generation and surface tesselation geonames Interface to www.geonames.org web service geophys Geophysics, Continuum Mechanics, Mogi Model geosphere Spherical Trigonometry geozoo Zoo of Geometric Objects getopt C-like getopt behavior ggcolpairs Combination of GGplot2 plots into a matrix based on data columns ggdendro Tools for extracting dendrogram and tree diagram plot data for use with ggplot 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 glm2 Fitting Generalized Linear Models glmc Fitting Generalized Linear Models Subject to Constraints glmdm R Code for Simulation of GLMDM glmmAK Generalized Linear Mixed Models glmmBUGS Generalised Linear Mixed Models and Spatial Models with WinBUGS, BRugs, or OpenBUGS glmmML Generalized linear models with clustering glmnet Lasso and elastic-net regularized generalized linear models glmnetcr Fit a penalized constrained continuation ratio model for predicting an ordinal response glmpath L1 Regularization Path for Generalized Linear Models and Cox Proportional Hazards Model glmpathcr Fit a penalized continuation ratio model for predicting an ordinal response glmperm Inference in Generalized Linear Models glmulti GLM model selection and multimodel inference made easy globalboosttest Testing the additional predictive value of high-dimensional data glogis Fitting and Testing Generalized Logistic Distributions glpk GNU Linear Programming Kit glpkAPI R Interface to C API of GLPK glrt Generalized Logrank Tests for Interval-censored Failure Time Data gmaps Wrapper and auxilliary functions for maps package to work with grid graphics system gmm Generalized Method of Moments and Generalized Empirical Likelihood 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 gnumeric Read data from files readable by gnumeric goalprog Weighted and lexicographical goal programming and optimization gof Model-diagnostics based on cumulative residuals gogarch Generalized Orthogonal GARCH (GO-GARCH) models gooJSON Google JSON Data Interpreter for R googleVis Interface between R and the Google Visualisation API googlebigquery R client library for communicating with the Google Bigquery service gpairs gpairs: The Generalized Pairs Plot gpclib General Polygon Clipping Library for R gplots Various R programming tools for plotting data gpls Classification using generalized partial least squares gptk Gaussian Processes Tool-Kit gputools A few GPU enabled functions grImport Importing Vector Graphics grade Provides functions for matching student-answers to teacher answers for a variety of data types granova Graphical Analysis of Variance granovaGG Graphical Analysis of Variance Using ggplot2 graphComp Visual graph comparison graphicsQC Quality Control for Graphics in R graphite GRAPH Interaction from pathway Topological Environment gregmisc Greg's Miscellaneous Functions gridBase Integration of base and grid graphics gridExtra functions in Grid graphics grofit The package was developed to fit fit many growth curves obtained under different conditions grouped Regression Analysis of Grouped and Coarse Data grplasso Fitting user specified models with Group Lasso penalty grpreg Regularization paths for regression models with grouped covariates grt General Recognition Theory gsDesign Group Sequential Design gsarima Two functions for Generalized SARIMA time series simulation gsc Generalised Shape Constraints gsl wrapper for the Gnu Scientific Library gsmoothr Smoothing tools gss General Smoothing Splines gstat spatial and spatio-temporal geostatistical modelling, prediction and simulation gstudio GeneticStudio packages for R gsubfn Utilities for strings and function arguments gtcorr Calculate efficiencies of group testing algorithms with correlated responses gtools Various R programming tools gumbel Gumbel copula gvlma Global Validation of Linear Models Assumptions gwerAM Controlling the genome-wide type I error rate in association mapping experiments HAC Estimation, simulation and visualization of Hierarchical Archimedean Copulae (HAC) HAPim HapIM HDMD Statistical Analysis Tools for High Dimension Molecular Data (HDMD) HDclassif High Dimensionnal Supervised Classification and Clustering HFWutils csv import, csv export, garbage collection,string matching and passing by reference HGLMMM Hierarchical Generalized Linear Models HH Statistical Analysis and Data Display: Heiberger and Holland HI Simulation from distributions supported by nested hyperplanes HLMdiag Diagnostic tools for two-level normal hierarchical linear models HMM HMM - Hidden Markov Models HMR Flux estimation with static chamber data HPbayes Heligman Pollard mortality model parameter estimation using Bayesian Melding with Incremental Mixture Importance Sampling HSAUR A Handbook of Statistical Analyses Using R HSAUR2 A Handbook of Statistical Analyses Using R (2nd Edition) HSROC Joint meta-analysis of diagnostic test sensitivity and specificity with or without a gold standard reference test HTMLUtils Facilitates automated HTML report creation HWEBayes Bayesian investigation of Hardy-Weinberg Equilibrium via estimation and testing HWEintrinsic Objective Bayesian Testing for the Hardy-Weinberg Equilibrium Problem HadoopStreaming Utilities for using R scripts in Hadoop streaming HapEstXXR HapEstXXR Haplin Analyzing case-parent triad and/or case-control data with SNP haplotypes HaploSim HaploSim HardyWeinberg Graphical tests for Hardy-Weinberg equilibrium HiDimDA High Dimensional Discriminant Analysis HiddenMarkov Hidden Markov Models HistData Data sets from the history of statistics and data visualization Hmisc Harrell Miscellaneous Hotelling Hotelling's T-squared test and variants HumMeth27QCReport HumMeth27QCReport: quality control and preprocessing of Illumina's Infinium methylation assays HybridMC Implementation of the Hybrid Monte Carlo and Multipoint Hybrid Monte Carlo sampling techniques HydroMe Estimation of Soil Hydraulic Parameters from Experimental Data HyperbolicDist The hyperbolic distribution haarfisz Software to perform Haar Fisz transforms hacks Convenient R Functions halp Show certain type of comments from function bodies as "live-help" hapassoc Inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm haplo.ccs Estimate Haplotype Relative Risks in Case-Control Data haplo.stats Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous hapsim Haplotype Data Simulation hash Full feature implementation of hash/associated arrays/dictionaries hbim Hill/Bliss Independence Model for Combination Vaccines hbmem Hierarchical Bayesian Analysis of Recognition Memory hda Heteroscedastic Discriminant Analysis 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 heavy Package for outliers accomodation using heavy-tailed distributions helloJavaWorld Hello Java World helpr Help for R heplots Visualizing Tests in Multivariate Linear Models hergm Hierarchical Exponential-Family Random Graph Models hett Heteroscedastic t-regression hexView Viewing Binary Files hexbin Hexagonal Binning Routines hgam High-dimensional Additive Modelling hglm Hierarchical Generalized Linear Models hier.part Hierarchical Partitioning highlight Syntax highlighter hints Provide hints on what to do next hisemi Hierarchical Semiparametric Regression of Test Statistics histogram Construction of regular and irregular histograms with different options for automatic choice of bins hive Hadoop InteractiVE hlr Hidden Logistic Regression hmm.discnp Hidden Markov models with discrete non-parametric observation distributions holdem Texas Holdem simulator homals Gifi Methods for Optimal Scaling homeR Functions useful for building physics homtest Homogeneity tests for Regional Frequency Analysis hopach Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) hot Computation on micro-arrays hotspots Hot spots howmany A lower bound for the number of correct rejections hsmm Hidden Semi Markov Models hts Hierarchical and grouped time series httpRequest Basic HTTP Request huge High-dimensional Undirected Graph Estimation hwde Models and tests for departure from Hardy-Weinberg equilibrium and independence between loci hwriter HTML Writer - Outputs R objects in HTML format hybridHclust Hybrid hierarchical clustering hydroGOF Goodness-of-fit functions for comparison of simulated and observed hydrological time series hydroTSM Time series management, analysis and interpolation for hydrological modelling hyperSpec Interface for hyperspectral data sets, i.e. spectra + meta information (spatial, time, concentration, …) hyperdirichlet A generalization of the Dirichlet distribution hypergeo The hypergeometric function hypred Simulation of genomic data in applied genetics IBrokers R API to Interactive Brokers Trader Workstation ICC Functions facilitating the estimation of the Intraclass Correlation Coefficient ICE Iterated Conditional Expectation ICEinfer Incremental Cost-Effectiveness (ICE) Statistical 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) IFP Identifying functional polymorphisms in genetic association studies IMIS Increamental Mixture Importance Sampling IPSUR Introduction to Probability and Statistics Using R IQCC Improved Quality Control Charts IQMNMR Identification and Quantification of Metabolites by Using 1D 1H NMR FID ISDA.R interval symbolic data analysis for R ISOcodes Selected ISO codes ISOweek Week of the year and weekday according to ISO 8601 ISwR Introductory Statistics with R Icens NPMLE for Censored and Truncated Data ImageMetrics Facilitates image analysis for social scientists Imap Interactive Mapping ImpactIV Identifying Causal Effect for Multi-Component Intervention Using Instrumental Variable Method IndependenceTests Nonparametric tests of independence between random vectors InfDim Infine-dimensional model (IDM) to analyse phenotypic variation in growth trajectories IniStatR Initiation à la Statistique avec R Interpol Interpolation of amino acid sequences Iso Functions to perform isotonic regression IsoGene Testing for monotonic relationship between gene expression and doses in a microarray experiment IsotopeR IsotopeR iBUGS An Interface to R2WinBUGS by gWidgets iCluster Integrative clustering of multiple genomic data types iGenomicViewer Tool for sending interactive bioinformatic heatmaps with tool-tip content iRefR iRefIndex Manager iRegression iRegression iSubpathwayMiner The package can implement the graph-based reconstruction, analyses, and visualization of the KEGG pathways iWebPlots Interactive web-based plots ibdreg Regression Methods for IBD Linkage With Covariates ibr Iterative Bias Reduction ic.infer Inequality constrained inference in linear normal situations ic50 Standardized high-throughput evaluation of cell-based compound screens icaOcularCorrection Independent Components Analysis (ICA) based eye-movement correction icomp ICOMP criterion identity Jacquard Condensed Coefficients of Identity idr Irreproducible discovery rate ieeeround Functions to set and get the IEEE rounding mode ifa Independent Factor Analysis ifs Iterated Function Systems ifultools Insightful Research Tools igraph Network analysis and visualization igraphtosonia Convert iGraph graps to SoNIA .son files iid.test iid-test imguR Share plots using the imgur.com image hosting service imprProbEst Minimum distance estimation in an imprecise probability model imputation imputation impute impute: Imputation for microarray data imputeMDR The Multifactor Dimensionality Reduction (MDR) Analysis for Imcomplete Data indicspecies Functions to assess the strength and significance of relationship of species site group associations ineq Measuring Inequality, Concentration, and Poverty inference Functions to extract inferential values of a fitted model object influence.ME Tools for detecting influential data in mixed effects models infoDecompuTE Information Decomposition of Two-phase Experiments infochimps An R wrapper for the infochimps.com API services informR informR: R Tools for Creating Sequence Statistics infotheo Information-Theoretic Measures inline Inline C, C++, Fortran function calls from R inlinedocs Convert inline comments to documentation insideRODE insideRODE includes buildin functions with deSolve solver and C/FORTRAN interfaces to nlme, together with compiled codes intamap procedures for automated interpolation intamapInteractive procedures for automated interpolation - methods only to be used interactively, not included in intamap package intcox Iterated Convex Minorant Algorithm for interval censored event data integrOmics end of integrOmics package integrativeME integrative mixture of experts interactivity toggle R interactive mode interval Weighted Logrank Tests and NPMLE for interval censored data intervals Tools for working with points and intervals introgress methods for analyzing introgression between divergent lineages ipdmeta Tools for Individual patient data and Mixed-level Meta-analysis iplots iPlots - interactive graphics for R ipptoolbox IPP Toolbox ipred Improved Predictors ipw Estimate inverse probability weights irlba Fast partial SVD by implicitly-restarted Lanczos bidiagonalization irr Various Coefficients of Interrater Reliability and Agreement irtProb Utilities and Probability Distributions Related to Multidimensional Person Item Response Models (IRT) irtoys Simple interface to the estimation and plotting of IRT models isa2 The Iterative Signature Algorithm isdals Provides datasets for Introduction to Statistical Data Analysis for the Life Sciences ismev An Introduction to Statistical Modeling of Extreme Values isocir Isotonic Inference for Circular data isopam Isopam (Clustering) isopat Calculation of isotopic pattern for a given molecular formula isotone Active set and generalized PAVA for isotone optimization isva Independent Surrogate Variable Analysis iteRates Parametric rate comparison iterLap Approximate probability densities by iterated Laplace Approximations iterators Iterator construct for R itertools Iterator Tools its Irregular Time Series itsmr Time series analysis package for students iv Information Visualisation with UML and Graphs ivivc A data analysis tool for in vitro-in vivo correlation (IVIVC) JADE JADE and ICA performance criteria JGR JGR - Java Gui for R JJcorr Calculates polychorical correlations for several copula families JM Joint Modelling of Longitudinal and Survival Data JOP Joint Optimization Plot JavaGD Java Graphics Device Johnson Johnson Transformation JointModeling Joint Modelling of Mean and Dispersion JudgeIt JudgeIt Julia Fractal Image Data Generator jit Just-in-time compiler for the R language jointDiag Joint Approximate Diagonalization of a set of square matrices jpeg Read and write JPEG images KFAS Kalman filter and smoothers for exponential family state space models 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) KernSmoothIRT Nonparametric Item Reponse Theory KrigInv Kriging-based Inversion for Deterministic and Noisy Computer Experiments KsPlot Check the power of a statistical model kappalab Non-additive measure and integral manipulation functions kerdiest Nonparametric kernel estimation of the distribution function. Bandwidth selection and estimation of related 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 kinfit Routines for fitting kinetic models to chemical degradation data kinship mixed-effects Cox models, sparse matrices, and modeling data from large pedigrees kinship2 Pedigree functions kknn Weighted k-Nearest Neighbors klaR Classification and visualization klausuR Multiple Choice Test Evaluation klin Linear equations with Kronecker structure km.ci Confidence intervals for the Kaplan-Meier estimator kmi Kaplan-Meier multiple imputation for the analysis of cumulative incidence functions in the competing risks setting kml K-Means for Longitudinal Data (KmL) kml3d K-means for joint Longitudinal data knn knn-gcv 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 kst Knowledge Space Theory kulife Data sets and functions from the Faculty of Life Sciences, University of Copenhagen kza Kolmogorov-Zurbenko Adaptive Filters kzft Kolmogorov-Zurbenko Fourier Transform and Applications kzs Kolmogorov-Zurbenko Spatial Smoothing and Applications LCAextend Latent Class Analysis (LCA) with familial dependence in extended pedigrees LDdiag Link Function and Distribution Diagnostic Test for Social Science Researchers LDheatmap Graphical display of pairwise linkage disequilibria between SNPs LDtests Exact tests for Linkage Disequilibrium and Hardy-Weinberg Equilibrium LGS simulating Linkage Group Selection (LGS) LIM Linear Inverse Model examples and solution methods LIStest Longest Increasing Subsequence Independence Test LLAhclust Hierarchical clustering of variables or objects based on the likelihood linkage analysis method LLdecomp Decomposes a set of variables into cliques and separators LMERConvenienceFunctions A suite of functions to back-fit fixed effects and forward-fit random effects, as well as other miscellaneous functions LN3GV LN3GV LPCM Local principal curve methods LS2W Locally stationary two-dimensional wavelet process estimation scheme LSD Lots of Superior Depictions LTPDvar LTPD plans for sampling inspection by variables LVQTools Learning Vector Quantization Tools LambertW Gaussianize and analyze skewed, heavy-tailed data LaplacesDemon Software for Bayesian Inference LargeRegression Large Regressions LeLogicielR Functions and datasets to accompany the book "Le logiciel R: Maitriser le langage, Effectuer des analyses statistiques" (french) LearnBayes Functions for Learning Bayesian Inference LearnEDA Functions for Learning Exploratory Data Analysis LiblineaR Linear Predictive Models Based On The Liblinear C/C++ Library LifeTables A package to implement HMD model life table system Lmoments L-moments and quantile mixtures LogConcDEAD Log-concave Density Estimation in Arbitrary Dimensions LogicForest Logic Forest LogicReg Logic Regression LogitNet Infer network based on binary arrays using regularized logistic regression LoopAnalyst A collection of tools to conduct Levins' Loop Analysis LowRankQP Low Rank Quadratic Programming labdsv Ordination and Multivariate Analysis for Ecology labeling Axis Labeling labeltodendro Convert labels or tables to a dendrogram labstatR Libreria del Laboratorio di Statistica con R laeken Estimation of indicators on social exclusion and poverty 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 landsat Radiometric and topographic correction of satellite imagery languageR Data sets and functions with "Analyzing Linguistic Data: A practical introduction to statistics" lars Least Angle Regression, Lasso and Forward Stagewise laser Likelihood Analysis of Speciation/Extinction Rates from Phylogenies lasso2 L1 constrained estimation aka ‘lasso’ lassoshooting L1 regularized regression (Lasso) solver using the Cyclic Coordinate Descent algorithm aka Lasso Shooting last.call Utility for returning previous commands as unevaluated calls and the full context of function calls latdiag Draws diagrams useful for checking latent scales latentnet Latent position and cluster models for statistical networks lattice Lattice Graphics latticeDensity Density estimation and nonparametric regression on irregular regions latticeExtra Extra Graphical Utilities Based on Lattice latticedl Lattice direct labels latticist A graphical user interface for exploratory visualisation lavaan Latent Variable Analysis lawstat An R package for biostatistics, public policy, and law lazy Lazy Learning for Local Regression lcd Learn Chain graphs via Decomposition lcda Latent Class Discriminant Analysis lcmm Estimation of various latent class mixed models and joint latent class mixed models lcmr lcmr package ldDesign Design of experiments for detection of linkage disequilibrium lda Collapsed Gibbs sampling methods for topic models lda.cv Cross-validation for linear discriminate analysis ldbounds Lan-DeMets Method for Group Sequential Boundaries ldlasso LD LASSO Regression for SNP Association Study leaps regression subset selection leiv Bivariate linear errors-in-variables estimation lemma Laplace approximated EM Microarray Analysis lessR Less Code, More Results lfe Linear Group Fixed Effects lga Tools for linear grouping analysis (LGA) lgtdl A set of methods for longitudinal data objects lhs Latin Hypercube Samples libamtrack libamtrack package lifecontingencies Package to perform actuarial evaluation of life contingencies limSolve Solving Linear Inverse Models limitplot Jitter/CI Plot with Ordered Points Below the Limit of Detection linkcomm Tools for Generating, Visualizing, and Analysing Link Communities in Networks linprog Linear Programming / Optimization list Statistical Methods for the Item Count Technique and List Experiment ljr Logistic Joinpoint Regression lmPerm Permutation tests for linear models lmSupport Support for Linear Models lme4 Linear mixed-effects models using S4 classes lmeSplines lmeSplines lmec Linear Mixed-Effects Models with Censored Responses lmm Linear mixed models lmmfit Goodness-of-fit-measures for linear mixed models with one-level-grouping lmmlasso Linear mixed-effects models with Lasso lmodel2 Model II Regression lmom L-moments lmomRFA Regional frequency analysis using L-moments lmomco L-moments, Censored L-moments, Trimmed L-moments, L-comoments, and Many Distributions lmtest Testing Linear Regression Models localdepth Local Depth locfdr Computes local false discovery rates locfit Local Regression, Likelihood and Density Estimation locpol Kernel local polynomial regression lodplot Plot a genome scan log10 Decimal log plotting in two and three dimensions log4r A simple logging system for R, based on log4j logcondens Estimate a Log-Concave Probability Density from iid Observations logcondiscr Estimate a Log-Concave Probability Mass function from Discrete i.i.d. Observations logging a tentative logging package 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 longRPart Recursive partitioning of longitudinal data using mixed-effects models longitudinal Analysis of Multiple Time Course Data longitudinalData Longitudinal Data longmemo Statistics for Long-Memory Processes (Jan Beran) – Data and Functions longpower Sample size calculations for longitudinal data lordif Logistic Regression Differential Item Functioning using IRT lossDev Robust Loss Development Using MCMC lpSolve Interface to Lp_solve v. 5.5 to solve linear/integer programs lpSolveAPI R Interface for lp_solve version 5.5.2.0 lpc Lassoed principal components for testing significance of features lpridge Local Polynomial (Ridge) Regression lqa Penalized Likelihood Inference for GLMs lsa Latent Semantic Analysis lspls LS-PLS Models lss the accelerated failure time model to right censored data based on least-squares principle ltm Latent Trait Models under IRT ltsa Linear time series analysis lubridate Make dealing with dates a little easier luca Likelihood inference from case-control data Under Covariate Assumptions (LUCA) M3 Reading M3 files MADAM This package provides some basic methods for meta-analysis MAINT.Data Model and Analize Interval Data MALDIquant Quantitative analysis of MALDI-TOF MS data MAMA Meta-Analysis of MicroArry MAMSE Calculation of Minimum Averaged Mean Squared Error (MAMSE) weights MAPLES Smoothed age profile estimation MARSS Multivariate Autoregressive State-Space Modeling MASS Support Functions and Datasets for Venables and Ripley's MASS MAT Multidimensional Adaptive Testing (MAT) MAc Meta-Analysis with Correlations MAclinical Class prediction based on microarray data and clinical parameters MAd Meta-Analysis with Mean Differences MBA Multilevel B-spline Approximation MBESS MBESS MCAPS MCAPS data and results MCE Tools for evaluating Monte Carlo Error MCLIME Simultaneous Estimation of the Regression Coefficients and Precision Matrix MCMCglmm MCMC Generalised Linear Mixed Models MCMChybridGP Hybrid Markov chain Monte Carlo using Gaussian Processes MCMCpack Markov chain Monte Carlo (MCMC) Package MCPAN Multiple comparisons using normal approximation MCPMod Design and Analysis of Dose-Finding Studies (see also DoseFinding package) MCUSUM Multivariate Cumulative Sum (MCUSUM) Control Chart MChtest Monte Carlo hypothesis tests with Sequential Stopping MDR Detect gene-gene interactions using multifactor dimensionality reduction MEMSS Data sets from Mixed-effects Models in S MEWMA Multivariate Exponentially Weighted Moving Average (MEWMA) Control Chart MFDA Model Based Functional Data Analysis MFDF Modeling Functional Data in Finance MFSAS Creation and Evaluation of Multilevel Fixed and Sequential Sampling Plans MHadaptive General Markov Chain Monte Carlo for Bayesian Inference using adaptive Metropolis-Hastings sampling MISA Bayesian Model Search and Multilevel Inference for SNP Association Studies MIfuns Pharmacometric tools for data preparation, modeling, simulation, and reporting MImix Mixture summary method for multiple imputation MKLE Maximum kernel likelihood estimation MKmisc Miscellaneous Functions from M. Kohl MLCM Maximum Likelihood Conjoint Measurement MLDA Methylation Linear Discriminant Analysis (MLDA) MLDS Maximum Likelihood Difference Scaling MLEcens Computation of the MLE for bivariate (interval) censored data MLPAstats MLPA analysis to detect gains and loses in genes MMG Mixture Model on Graphs MMIX Model selection uncertainty and model mixing MMST DATASETS FROM MMST MNM Multivariate Nonparametric Methods. An Approach Based on Spatial Signs and Ranks MNP R Package for Fitting the Multinomial Probit Model MOCCA Multi-objective optimization for collecting cluster alternatives MPV Data Sets from Montgomery, Peck and Vining's Book MSBVAR Markov-Switching, Bayesian, Vector Autoregression Models MSG Data and functions for the book Modern Statistical Graphics MSToolkit The MSToolkit library for clinical trial design MTSKNN Multivariate two-sample tests based on K-nearest-neighbors MUCflights Munich Franz-Josef-Strauss Airport Pattern Analysis MVA An Introduction to Applied Multivariate Analysis with R MVR Mean-Variance Regularization MVpower Give power for a given effect size using multivariate classification methods MaXact Exact max-type Cochran-Armitage trend test(CATT) 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 MatrixEQTL Matrix eQTL: Ultra fast eQTL analysis via large matrix operations MatrixModels Modelling with Sparse And Dense Matrices McParre Run a Regenerative Markov chain in Parallel on a Cluster Mcomp Data from the M-competitions MeDiChI MeDiChI ChIP-chip deconvolution library MergeGUI A GUI for Merging Datasets in R MetABEL meta-analysis of genome-wide SNP association results MetaPCA MetaPCA: Meta-analysis in the Dimension Reduction of Genomic data MetaQC MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis MetabolAnalyze Probabilistic latent variable models for metabolomic data Metabonomic GUI for Metabonomic Analysis Meth27QC Meth27QC: sample quality analysis, and sample control analysis MethComp Functions for analysis of method comparison studies Miney Implementation of the Well-Known Game to Clear Bombs from a Given Field (Matrix) MiscPsycho Miscellaneous Psychometric Analyses MissingDataGUI A GUI for Missing Data Exploration MixSim Simulating Data to Study Performance of Clustering Algorithms Modalclust Hierarchical Modal Clustering ModelGood Validation of prediction models ModelMap Creates Random Forest and Stochastic Gradient Boosting Models, and applies them to GIS .img files to build detailed prediction maps MortalitySmooth Smoothing Poisson counts with P-splines MplusAutomation Automating Mplus Model Estimation and Interpretation MsatAllele Visualizes the scoring and binning of microsatellite fragment sizes MuMIn Multi-model inference MultEq Multiple equivalence tests and simultaneous confidence intervals MultiPhen MultiPhen, a package for the genetic association testing of multiple phenotypes Multiclasstesting Performance of N-ary classification testing mAr Multivariate AutoRegressive analysis mFilter Miscellaneous time series filters mRm mRm: An R package for conditional maximum likelihood estimation in mixed Rasch models maRketSim Market simulator for R maanova Tools for analyzing Micro Array experiments magic create and investigate magic squares magma Matrix Algebra on GPU and Multicore Architectures magnets Simulate micro-magnets dynamics makesweave Literate Programming with Make and Sweave mapLD Linkage Disequilibrium Mapping mapReduce mapReduce - flexible mapReduce algorithm for parallel computation 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 mar1s Multiplicative AR(1) with Seasonal Processes marelac Tools for Aquatic Sciences marelacTeaching Datasets and tutorials for use in aquatic sciences margLikArrogance Marginal Likelihood Computation via Arrogance Sampling marginTree marginTree: margin trees for high-dimensional classification marginalmodelplots Marginal Mean Model Plots mathgraph Directed and undirected graphs maticce Mapping Transitions in Continuous Character Evolution matlab MATLAB emulation package matrixStats Methods that apply to rows and columns of a matrix matrixcalc Collection of functions for matrix differential calculus maxLik Maximum Likelihood Estimation maxLinear Conditional Samplings for Max-Linear Models maxent Text Classification Using Low-memory Multinomial Logistic Regression maxstat Maximally Selected Rank Statistics mblm Median-Based Linear Models mbmdr Model Based Multifactor Dimensionality Reduction mboost Model-Based Boosting mc2d Tools for Two-Dimensional Monte-Carlo Simulations mcclust Process an MCMC Sample of Clusterings mcga Machine coded genetic algorihms for real-valued optimization problems mcgibbsit Warnes and Raftery's MCGibbsit MCMC diagnostic mclogit Mixed Conditional Logit mclust Model-Based Clustering / Normal Mixture Modeling mcmc Markov Chain Monte Carlo mcmcplots Create Plots from MCMC Output mco Multi criteria optimization algorithms and related functions mcprofile Multiple Contrast Profiles mcsm Functions for Monte Carlo Methods with R mda Mixture and flexible discriminant analysis meboot Maximum Entropy Bootstrap for Time Series mecdf Multivariate Empirical Cumulative Distribution Functions medAdherence Medication Adherence: Commonly Used Definitions mederrRank Bayesian Methods for Identifying the Most Harmful Medication Errors mediation R Package for Causal Mediation Analysis mefa Multivariate Data Handling in Ecology and Biogeography mefa4 Multivariate Data Handling with S4 Classes and Sparse Matrices meifly Interactive model exploration using GGobi mem Moving Epidemics Method R Package memisc Tools for Management of Survey Data, Graphics, Programming, Statistics, and Simulation memoise Memoise functions merror Accuracy and Precision of Measurements meta Meta-Analysis with R metaLik Likelihood inference in meta-analysis and meta-regression models metaMA Meta-analysis for MicroArrays metacor Meta-analysis of correlation coefficients metafor Meta-Analysis Package for R metatest Fit and test metaregression models mfp Multivariable Fractional Polynomials mfr Minimal Free Resolutions of Graph Edge Ideals mgcv GAMs with GCV/AIC/REML smoothness estimation and GAMMs by PQL mgpd Functions for multivariate generalized Pareto distribution (MGPD of Type II) mhsmm Parameter estimation and prediction for hidden Markov and semi-Markov models for data with multiple observation sequences mht Multiple Hypotheses Testing For Variable Selection mhurdle Estimation of models with limited dependent variables mi Missing Data Imputation and Model Checking miP Multiple Imputation Plots miRtest combined miRNA- and mRNA-testing micEcon Microeconomic Analysis and Modelling micEconAids Demand Analysis with the Almost Ideal Demand System (AIDS) micEconCES Analysis with the Constant Elasticity of Scale (CES) function micEconSNQP Symmetric Normalized Quadratic Profit Function mice Multivariate Imputation by Chained Equations microbenchmark Sub microsecond accurate timing functions migui Graphical User Interface of the mi Package mimR A package for graphical modelling in R minPtest Gene region-level testing procedure for SNP data, using the min P test resampling approach miniGUI tktcl quick and simple function GUI minimax Minimax distribution family minpack.lm R interface to the Levenberg-Marquardt nonlinear least-squares algorithm found in MINPACK minqa Derivative-free optimization algorithms by quadratic approximation minxent Entropy Optimization Distributions mirf MULTIPLE IMPUTATION AND RANDOM FORESTS FOR UNOBSERVABLE PHASE, HIGH-DIMENSIONAL DATA mirt Multidimensional Item Response Theory misc3d Miscellaneous 3D Plots miscTools Miscellanneous Tools and Utilities missForest Nonparametric Missing Value Imputation using Random Forest missMDA Handling missing values with/in multivariate data analysis (principal component methods) mitools Tools for multiple imputation of missing data mix Estimation/multiple Imputation for Mixed Categorical and Continuous Data mixAK Mixture of methods including mixtures mixOmics Omics Data Integration Project mixPHM Mixtures of proportional hazard models mixRasch Mixture Rasch Models with JMLE mixdist Finite Mixture Distribution Models mixedQF Estimator with Qudratics Forms in Mixeds Models mixer Random graph clustering mixexp Design and analysis of mixture experiments mixfdr Computes false discovery rates and effect sizes using normal mixtures mixlow Mixlow Method for Assessing Drug Synergism/Antagonism mixreg Functions to fit mixtures of regressions mixsep Forensic Genetics DNA Mixture Separation mixsmsn Fitting finite mixture of scale mixture of skew-normal distributions mixstock functions for mixed stock analysis mixtools Tools for analyzing finite mixture models mkin Routines for fitting kinetic models with one or more state variables to chemical degradation data mkssd Efficient multi-level k-circulant supersaturated designs mlbench Machine Learning Benchmark Problems mlegp Maximum Likelihood Estimates of Gaussian Processes mleur Maximum likelihood unit root test mlmRev Examples from Multilevel Modelling Software Review mlmmm ML estimation under multivariate linear mixed models with missing values mlogit multinomial logit model mlogitBMA Bayesian Model Averaging for Multinomial Logit Models mmap Map Pages of Memory mmcm Modified Maximum Contrast Method mnormt The multivariate normal and t distributions mnspc Multivariate Nonparametric Statistical Process Control moc GENERAL NONLINEAR MIXTURES OF CURVES modTempEff Modelling temperature effects using time series data modeest Mode Estimation modehunt Multiscale Analysis for Density Functions modelcf Modeling physical computer codes with functional outputs using clustering and dimensionality reduction modelfree Model-free estimation of a psychometric function 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 mondate Keep track of dates in terms of months monmlp Monotone multi-layer perceptron neural network monoProc strictly monotone smoothing procedure monomvn Estimation for multivariate normal and Student-t data with monotone missingness monreg Nonparametric monotone regression moonsun Basic astronomical calculations with R mosaic Project MOSAIC (mosaic-web.org) math and stats teaching utilities motmot Models of Trait Macroevolution on Trees moult Models for Analysing Moult Data movMF Mixtures of von Mises Fisher Distributions mpa CoWords Method mpc MPC - Multiple Precision Complex Library mpm Multivariate Projection Methods mpmcorrelogram Multivariate Partial Mantel Correlogram mprobit Multivariate probit model for binary/ordinal response mpt Multinomial Processing Tree (MPT) Models mra Analysis of Mark-Recapture data mratios Inferences for ratios of coefficients in the general linear model mrdrc Model-robust concentration-response analysis mritc MRI tissue classification mrt Wright & London's Modern Regression Techniques 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 msSurv Nonparametric Estimation for Multistate Models mseq Modeling non-uniformity in short-read rates in RNA-Seq data msir Model-based Sliced Inverse Regression msm Multi-state Markov and hidden Markov models in continuous time mspath Multi-state Path-Dependent Models in Discrete Time msr Morse-Smale approximation, regression and visualization mstate Data preparation, estimation and prediction in multi-state models mtcreator Creating MAGE-TAB files using mtcreator mtsc Multivariate Timeseries Clusters mtsdi Multivariate time series data imputation muRL Mailmerge using R, LaTeX, and the Web muS2RC Splus to R Compatibility for package muStat muStat Prentice Rank Sum Test and McNemar Test muUtil muStat Utility Functions mugnet Mixture of Gaussian Bayesian Network Model muhaz Hazard Function Estimation in Survival Analysis multcomp Simultaneous Inference in General Parametric Models multcompView Visualizations of Paired Comparisons multiPIM Variable Importance Analysis with Population Intervention Models multibiplotGUI Multibiplot Analysis in R multic Quantitative linkage analysis tools using the variance components approach multicore Parallel processing of R code on machines with multiple cores or CPUs multilevel Multilevel Functions multinomRob Robust Estimation of Overdispersed Multinomial Regression Models multipol multivariate polynomials multisensi Multivariate Sensitivity Analysis multitaper Multitaper Spectral Analysis multmod Testing of multiple outcomes multxpert Common Multiple Testing Procedures and Gatekeeping Procedures munfold Metric Unfolding munsell Munsell colour system mutatr Mutable objects for R mutoss Unified multiple testing procedures mutossGUI A graphical user interface for the MuToss Project mvShapiroTest Generalized Shapiro-Wilk test for multivariate normality mvabund statistical methods for analysing multivariate abundance data mvbutils Workspace organization, code and documentation editing, package prep and editing, etc mvgraph Multivariate, Interactive Visualization mvmeta Multivariate meta-analysis and meta-regression mvna Nelson-Aalen estimator of the cumulative hazard in multistate models mvngGrAd Software for moving grid adjustment in plant breeding field trials 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 mvsf Shapiro-Francia Multivariate Normality Test mvtBinaryEP Generates Correlated Binary Data mvtnorm Multivariate Normal and t Distributions mvtnormpcs Multivariate Normal and T Distribution functions of (Dunnett, 1989) mvtsplot Multivariate Time Series Plot mxkssd Efficient mixed-level k-circulant supersaturated designs NADA Nondetects And Data Analysis for environmental data NBPSeq The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq NCBI2R NCBI2R-An R package to navigate and annotate genes and SNPs NISTnls Nonlinear least squares examples from NIST NMF Algorithms and framework for Nonnegative Matrix Factorization (NMF) NMFN Non-negative Matrix Factorization NMMAPSlite NMMAPS Data Lite NMRS NMR Spectroscopy NORMT3 Evaluates complex erf, erfc, Faddeeva, and density of sum of Gaussian and Student's t NRAIA Data sets from "Nonlinear Regression Analysis and Its Applications" NeMo Exceptionnal Network Motifs in biological networks NeatMap Non-clustered heatmap alternatives NestedCohort Survival Analysis for Cohorts with Missing Covariate Information NetCluster Clustering for networks NetData Network Data for McFarland's SNA R labs NetIndices Estimating network indices, including trophic structure of foodwebs in R NetworkAnalysis Statistical inference on populations of weighted or unweighted networks NightDay Night and Day Boundary Plot Funtion Nippon Japanese utility functions and data nFDR Nonparametric Estimate of FDR Based on Bernstein Polynomials nFactors Parallel Analysis and Non Graphical Solutions to the Cattell Scree Test nacopula Nested Archimedean Copulas nanop tools for nanoparticle simulation and PDF calculation nbpMatching functions for non-bipartite optimal matching ncdf Interface to Unidata netCDF data files ncdf4 Interface to Unidata netCDF (version 4 or earlier) format data files ncf spatial nonparametric covariance functions ncomplete ncomplete ncvreg Regularization paths for SCAD- and MCP-penalized regression models ndl Naive Discriminative Learning ndvits NDVI Time series extraction and analysis neariso Near-Isotonic Regression negenes Estimating the number of essential genes in a genome neldermead R port of the Scilab neldermead module network Classes for Relational Data networksis Simulate bipartite graphs with fixed marginals through sequential importance sampling neuRosim Functions to generate fMRI data including activated data, noise data and resting state data neuralnet Training of neural networks nga NGA Earthquake Ground Motion Prediction Equations nice Get or Set UNIX Niceness nlADG Regression in the Normal Linear ADG Model nleqslv Solve systems of non linear equations nlme Linear and Nonlinear Mixed Effects Models nlmeODE Non-linear mixed-effects modelling in nlme using differential equations nloptr R interface to NLopt nlreg Higher Order Inference for Nonlinear Heteroscedastic Models nlrwr Nonlinear 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 nnDiag k-Nearest Neighbor Diagnostic Tools nnc Nearest Neighbor Autocovariates nncRda Improved RDA Using nnc nnclust Nearest-neighbour tools for clustering nnet Feed-forward Neural Networks and Multinomial Log-Linear Models nnls The Lawson-Hanson algorithm for non-negative least squares (NNLS) nodeHarvest Node Harvest for regression and classification noia Implementation of the Natural and Orthogonal InterAction (NOIA) model nonbinROC ROC-type analysis for non-binary gold standards nonparaeff Nonparametric Methods for Measuring Efficiency and Productivity nonrandom Stratification and matching by the propensity score 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) normwhn.test Normality and White Noise Testing nortest Tests for Normality noverlap ncomplete np Nonparametric kernel smoothing methods for mixed data types npRmpi Parallel nonparametric kernel smoothing methods for mixed data types nparLD Nonparametric Analysis of Longitudinal Data in Factorial Experiments nparcomp nparcomp-package npde Normalised prediction distribution errors for nonlinear mixed-effect models nplplot Plotting non-parametric linkage results npmc Nonparametric Multiple Comparisons npmlreg Nonparametric maximum likelihood estimation for random effect models nppbib Nonparametric Partially-Balanced Incomplete Block Design Analysis npst Generalization of Hewitt's Seasonality Test nsRFA Non-supervised Regional Frequency Analysis nullabor Tools for graphical inference numConversion Test of accuracy of as.character() for a numeric input using the standard arithmetic numDeriv Accurate Numerical Derivatives nutshell Data for "R in a Nutshell" nutshellDE Beispieldaten zu "R in a Nutshell" [deutsche Ausgabe] nvis Combination of visualization functions for nuclear data using ggplot2 and ggcolpairs nws R functions for NetWorkSpaces and Sleigh OAIHarvester Harvest Metadata Using OAI-PMH v2.0 ODB Open Document Databases (.odb) management OPE Outer-product emulator ORDER2PARENT Estimate parent distributions with data of several order statistics ORIClust Order-restricted Information Criterion-based Clustering Algorithm ORMDR ORMDR OSACC Ordered Subset Analysis for Case-Control Studies Oarray Arrays with arbitrary offsets OjaNP Multivariate Methods Based on the Oja Median and Related Concepts OligoSpecificitySystem Oligo Specificity System Oncotree Estimating oncogenetic trees OpenCL Interface allowing R to use OpenCL OpenRepGrid Tools to analyse repertory grid data OrdFacReg Least squares, logistic, and Cox-regression with ordered predictors OrdMonReg Compute least squares estimates of one bounded or two ordered isotonic regression curves OrgMassSpecR Organic Mass Spectrometry objectProperties A factory of self-describing properties objectSignals objectSignals oblique.tree Oblique Trees for Classification Data obsSens Sensitivity analysis for Observational studies oc OC Roll Call Analysis Software oce Analysis of Oceanographic data ocomposition Gibbs sampler for ordered compositional data odesolve Solvers for Ordinary Differential Equations odfWeave Sweave processing of Open Document Format (ODF) files odfWeave.survey Support for odfWeave on the survey package odprism Optimal design and performance of random intercept and slope models ofp Object-Functional Programming omd filter the molecular descriptors for QSAR oncomodel Maximum likelihood tree models for oncogenesis onemap Software for constructing genetic maps in experimental crosses: full-sib, RILs, F2 and backcrosses onion octonions and quaternions opefimor Option Pricing and Estimation of Financial Models in R openNLP openNLP Interface openNLPmodels.en openNLP Models for English openNLPmodels.es openNLP Models for Spanish openair Tools for the analysis of air pollution data opencpu.encode opencpu object encoder/decoder openintro OpenIntro data sets and supplement functions operator.tools Utilities for working with R's operators operators Additional binary operators for the R language oposSOM Package for analysis and visualization of metagenes optBiomarker Estimation of optimal number of biomarkers for two-group microarray based classifications at a given error tolerance level for various classification rules optimbase R port of the Scilab optimbase module optimsimplex R port of the Scilab optimsimplex module optimx A Replacement and Extension of the optim() Function optmatch Functions for optimal matching optparse Command line option parser optpart Optimal partitioning of similarity relations orQA Order Restricted Assessment Of Microarray Titration Experiments orclus ORCLUS subspace clustering ordPens Selection and/or Smoothing of Ordinal Predictors orddom Ordinal Dominance Statistics ordinal Regression Models for Ordinal Data orientlib Support for orientation data orloca The package deals with Operations Research LOCational Analysis models orloca.es Spanish version of orloca package oro.dicom Rigorous - DICOM Input / Output oro.nifti Rigorous - NIfTI+ANALYZE+AFNI Input / Output orsk Convertinging Odds Ratio to Relative Risk with Partial Data Information orth Multivariate Logistic Regressions Using Orthogonalized Residuals orthogonalsplinebasis Orthogonal Bspline Basis Functions orthopolynom Collection of functions for orthogonal and orthonormal polynomials osDesign Design and analysis of observational studies osmar Importing and working with OpenStreetMap-Data ouch Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses outliers Tests for outliers oz Plot the Australian coastline and states PASWR PROBABILITY and STATISTICS WITH R PBImisc A set of datasets used in my classes or in the book ,,Modele liniowe i mieszane w R, wraz z przykladami w analizie danych” PBSadmb PBS ADMB PBSddesolve Solver for Delay Differential Equations PBSmapping Mapping Fisheries Data and Spatial Analysis Tools PBSmodelling GUI Tools Made Easy: Interact with Models, Explore Data, Give Dynamic Presentations PCIT PCIT algorithm - Partial Correlation Coefficient with Information Theory PCS Calculate the probability of correct selection (PCS) PERregress Regression Functions and Datasets PET Simulation and Reconstruction of PET Images PHYLOGR Functions for phylogenetically based statistical analyses PK Basic Non-Compartmental Pharmacokinetics PKfit A Data Analysis Tool for Pharmacokinetics PKgraph Model diagnostics for population pharmacokinetic models PKmodelFinder Software for Pharmacokinetic model PKreport A reporting pipeline for checking population pharmacokinetic model assumption PKtools unified computational interfaces for pop PK PL.popN Population Size Estimation PLIS Multiplicity control using Pooled LIS statisitcs PMA Penalized Multivariate Analysis POT Generalized Pareto Distribution and Peaks Over Threshold PSAgraphics Propensity Score Analysis Graphics PSCBS Analysis of Parent-Specific DNA Copy Numbers PSCN Parent Specific DNA Copy Number Estimation PSM Non-Linear Mixed-Effects modelling using Stochastic Differential Equations PTAk Principal Tensor Analysis on k modes PairViz Visualization using Eulerian tours and Hamiltonian decompositions Peak2Trough Estimation of the peak-to-trough ratio of a seasonal variation component Peaks Peaks PearsonDS Pearson Distribution System PearsonICA Independent component analysis using score functions from the Pearson system PerformanceAnalytics Econometric tools for performance and risk analysis PermAlgo Permutational algorithm to simulate survival data PhViD PhViD: a R package for PharmacoVigilance signal Detection PhysicalActivity Process Physical Activity Accelerometer Data PoMoS Polynomial (ordinary differential equation) Model Search PoiClaClu Classification and clustering of sequencing data based on a Poisson model PoissonSeq Significance analysis of sequencing data based on a Poisson log linear model PolynomF Polynomials in R Pomic Pattern Oriented Modelling Information Criterion PopGenKit Useful functions for (batch) file conversion and data resampling in microsatellite datasets PottsUtils Utility Functions of the Potts Models PowerTOST Power and Sample size based on two one-sided t-tests (TOST) for bioequivalence studies PredictABEL Assessment of risk prediction models PredictiveRegression Prediction Intervals for Three Basic Statistical Models PresenceAbsence Presence-Absence Model Evaluation ProDenICA Product Density Estimation for ICA using tilted Gaussian density estimates ProbForecastGOP Probabilistic weather forecast using the GOP method ProfessR Grades Setting and Exam Maker ProfileLikelihood Profile Likelihood for a Parameter in Commonly Used Statistical Models ProjectTemplate Automates the creation of new statistical analysis projects PropCIs Computes confidence intervals for single proportions, for differences in proportions, for an odds-ratio and for the relative risk in a 2x2 table PtProcess Time Dependent Point Process Modelling PwrGSD Power in a Group Sequential Design p3state.msm Analyzing survival data pGLS Generalized Least Square in comparative Phylogenetics pROC display and analyze ROC curves pack Convert values to/from raw vectors packClassic Toy example of Pack Classic packS4 Toy example of S4 package packdep Mapping dependencies among R packages pairwiseCI Confidence intervals for two sample comparisons palaeoSig Significance tests for palaeoenvironmental reconstructions paleoMAS Paleoecological Analysis paleoTS Analyze paleontological time-series paloma Poisson Approximation for LOcal Motif Assessment paltran WA, WA-PLS, MW for paleolimnology pamctdp Principal Axes Methods for Contingency Tables with Partition Structures on Rows and Columns pamm Power analysis for random effects in mixed models pamr Pam: prediction analysis for microarrays pan Multiple imputation for multivariate panel or clustered data panel Panel papply Parallel apply function using MPI paramlink Parametric linkage analysis paran Horn's Test of Principal Components/Factors parcor Regularized estimation of partial correlation matrices parfossil Parallelized functions for palaeoecological and palaeogeographical analysis parmigene Parallel Mutual Information estimation for Gene Network reconstruction parser Detailed R source code parser partDSA Partitioning using deletion, substitution, and addition moves partitionMap Partition Maps partitionMetric Compute a distance metric between two partitions of a set partitions Additive partitions of integers party A Laboratory for Recursive Partytioning parviol Parviol pastecs Package for Analysis of Space-Time Ecological Series pathClass Classification using biological pathways as prior knowledge pathmox Segmentation Trees in Partial Least Squares Path Modeling pbapply Adding Progress Bar to '*apply' Functions pbatR P2BAT pbivnorm Vectorized Bivariate Normal CDF pcaPP Robust PCA by Projection Pursuit pcalg Estimation of CPDAG/PAG and causal inference using the IDA algorithm pcse Panel-Corrected Standard Error Estimation in R pcurve Principal curve analysis pdfCluster Cluster analysis via nonparametric density estimation pdist Partitioned Distance Function pear Package for Periodic Autoregression Analysis pec Prediction Error Curves for Survival Models pedantics Functions to facilitate power and sensitivity analyses for genetic studies of natrual popualtions pedigree Pedigree functions pedigreemm Pedigree-based mixed-effects models pegas Population and Evolutionary Genetics Analysis System penalized L1 (lasso) and L2 (ridge) penalized estimation in GLMs and in the Cox model penalizedLDA Penalized classification using Fisher's linear discriminant penalizedSVM Feature Selection SVM using penalty functions pencopula Flexible Copula Density Estimation with Penalized Hierarchical B-Splines pendensity Density Estimation with a Penalized Mixture Approach pensim Simulation of high-dimensional data and parallelized repeated penalized regression peperr Parallelised Estimation of Prediction Error pequod Moderated regression package perm Exact or Asymptotic permutation tests permax permax permtest Permutation test to compare variability within and distance between two groups perturb Tools for evaluating collinearity pesticides Analysis of single serving and composite pesticide residue measurements pfda Paired Functional Data Analysis pgam Poisson-Gamma Additive Models pgfSweave Quality speedy graphics compilation and caching with Sweave pgirmess Data analysis in ecology pglm panel generalized linear model pgs Precision of Geometric Sampling phangorn Phylogenetic analysis in R pheatmap Pretty Heatmaps pheno Auxiliary functions for phenological data analysis phitest Nonparametric goodness-of-fit methods based on phi-divergences phmm Proportional Hazards Mixed-effects Model (PHMM) phpSerialize Serialize R to PHP associative array phull p-hull: a generalization of convex hull, X-Y hull and bounding rectangle phybase Basic functions for phylogenetic analysis phyclust Phylogenetic Clustering (Phyloclustering) phyext An extension of some of the classes in phylobase. Tree objects now support subnodes on branches phylobase Base package for phylogenetic structures and comparative data phyloclim Integrating phylogenetics and climatic niche modelling phylosim R packge for simulating biological sequence evolution phylotools Phylogenetic tools for Eco-phylogenetics phytools Phylogenetic Tools for comparative biology (and other things) pi0 Estimating the proportion of true null hypotheses for FDR picante R tools for integrating phylogenies and ecology pixmap Bitmap Images (“Pixel Maps”) pkDACLASS A complete statistical analysis of MALDI-TOF Mass Spectrometry Proteomics data plRasch Log Linear by Linear Asscociation models plan Tools for project planning planar Multilayer optics playitbyr Representing and exploring data through sound playwith A GUI for interactive plots using GTK+ plgp Particle Learning of Gaussian Processes plink IRT Separate Calibration Linking Methods plm Linear Models for Panel Data plotGoogleMaps Plot HTML output with Google Maps API and your own data plotSEMM Graphing nonlinear latent variable interactions in SEMM plotmo Plot a model's response while varying the values of the predictors plotpc Plot principal component histograms around a scatter plot plotrix Various plotting functions pls Partial Least Squares Regression (PLSR) and Principal Component Regression (PCR) plsRcox Partial least squares Regression for Cox models and related techniques plsRglm Partial least squares Regression for generalized linear models plsdof Degrees of Freedom and Statistical Inference for Partial Least Squares Regression plsgenomics PLS analyses for genomics plspm Partial Least Squares Data Analysis Methods plugdensity Plug-in Kernel Density Estimation plus Penalized Linear Unbiased Selection plyr Tools for splitting, applying and combining data pmg Poor Man's GUI pmlr Penalized Multinomial Logistic Regression pmml Generate PMML for various models pmr Probability Models for Ranking Data png Read and write PNG images poLCA Polytomous variable Latent Class Analysis poibin The Poisson Binomial Distribution poilog Poisson lognormal and bivariate Poisson lognormal distribution poistweedie Poisson-Tweedie exponential family models polspline Polynomial spline routines polySegratio Simulate and test marker dosage for dominant markers in autopolyploids polySegratioMM Bayesian mixture models for marker dosage in autopolyploids polyapost Simulating from the Polya posterior polycor Polychoric and Polyserial Correlations polydect polydect polynom A collection of functions to implement a class for univariate polynomial manipulations polysat Tools for Polyploid Microsatellite Analysis polytomous Polytomous logistic regression for fixed and mixed effects pomp Statistical inference for partially observed Markov processes pooh Partial Orders and Relations popPK Summary of Population Pharmacokinetic Analysis popbio Construction and analysis of matrix population models popgen Statistical and Population Genetics portes Portmanteau Tests for Time Series Models portfolio Analysing equity portfolios portfolioSim Framework for simulating equity portfolio strategies potts Markov Chain Monte Carlo for Potts Models powell Powell's UObyQA algorithm powerGWASinteraction Power Calculations for Interactions for GWAS powerMediation Power/Sample size calculation for mediation analysis powerSurvEpi Power and sample size calculation for survival analysis of epidemiological studies powerpkg Power analyses for the affected sib pair and the TDT design ppMeasures Point pattern distances and prototypes ppcor Partial and Semi-partial (Part) correlation ppls Penalized Partial Least Squares pps Functions for PPS sampling ppstat Point Process Statistics prLogistic Estimation of Prevalence Ratios using Logistic Models prabclus Functions for clustering of presence-absence, abundance and multilocus genetic data pracma Practical Numerical Math Functions pragma Provides a pragma / directive / keyword syntax for R predbayescor Classification rule based on Bayesian naive Bayes models with feature selection bias corrected predmixcor Classification rule based on Bayesian mixture models with feature selection bias corrected prefmod Utilities to fit paired comparison models for preferences press Protein REsidue-level Structural Statistics pressData Data sets for package PRESS–Protein REsidue-level Structural Statistics prettyR Pretty descriptive stats prim Patient Rule Induction Method (PRIM) primer Functions and data for the forthcoming, A Primer of Ecology with R princurve Fits a Principal Curve in Arbitrary Dimension prob Elementary Probability on Finite Sample Spaces probemapper Connects to QBRC's ProbeMapper platform processdata Process Data prodlim Product Limit Estimation productplots NA profdpm Profile Dirichlet Process Mixtures 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 protoclust Hierarchical clustering with prototypes proxy Distance and Similarity Measures pscl Political Science Computational Laboratory, Stanford University pseudo Pseudo - observations psgp Projected Spatial Gaussian Process (psgp) methods pso Particle Swarm Optimization pspearman Spearman's rank correlation test pspline Penalized Smoothing Splines psy Various procedures used in psychometry psych Procedures for Psychological, Psychometric, and Personality Research psychometric Applied Psychometric Theory psychotree Recursive Partitioning Based on Psychometric Models psyphy Functions for analyzing psychophysical data in R ptinpoly Point-In-Polyhedron Test (3D) ptw Parametric Time Warping pvclass P-values for Classification pvclust Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling pwr Basic functions for power analysis pwt Penn World Table pxR PC-Axis with R pycno Pycnophylactic Interpolation pyramid Functions to draw population pyramid QCA Qualitative Comparative Analysis QCA3 Yet another package for Qualitative Comparative Analysis QCAGUI QCA Graphical User Interface QRMlib Provides R-language code to examine Quantitative Risk Management concepts QSARdata Quantitative Structure Activity Relationship (QSAR) Data Sets QT QT Knowledge Management System QTLNetworkR Interactive software package for QTL visualization QTLRel Tools for mapping of quantitative traits of genetically related individuals and calculating identity coefficients from a pedigree QuACN This package offers a set of topological network measures to analyze complex Networks structurally QuantPsyc Quantitative Psychology Tools qAnalyst Control Charts, Capability and Distribution Identification qat Quality Assurance Toolkit qcc Quality Control Charts qgraph Network representations of relationships in data qlspack Quasi Least Square Package qp q-order partial correlation graph search algorithm qpcR Modelling and analysis of real-time PCR data qrnn Quantile regression neural network qtl Tools for analyzing QTL experiments qtlDesign Design of QTL experiments qtlbim QTL Bayesian Interval Mapping qtlbook Datasets for the R/qtl book qtlmt Tools for mapping multiple complex traits quadprog Functions to solve Quadratic Programming Problems qualV Qualitative Validation Methods qualityTools Statistical Methods for Quality Science quantchem Quantitative chemical analysis: calibration and evaluation of results quantmod Quantitative Financial Modelling Framework quantreg Quantile Regression quantregForest Quantile Regression Forests quaternions Arithmetics and linear algebra with Quaternions queueing Basic Markovian queueing models 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 (memoization) of objects R.filesets Easy handling of and access to files organized in structured directories R.huge Methods for accessing huge amounts of data [DEPRECATED] 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 Dynamic generation of scientific reports R.utils Various programming utilities R1magic Compressive Sampling: Sparse signal recovery utilities R2Cuba Multidimensional Numerical Integration R2HTML HTML exportation for R objects R2PPT Simple R Interface to Microsoft PowerPoint using rcom R2SWF Convert R Graphics to Flash Animations R2WinBUGS Running WinBUGS and OpenBUGS from R / S-PLUS R2jags A Package for Running jags from R R2wd Write MS-Word documents from R R4dfp 4dfp MRI Image Read and Write Routines RAD Fit RAD models to biological data RANN Fast Nearest Neighbour Search RArcInfo Functions to import data from Arc/Info V7.x binary coverages RAtmosphere Standard Atmosperic profiles RBGL An interface to the BOOST graph library RBerkeley R API to Oracle Berkeley DB RBloomberg R/Bloomberg RBrownie Continuous and discrete ancestral character reconstruction and evolutionary rate tests RC Reproducible Computing RColorBrewer ColorBrewer palettes RCurl General network (HTTP/FTP/…) client interface for R RDS R Functions for Respondent-Driven Sampling RDieHarder R interface to the dieharder RNG test suite REEMtree Regression Trees with Random Effects for Longitudinal (Panel) Data REQS R/EQS Interface RExcelInstaller Integration of R and Excel, (use R in Excel, read/write XLS files) RFA Regional Frequency Analysis RFLPtools Tools to analyse RFLP data RFOC Graphics for Spherical Distributions and Earthquake Focal Mechanisms RFinanceYJ RFinanceYJ RFreak R/FrEAK interface RGCCA Regularized Generalized Canonical Correlation Analysis RGraphics Data and Functions from the book R Graphics, Second Edition RGtk2 R bindings for Gtk 2.8.0 and above RGtk2Extras Data frame editor and dialog making wrapper for RGtk2 RH2 DBI/RJDBC interface to h2 Database RHRV Heart rate variability analysis of ECG data RHmm Hidden Markov Models simulations and estimations RISmed Search Pubmed, Make bibliographic content analyzable RImageJ R bindings for ImageJ RInside C++ classes to embed R in C++ applications RItools Randomization inference tools RJDBC Provides access to databases through the JDBC interface RJSONIO Serialize R objects to JSON, JavaScript Object Notation 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 RLastFM R interface to last.fm API RM2 Revenue Management and Pricing Package RMAWGEN RMAWGEN (R Multi-site Auto-regressive Weather GENeretor): a package to generate daily time series from monthly mean values RMC Functions for fitting Markov models RMTstat Distributions, Statistics and Tests derived from Random Matrix Theory RMark R Code for MARK Analysis RMediation An R Package for Mediation Analysis RMySQL R interface to the MySQL database RNCBI The java ncbi interface to R RNCBIAxis2Libs Axis2 libraries for use in the R environment RNCBIEUtilsLibs EUtils libraries for use in the R environment RNCEP Obtain, organize, and visualize NCEP weather data RNetCDF R Interface to NetCDF Datasets RNetLogo Provides an interface to the agent-based modelling plattform NetLogo RNiftyReg Medical image registration using the NiftyReg library ROAuth R interface for OAuth ROCR Visualizing the performance of scoring classifiers ROCwoGS Non-parametric estimation of ROC curves without Gold Standard Test RODBC ODBC Database Access RODM R interface to Oracle Data Mining ROptEst Optimally robust estimation ROptEstOld Optimally robust estimation - old version ROptRegTS Optimally robust estimation for regression-type models ROracle Oracle database interface for R ROracleUI Convenient Tools for Working with Oracle Databases RPMG Graphical User Interface (GUI) for interactive R analysis sessions RPMM Recursively Partitioned Mixture Model RPPanalyzer Reads, annotates, and normalizes reverse phase protein array data RPostgreSQL R interface to the PostgreSQL database system RProtoBuf R Interface to the Protocol Buffers API RPyGeo ArcGIS Geoprocessing in R via Python RQDA R-based Qualitative Data Analysis RQuantLib R interface to the QuantLib library RSAGA SAGA Geoprocessing and Terrain Analysis in R RSEIS Seismic Time Series Analysis Tools RSNNS Neural Networks in R using the Stuttgart Neural Network Simulator (SNNS) RSQLite SQLite interface for R RSQLite.extfuns Math and String Extension Functions for RSQLite RSVGTipsDevice An R SVG graphics device with dynamic tips and hyperlinks RScaLAPACK A seamless interface to perform parallel computation on linear algebra problems using the ScaLAPACK library RSearchYJ RSearchYJ RSiena Siena - Simulation Investigation for Empirical Network Analysis RSiteSearch RSiteSearch RStackExchange R based StackExchange client RSurvey Analysis of Spatially Distributed Data RSvgDevice An R SVG graphics device RTAQ RTAQ: Tools for the analysis of trades and quotes in R RTOMO Visualization for seismic tomography RTextTools Automatic Text Classification via Supervised Learning RTisean R interface to Tisean algorithms RUnit R Unit test framework RVAideMemoire Diverse basic statistical and graphical functions accompanying the french book 'Aide-memoire de statistique appliquee a la biologie' RWebMA RWebMA RWeka R/Weka interface RWekajars R/Weka interface jars RWinEdt R-WinEdt RXKCD Get XKCD comic from R RXMCDA RXMCDA RXshrink Maximum Likelihood Shrinkage via Generalized Ridge or Least Angle Regression RadioSonde Tools for plotting skew-T diagrams and wind profiles RandForestGUI RandForestGUI RandVar Implementation of random variables RandomFields Simulation and Analysis of Random Fields RankAggreg Weighted rank aggregation RaschSampler Rasch Sampler Rassoc Robust tests for case-control genetic association studies Ratings Model-based Ratings Figures Rcapture Loglinear Models for Capture-Recapture Experiments Rcgmin Conjugate gradient minimization of nonlinear functions with box constraints Rcmdr R Commander RcmdrPlugin.BCA Rcmdr Plug-In for Business and Customer Analytics RcmdrPlugin.DoE R Commander Plugin for (industrial) Design of Experiments RcmdrPlugin.EHESsampling Tools for sampling in European Health Examination Surveys (EHES) RcmdrPlugin.Export Graphically export output to LaTeX or HTML RcmdrPlugin.FactoMineR Graphical User Interface for FactoMineR RcmdrPlugin.HH Rcmdr support for the HH package RcmdrPlugin.IPSUR An IPSUR Plugin for the R Commander RcmdrPlugin.KMggplot2 Rcmdr Plug-In for Kaplan-Meier Plot and Other Plots by Using the ggplot2 Package RcmdrPlugin.MAc Meta-Analysis with Correlations (MAc) Rcmdr Plug-in RcmdrPlugin.MAd Meta-Analysis with Mean Differences (MAd) Rcmdr Plug-in RcmdrPlugin.PT Some discrete exponential dispersion models: Poisson-Tweedie RcmdrPlugin.SLC SLC Rcmdr Plug-in RcmdrPlugin.SensoMineR Graphical User Interface for SensoMineR RcmdrPlugin.SurvivalT Rcmdr Survival Plug-In RcmdrPlugin.TeachingDemos Rcmdr Teaching Demos Plug-In RcmdrPlugin.TextMining Rcommander plugin for "tm" package RcmdrPlugin.coin Rcmdr Coin Plug-In RcmdrPlugin.depthTools R commander Depth Tools Plug-In RcmdrPlugin.doex Rcmdr plugin for Stat 4309 course RcmdrPlugin.epack Rcmdr plugin for time series RcmdrPlugin.mosaic Adds menu items to produce mosaic plots and assoc plots to Rcmdr RcmdrPlugin.orloca orloca Rcmdr Plug-in RcmdrPlugin.qcc Rcmdr qcc Plug-In RcmdrPlugin.qual Rcmdr plugin for quality control course RcmdrPlugin.sos Efficiently search R Help pages RcmdrPlugin.steepness Steepness Rcmdr Plug-in RcmdrPlugin.survival R Commander Plug-in for the survival Package Rcplex R interface to CPLEX Rcpp Seamless R and C++ Integration RcppArmadillo Rcpp integration for Armadillo templated linear algebra library RcppBDT Rcpp bindings for the Boost Date_Time library RcppClassic Deprecated 'classic' Rcpp API RcppDE Global optimization by differential evolution in C++ RcppEigen Rcpp integration for the Eigen templated linear algebra library RcppExamples Examples using Rcpp to interface R and C++ RcppGSL Rcpp integration for GNU GSL vectors and matrices Rcsdp R interface to the CSDP semidefinite programming library Rd2roxygen Convert Rd to roxygen documentation and utilities to improve documentation Rdsm Threads Environment for R ReacTran Reactive transport modelling in 1D, 2D and 3D Read.isi Automated access to old World Fertility Survey data saved in fixed-width format based on ISI-formatted codebooks ReadImages Image Reading Module for R RecordLinkage Record Linkage in R Records Record Values and Record Times RelativeRisk Relative Risk Reliability Functions for estimating parameters in software reliability models Renext Renewal method for extreme values extrapolation RepeatedHighDim Detection of global group effect in microarrays data ResearchMethods Using GUIs to help teach statistics to non-statistics students ResistorArray electrical properties of resistor networks ResourceSelection Resource Selection (Probability) Functions for Use-Availability Data Rfit Rank Estimation for Linear Models Rfun Funy application of R RghcnV3 Global Historical Climate Network Version 3 Rglpk R/GNU Linear Programming Kit Interface RgoogleMaps Overlays on Google map tiles in R Rhh Calculating multilocus heterozygosity and heterozygosity-heterozygosity correlation RiDMC R interface to the idmclib library Rigroup Rigroup: Provides small integer group functions Rjms R messaging using ActiveMQ and jms Rjmsjars Rjms jars Rknots Rknots Rlab Functions and Datasets Required for ST370 class Rlabkey Data exchange between R and LabKey Server Rmpfr R MPFR - Multiple Precision Floating-Point Reliable Rmpi Interface (Wrapper) to MPI (Message-Passing Interface) RnavGraph Using graphs as a navigational infrastructure RnavGraphImageData Some image data used in the RnavGraph package demos Rniftilib Rniftilib - R Interface to NIFTICLIB (V1.1.0) RobAStBase Robust Asymptotic Statistics RobLox Optimally robust influence curves and estimators for location and scale RobLoxBioC Infinitesimally robust estimators for preprocessing omics data RobRex Optimally robust influence curves for regression and scale RobustAFT Truncated Maximum Likelihood fit and Robust Accelerated Failure Time regression for Gaussian and logWeibull case RobustRankAggreg Methods for robust rank aggregation Rook Rook - a web server interface for R Rpad Workbook-style, web-based interface to R RpgSQL DBI/RJDBC interface to PostgreSQL Database Rramas Matrix population models Rserve Binary R server Rsge Interface to the SGE Queuing System Rsolnp General Non-linear Optimization Rssa A collection of methods for singular spectrum analysis Rstem Interface to Snowball implementation of Porter's word stemming algorithm Rsundials Suite of Nonlinear Differential Algebraic Equations Solvers in R Rsymphony Symphony in R RthroughExcelWorkbooksInstaller Excel Workbooks supporting Statistics courses using 'R through Excel' Runiversal Runiversal - Package for converting R objects to Java variables and XML Runuran R interface to the UNU.RAN random variate generators RunuranGUI A GUI for the UNU.RAN random variate generators Rvelslant Downhole Seismic Analysis in R Rvmmin Variable metric nonlinear function minimization with bounds constraints Rwave Time-Frequency analysis of 1-D signals Rwinsteps Running Winsteps in R RxCEcolInf R x C Ecological Inference With Optional Incorporation of Survey Information Ryacas R interface to the yacas computer algebra system Rz GUI Tool for Data Management like SPSS or Stata r2dRue 2d Rain Use Efficience model r2lh R to LaTeX and HTML r4ss R code for Stock Synthesis rAverage Parameter estimation for the Averaging model of Information Integration Theory rCUR CUR decomposition package rChoiceDialogs rChoiceDialogs collection rDNA R Bindings for the Discourse Network Analyzer rEMM Extensible Markov Model (EMM) for Data Stream Clustering in R rJPSGCS R-interface to gene drop Java Programs for Statistical Genetics and Computational Statistics (JPSGCS) rJava Low-level R to Java interface rJavax rJava extensions rJython R interface to Python via Jython rPorta R/PORTA interface rSymPy R interface to SymPy computer algebra system rTOFsPRO Time-of-flight mass spectra signal processing rWMBAT The William and Mary Bayesian Analysis Tool race Racing methods for the selection of the best rainbow Rainbow plots, bagplots and boxplots for functional data 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 random.polychor.pa A Parallel Analysis With Polychoric Correlation Matrices randomForest Breiman and Cutler's random forests for classification and regression randomLCA Random Effects Latent Class Analysis randomNames Random name generating function and data set randomSurvivalForest Random Survival Forests randtoolbox toolbox for pseudo and quasi random number generation and RNG tests rangeMapper A platform for the study of macroecology of life history traits rankhazard Rank-hazard plots rasclass Supervised Raster Image Classification raster Geographic analysis and modeling with raster data rasterVis Visualization methods for the raster package rateratio.test Exact rate ratio test rattle Graphical user interface for data mining in R rbenchmark Benchmarking routine for R 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 rcdklibs rcdklib - CDK libraries packaged for R rcom R COM Client Interface and internal COM Server rconifers R interface to the CONIFERS forest growth model rda Shrunken Centroids Regularized Discriminant Analysis rdatamarket Data access API for DataMarket.com rdetools Relevant Dimension Estimation (RDE) in Feature Spaces rdyncall Improved Foreign Function Interface (FFI) and Dynamic Bindings to C Libraries (e.g. OpenGL) readBrukerFlexData Reads mass spectrometry data in Bruker *flex format readMzXmlData Reads mass spectrometry data in mzXML format realized Realized rebmix The Rebmix Package recommenderlab Lab for Testing and Developing Recommender Algorithms for Binary Data ref References for R refund Regression with Functional Data registry Registry infrastructure reglogit Simulation-based Regularized Logistic Regression regress Gaussian linear models with linear covariance structure regsubseq Detect and Test Regular Sequences and Subsequences regtest Regression testing rela Item Analysis Package with Standard Errors 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 relevent Relational Event Models reliaR Package for some probability distributions relimp Relative Contribution of Effects in a Regression Model relsurv Relative survival remMap Regularized Multivariate Regression for Identifying Master Predictors remix Remix your data repolr Repeated measures proportional odds logistic regression reportr A general message and error reporting system reporttools Generate LaTeX tables of descriptive statistics reshape Flexibly reshape data reshape2 Flexibly reshape data: a reboot of the reshape package reshapeGUI A GUI for the reshape2 and plyr packages review Manage Review Logs revoIPC Shared memory parallel framework for multicore machines reweight Adjustment of Survey Respondent Weights rfPermute Estimate permutation p-values for importance metrics rgam Robust Generalized Additive Model rgcvpack R Interface for GCVPACK Fortran Package rgdal Bindings for the Geospatial Data Abstraction Library rgenoud R version of GENetic Optimization Using Derivatives rgeos Interface to Geometry Engine - Open Source (GEOS) rggobi Interface between R and GGobi rgl 3D visualization device system (OpenGL) rgp R genetic programming framework rgr The GSC Applied Geochemistry EDA Package rgrs Functions to make R usage in social sciences easier (in french) rhosp Side effect risks in hospital : simulation and estimation rich Species richness estimation and comparison richards Richards curves rimage Image Processing Module for R rindex Indexing for R ringscale Ringscale rioja Analysis of Quaternary Science Data risksetROC Riskset ROC curve estimation from censored survival data rjags Bayesian graphical models using MCMC rje Miscellaneous useful functions rjson JSON for R rlecuyer R interface to RNG with multiple streams rmac calculate RMAC or FMAC agreement coefficients rmeta Meta-analysis rmetasim An individual-based population genetic simulation environment rminer Simpler use of data mining methods (e.g. NN and SVM) in classification and regression rms Regression Modeling Strategies rneos rneos: XML-RPC Interface to NEOS rngWELL toolbox for WELL random number generators rngwell19937 WELL19937a random number generator implemented with 53 bit output robCompositions Robust Estimation for Compositional Data robeth R functions for robust statistics robfilter Robust Time Series Filters robust Insightful Robust Library robustX eXperimental eXtraneous eXtraordinary … Functionality for Robust Statistics robustbase Basic Robust Statistics robustreg Robust Regression Functions rocc ROC based classification rocplus ROC, Precision-Recall, Convex Hull and other plots rootSolve Nonlinear root finding, equilibrium and steady-state analysis of ordinary differential equations roxygen Literate Programming in R roxygen2 In-source documentation for R rpanel Simple Interactive Controls for R Using the tcltk Package rpart Recursive Partitioning rpart.plot Plot rpart models. An enhanced version of plot.rpart rpartOrdinal Ordinal classification tree functions rphast R interface to PHAST software for comparative genomics rpsychi Statistics for psychiatric research rpubchem rpubchem - Interface to the PubChem Collection rpud R functions for computation on GPU rpvm R interface to PVM (Parallel Virtual Machine) rqmcmb2 Markov Chain Marginal Bootstrap for Quantile Regression rrBLUP Ridge Regression-BLUP and related methods for genomic selection rrcov Scalable Robust Estimators with High Breakdown Point rrcovNA Scalable Robust Estimators with High Breakdown Point for Incomplete Data rrdf rrdf - support for the Resource Description Framework rrdflibs rrdflibs - package with Jena libraries for use with rrdf rredis Redis client for R rrp Random Recursive Partitioning rrules Generic rule engine for R rrv Random Return Variables rsae Robust Small Area Estimation rscproxy statconn: provides portable C-style interface to R (StatConnector) rsdepth Ray Shooting Depth (i.e. RS Depth) functions for bivariate analysis rseedcalc Estimation of Proportion of GM Stacked Seeds in Seed Lots rsm Response-surface analysis rsprng R interface to SPRNG (Scalable Parallel Random Number Generators) rstream Streams of random numbers rtape Manage and manipulate large collections of R objects stored as tape-like files rtfbs R Transcription Factor Binding Site identification tool rtiff A tiff reader for R rtv Random Time Variables runjags Interface utilities for JAGS (using BUGS syntax) and Apple Xgrid distributed computing clusters rv Simulation-based random variable object class in R rvgtest Tools for Analyzing Non-Uniform Pseudo-Random Variate Generators rvmbinary RVM Binary Classification rwm R Workspace Management rworldmap For mapping global data : rworldmap rwt Rice Wavelet Toolbox wrapper rysgran Grain size analysis, textural classifications and distribuition of uncosolidated sediments SAFD Statistical Analysis of Fuzzy Data SAPP Statistical Analysis of Point Processes SASPECT Significant AnalysiS of PEptide CounTs SASmixed Data sets from "SAS System for Mixed Models" SASxport Read and Write SAS XPORT Files SBSA Simplified Bayesian Sensitivity Analysis SDDA Stepwise Diagonal Discriminant Analysis SDMTools Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises SDaA Sampling: Design and Analysis SDisc Integrated methodology for the identification of homogeneous profiles in data distribution SE.IGE Standard errors of estimated genetic parametes SEL Semiparametric elicitation SEMModComp Model Comparisons for SEM SGCS Spatial Graph based Clustering Summaries for spatial point patterns SGP An R Package for the Calculation and Visualization of Student Growth Percentiles SHARE SNP-Haplotype Adaptive REgression (SHARE) SHIP SHrinkage covariance Incorporating Prior knowledge SII Calculate ANSI S3.5-1997 Speech Intelligibility Index SIN A SINful Approach to Selection of Gaussian Graphical Markov Models SIS Sure Independence Screening SLC Slope and level change SMCP Smoothed minimax concave penalization (SMCP) method for genome-wide association studies SMIR Companion to Statistical Modelling in R SMPracticals Practicals for use with Davison (2003) Statistical Models SMVar Structural Model for variances SNPRelate Parallel Computing Toolset for genome-wide association studies SNPassoc SNPs-based whole genome association studies SNPmaxsel Maximally selected statistics for SNP data SOAR Memory management in R by delayed assignments SPACECAP A Program to Estimate Animal Abundance and Density using Spatially-Explicit Capture-Recapture SPARQL SPARQL client SPECIES Statistical package for species richness estimation SPIAssay A genetic-based assay for the identification of cell lines SPOT Sequential Parameter Optimization SQLiteDF Stores data frames & matrices in SQLite tables SQLiteMap Wrapper to spatialite functions SQN subset quantile normalization SQUAREM Squared extrapolation methods for accelerating fixed-point iterations SRPM Shared Reproducibility Package Management SSSR Server Side Scripting with R SSsimple State space models STAR Spike Train Analysis with R SV Quasi-likelihood and indirect inference in non-Gaussian stochastic volatility models SVGMapping Map experimental data on custom-made SVG file SVMMaj SVMMaj algorithm SWordInstaller SWord: Use R in Microsoft Word (Installer) SYNCSA SYNCSA - Analysis of functional and phylogenetic patterns in metacommunities SampleSizeMeans Sample size calculations for normal means SampleSizeProportions Calculating sample size requirements when estimating the difference between two binomial proportions SamplerCompare A framework for comparing the performance of MCMC samplers SamplingStrata Optimal stratification of sampling frames for multipurpose sampling surveys SciViews SciViews GUI API - Main package ScottKnott The ScottKnott Clustering Algoritm SearchTrees Spatial Search Trees SemiPar Semiparametic Regression SemiParBIVProbit Semiparametric Bivariate Probit Modelling SenSrivastava Datasets from Sen & Srivastava SensoMineR Sensory data analysis with R SeqKnn Sequential KNN imputation method SiZer SiZer: Significant Zero Crossings SigWinR SigWin-detector implementation in R Sim.DiffProc Simulation of Diffusion Processes Sim.DiffProcGUI Graphical User Interface for Simulation of Diffusion Processes SimComp Simultaneous Comparisons for Multiple Endpoints SimpleTable Bayesian Inference and Sensitivity Analysis for Causal Effects from 2 x 2 and 2 x 2 x K Tables in the Presence of Unmeasured Confounding SimultAnR Correspondence and Simultaneous Analysis SixSigma Six Sigma Tools for Quality and Process Improvement SkewHyperbolic The Skew Hyperbolic Student t-distribution Sleuth2 Data sets from Ramsey and Schafer's "Statistical Sleuth (2nd ed)" SlimPLS SlimPLS multivariate feature selection Snowball Snowball Stemmers SoDA Functions and Exampels for "Software for Data Analysis" SortableHTMLTables Turns a data frame into an HTML file containing a sortable table SparseM Sparse Linear Algebra SpatialEpi Performs various spatial epidemiological analyses SpatialExtremes Modelling Spatial Extremes SpatialNP Multivariate nonparametric methods based on spatial signs and ranks SpatioTemporal Spatio-Temporal Model Estimation SpeciesMix Fit Mixtures of Archetype species SpectralGEM Discovering Genetic Ancestry Using Spectral Graph Theory SpherWave Spherical Wavelets and SW-based Spatially Adaptive Methods StMoSim Simulate QQ-Norm-Plot StatDA Statistical Analysis for Environmental Data StatDataML implementation of the StatDataML proposal StatFingerprints StatFingerprints StatMatch Statistical Matching Stem Spatio-temporal models in R StreamMetabolism Stream Metabolism-A package for calculating single station metabolism from diurnal Oxygen curves SubpathwayMiner A software package for annotation and identification of the KEGG pathways SuppDists Supplementary distributions SweaveListingUtils Utilities for Sweave together with TeX listings package 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 s3x Enhanced S3-Based Programming s4vd Biclustering via sparse singular value decomposition incorporating stability selection sBF Smooth Backfitting sabreR Multivariate Generalized Linear Mixed Models sac Semiparametric Analysis of Changepoint saemix Stochastic Approximation Expectation Maximization (SAEM) algorithm safeBinaryRegression Safe Binary Regression sampSurf Sampling Surface Simulation for Areal Sampling Methods sampfling Sampford sampling (w/o replacement and unequal probabilities) sampleSelection Sample Selection Models samplesize a collection of sample size functions sampling Survey Sampling samplingbook Survey Sampling Procedures samr SAM: Significance Analysis of Microarrays sandwich Robust Covariance Matrix Estimators sapa Insightful Spectral Analysis for Physical Applications sas7bdat SAS Database Reader (experimental) satin Functions for reading and displaying satellite data for oceanographic applications with R saves Fast load variables saws Small-Sample Adjustments for Wald tests Using Sandwich Estimators sbgcop Semiparametric Bayesian Gaussian copula estimation and imputation sca Simple Component Analysis scaRabee Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models scagnostics Compute scagnostics - scatterplot diagnostics scaleCoef Scale regression coefficients 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 schwartz97 A package on the Schwartz two-factor commodity model sciplot Scientific Graphing Functions for Factorial Designs scout Implements the Scout method for Covariance-Regularized Regression scrapeR Tools for Scraping Data from HTML and XML Documents scrime Analysis of High-Dimensional Categorical Data such as SNP Data scriptests Transcript-based unit tests that are easy to create and maintain scuba Scuba diving calculations and decompression models sculpt3d A simple toolbar GUI for brushing RGL plots sda Shrinkage Discriminant Analysis and CAT Score Variable Selection sdcMicro Statistical Disclosure Control methods for the generation of public- and scientific-use files sdcMicroGUI Graphical user interface for package sdcMicro sdcTable statistical disclosure control for tabular data sddpack Semidiscrete Decomposition sde Simulation and Inference for Stochastic Differential Equations sdef Synthesizing List of Differentially Expressed Features sdtalt Signal detection theory and alternatives sdtoolkit Scenario Discovery Tools to Support Robust Decision Making seacarb seawater carbonate chemistry with R seas Seasonal analysis and graphics, especially for climatology season Seasonal analysis of health data secr Spatially explicit capture-recapture seewave Time wave analysis and graphical representation seg A set of tools for residential segregation research segclust SegClust : a package for Segmentation and Segmentation/Clustering segmented Segmented relationships in regression models selectMeta Estimation of weight functions in meta analysis selectiongain gain of a model selection sem Structural Equation Models semPLS Structural Equation Modeling Using Partial Least Squares sendmailR send email using R sendplot Tool for sending interactive plots with tool-tip content sensR Thurstonian models for sensory discrimination sensitivity Sensitivity Analysis sensitivityPStrat Principal Stratification Sensitivity Analysis Functions separationplot Separation Plots seqCBS CN Profiling using Sequencing and CBS seqRFLP Simulation and visualization of restriction enzyme cutting pattern from DNA sequences 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, Customizable Sets and Intervals sfa Stochastic Frontier Analysis 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 sharx Models and Data Sets for the Study of Species-Area Relationships siar Stable Isotope Analysis in R siatclust Shenzhen Institutes of Advanced Technology Clustering Suite sideChannelAttack Side Channel Attack sifds Swedish inflation forecast data set sigclust Statistical Significance of Clustering signal Signal processing signalextraction Real-Time Signal Extraction (Direct Filter Approach) simFrame Simulation framework simPopulation Simulation of synthetic populations for surveys based on sample data simba A Collection of functions for similarity analysis of vegetation data simboot Simultaneous Confidence Intervals and Adjusted p–values for Diversity Indices simco A package to import Structure files and deduce similarity coefficients from them simctest Sequential (or Safe) Implementation of Monte Carlo tests with uniformly bounded resampling risk simecol Simulation of ecological (and other) dynamic systems simex SIMEX- and MCSIMEX-Algorithm for measurement error models simexaft simexaft similarityRichards Similarity of Richards curves simone Statistical Inference for MOdular NEtworks (SIMoNe) simpleboot Simple Bootstrap Routines sinartra A simple web app framework for R, based on sinatra sisus SISUS: Stable Isotope Sourcing using Sampling skellam Skellam distribution skewt The Skewed Student-t Distribution skills Skills in Knowledge Space Theory skmeans Spherical k-Means Clustering slam Sparse Lightweight Arrays and Matrices sm Smoothing methods for nonparametric regression and density estimation smacof SMACOF for Multidimensional Scaling smatr (Standardised) Major Axis Estimation and Testing Routines smco A simple Monte Carlo optimizer using adaptive coordinate sampling smirnov Provides two taxonomic coefficients from E. S. Smirnov "Taxonomic analysis" (1969) book smoothSurv Survival Regression with Smoothed Error Distribution smoothmest Smoothed M-estimators for 1-dimensional location smoothtail Smooth Estimation of GPD Shape Parameter sn The skew-normal and skew-t distributions sna Tools for Social Network Analysis snort Social Network-Analysis On Relational Tables 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 softclassval Soft classification performance measures soil.spec Soil spectral data exploration and regression functions soiltexture Functions for soil texture plot, classification and transformation solaR Solar Photovoltaic Systems som Self-Organizing Map soma General-purpose optimisation with the Self-Organising Migrating Algorithm someKfwer Controlling the Generalized Familywise Error Rate someMTP Some Multiple Testing Procedures somplot Visualisation of hexagonal Kohonen maps sos sos sos4R An R client for the OGC Sensor Observation Service sound A Sound Interface for R sp classes and methods for spatial data spBayes Univariate and Multivariate Spatial Modeling spa Implements The Sequential Predictions Algorithm spaa SPecies Association Analysis space Sparse PArtial Correlation Estimation spacetime classes and methods for spatio-temporal data spacodiR Spatial and Phylogenetic Analysis of Community Diversity spam SPArse Matrix sparcl Perform sparse hierarchical clustering and sparse k-means clustering sparkTable Sparklines and graphical tables for tex and html sparr The sparr package: SPAtial Relative Risk sparseLDA Sparse Discriminant Analysis spatcounts Spatial count regression spatgraphs Graphs for spatial point patterns spatial Functions for Kriging and Point Pattern Analysis spatialCovariance Computation of spatial covariance matrices for data on rectangles spatialkernel Nonparameteric estimation of spatial segregation in a multivariate point process spatialsegregation Segregation measures for multitype spatial point patterns spatstat Spatial Point Pattern analysis, model-fitting, simulation, tests spc Statistical Process Control spcosa Spatial Coverage Sampling and Random Sampling from Compact Geographical Strata spd Semi Parametric Distribution spdep Spatial dependence: weighting schemes, statistics and models spe Stochastic Proximity Embedding spectralGP Approximate Gaussian processes using the Fourier basis speedR A GUI based importing and filtering tool speedRlibTF speedR's table filter library speedRlibs Package containing the required libraries (jars) for speedR speedglm Fitting Linear and Generalized Linear Models to large data sets spef Semiparametric estimating functions speff2trial Semiparametric efficient estimation for a two-sample treatment effect sperich Auxiliary functions to estimate centers of biodiversity spgrass6 Interface between GRASS 6+ geographical information system and R spgwr Geographically weighted regression sphet Spatial Models with heteroskedastic innovations spi Compute SPI index spikeSlabGAM Bayesian variable selection and model choice for generalized additive mixed models spikeslab Prediction and variable selection using spike and slab regression splancs Spatial and Space-Time Point Pattern Analysis splinesurv Nonparametric bayesian survival analysis spls Sparse Partial Least Squares (SPLS) Regression and Classification splus2R S-PLUS functionality missing from R sporm Semiparametric proportional odds rate model sprint Simple Parallel R INTerface spssDDI Read SPSS System files and produce valid DDI Version 3.0 documents spsurvey Spatial Survey Design and Analysis spuRs Functions and Datasets for "Introduction to Scientific Programming and Simulation Using R" sqldf Perform SQL Selects on R Data Frames squash Color-based plots for multivariate visualization sra Selection Response Analysis 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 and CAT Score stab data analysis of drug stability for shelf life estimation stabledist Stable Distribution Functions stam Spatio-Temporal Analysis and Modelling 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 steepness Testing Steepness of Dominance Hierarchies stepPlr L2 penalized logistic regression with a stepwise variable selection stepp Subpopulation Treatment Effect Pattern Plot (STEPP) stepwise Stepwise detection of recombination breakpoints stinepack Stineman, a consistently well behaved method of interpolation stochmod Stochastic Modeling stockPortfolio Build stock models and analyze stock portfolios stoichcalc R Functions for Solving Stoichiometric Equations stratasphere Stratified Spherical Approximate Conditional Modeling stratification Univariate Stratification of Survey Populations stratigraph Toolkit for the plotting and analysis of stratigraphic and palaeontological data stream.net Building and analyzing binary stream networks stringkernels String Kernel Methods for kernlab stringr Make it easier to work with strings strucchange Testing, Monitoring, and Dating Structural Changes subplex Subplex optimization algorithm subselect Selecting variable subsets sudoku Sudoku Puzzle Generator and Solver sugaR Plots to help optimising diabetes therapy supclust Supervised Clustering of Predictor Variables such as Genes superMDS Implements the supervised multidimensional scaling (superMDS) proposal of Witten and Tibshirani (2011) superpc Supervised principal components support.CEs Basic functions for supporting an implementation of choice experiments surv2sample Two-Sample Tests for Survival Analysis survAUC Estimators of prediction accuracy for time-to-event data survBayes Fits a proportional hazards model to time to event data by a Bayesian approach survJamda Survival prediction by joint analysis of microarray gene expression data survJamda.data survJamda.data survPresmooth Presmoothed Estimation in Survival Analysis surveillance Modeling and monitoring discrete response time series survey analysis of complex survey samples survival Survival analysis, including penalised likelihood survivalBIV Estimation of the bivariate distribution function survivalROC Time-dependent ROC curve estimation from censored survival data survrec Survival analysis for recurrent event data svDialogs SciViews GUI API - Dialog boxes svGUI SciViews GUI API - Functions to manage GUI client svIDE SciViews GUI API - IDE and code editor functions svMisc SciViews GUI API - Miscellaneous functions svSocket SciViews GUI API - R Socket Server svSweave SciViews GUI API - Sweave functions svTools SciViews GUI API - Tools (wrapper for packages tools and codetools) svUnit SciViews GUI API - Unit testing svWidgets SciViews GUI API - Widgets & Windows svcR svcR package svcm 2d and 3d Space-Varying Coefficient Models svd Interfaces to various state-of-art SVD and eigensolvers svmpath svmpath: the SVM Path algorithm swamp Analysis and visualization of high-dimensional data in respect to sample annotations symbols Symbol plots symmoments Symbolic Central Moments of the Multivariate Normal Distribution synchronicity Boost mutex functionality for R systemfit Estimating Systems of Simultaneous Equations TAHMMAnnot Mixture model approach to compare two samples of Tiling Array data TANOVA Time Course Analysis of Variance for Microarray TEQR Target Equavelence Range Design TERAplusB Test for A+B Traditional Escalation Rule TGUICore Teaching GUI - Core functionality TGUITeaching Teaching GUI - prototype TIMP a problem solving environment for fitting separable nonlinear models in physics and chemistry applications TRAMPR TRFLP Analysis and Matching Package for R TRIANG Symmetric discrete triangular distributions TRIANGG General discrete triangular distribution TSA Time Series Analysis TSAgg Time series Aggregation TSHRC Two Stage Hazard Rate Comparison TSMySQL Time Series Database Interface extensions for MySQL TSP Traveling Salesperson Problem (TSP) TSPostgreSQL Time Series Database Interface extensions for PostgreSQL TSSQLite Time Series Database Interface extentions for SQLite TSdbi Time Series Database Interface TSfame Time Series Database Interface extensions for fame TSgetSymbol Time Series Database Interface extension to connect with getSymbols TShistQuote Time Series Database Interface extensions for get.hist.quote TSodbc Time Series Database Interface extensions for ODBC TSpadi Time Series Database Interface extensions for PADI Time Series Server TSxls Time Series Database Interface extension to connect to spreadsheets TSzip Time Series Database Interface extension to connect to zip files TTR Technical Trading Rules TWIX Trees WIth eXtra splits TauP.R Earthquake Traveltime Calculations for 1-D Earth Models TeachingDemos Demonstrations for teaching and learning TeachingSampling Sampling designs and parameter estimation in finite population ThreeGroups ML Estimator for Baseline-Placebo-Treatment (Three-group) designs TilePlot Characterization of functional genes in complex microbial communities using tiling DNA microarrays Tinflex Tinflex - Universal non-uniform random number generator TinnR Resources of Tinn-R GUI/Editor for R Environment ToxLim Incorporating Ecological Data and Associated Uncertainty in Bioaccumulation Modeling TraMineR Sequences and trajectories mining for social scientists TradeStrategyAnalyzer Trade Strategy Analyzer TreePar Estimating speciation and extinction rates based on phylogenies TreeRank TreeRank TreeSim Simulating trees under the birth-death model TripleR Social Relation Model (SRM) analyses for single or multiple round-robin groups TunePareto Multi-objective parameter tuning for classifiers TwoPhaseInd Two-Phase Independence TwoStepCLogit Conditional logistic regression: A two-step estimation method TwoWaySurvival Additiv Two-Way Hazards Modelling of Right Censored Survival Data taRifx Collection of utility and convenience functions, and some interesting spatial functions tableplot Represents tables as semi-graphic displays tabplot Tableplot, a visualization of large statistical datasets taskPR Task-Parallel R Package tau Text Analysis Utilities tawny Provides various portfolio optimization strategies including random matrix theory and shrinkage estimators tcltk2 Tcl/Tk Additions tclust Robust Trimmed Clustering 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 testthat Testthat code. Tools to make testing fun :) texmex Threshold exceedences and multivariate extremes textcat N-Gram Based Text Categorization textir Inverse Regression for Text Analysis tfer Forensic Glass Transfer Probabilities tframe Time Frame coding kernel tframePlus Time Frame coding kernel extensions tgp Bayesian treed Gaussian process models tgram Functions to compute and plot tracheidograms thgenetics Genetic Rare Variants Tests tiger TIme series of Grouped ERrors tikzDevice A Device for R Graphics Output in PGF/TikZ Format tileHMM Hidden Markov Models for ChIP-on-Chip Analysis time Time tracking for developers timeDate Rmetrics - Chronological and Calendarical Objects timeSeries Rmetrics - Financial Time Series Objects timeordered Time-ordered and time-aggregated network analyses timereg timereg package for Flexible regression models for survival data timsac TIMe Series Analysis and Control package tis Time Indexes and Time Indexed Series titan Titration analysis for mass spectrometry data tkrgl TK widget tools for rgl package tkrplot TK Rplot tlemix Trimmed Maximum Likelihood Estimation tlnise Two-level normal independent sampling estimation tm Text Mining Package tm.plugin.dc Text Mining Distributed Corpus Plug-In tm.plugin.mail Text Mining E-Mail Plug-In tmle Targeted Maximum Likelihood Estimation of additive treatment effect tmvtnorm Truncated Multivariate Normal and Student t Distribution tnet tnet: Software for Analysis of Weighted, Two-mode, and Longitudinal networks tolerance Functions for calculating tolerance intervals tonymisc Functions for Econometrics Output topicmodels Topic models topmodel Implementation of the hydrological model TOPMODEL in R topologyGSA topologyGSA tourr Implement tour methods in pure R code tourrGui A Tour GUI using gWidgets tpr Temporal Process Regression track Track Objects trackObjs Track Objects tractor.base A package for reading, manipulating and visualising magnetic resonance images traitr An interface for creating GUIs modeled in part after traits UI module for python trapezoid The Trapezoidal Distribution tree Classification and regression trees treecm Estimating and plotting the centre of mass of a tree treelet Treelet treemap Treemap visualization treethresh Methods for Tree-based Local Adaptive Thresholding trex Truncated exact test for two-stage case-control design for studying rare genetic variants triads Triad census for networks triangle Provides the standard distribution functions for the triangle distribution trifield Some basic facilities for ternary fields and plots triggr Fast, simple RPC controller for R trimcluster Cluster analysis with trimming trio Detection of disease-associated SNP interactions in case-parent trio data trip Spatial analysis of animal track data tripEstimation Metropolis sampler and supporting functions for estimating animal movement from archival tags and satellite fixes tripack Triangulation of irregularly spaced data truncSP Semi-parametric estimators of truncated regression models truncgof GoF tests allowing for left truncated data truncnorm Truncated normal distribution truncreg Truncated Regression Models trust Trust Region Optimization tsDyn Nonlinear time series models with regime switching 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 tslars Least angle regression for time series analysis tsne T-distributed Stochastic Neighbor Embedding for R (t-SNE) ttime Translate Neurodevelopmental Event Timing Across Species ttrTests Standard Backtests for Technical Trading Rules in Financial Data ttutils Utility functions tuneR Analysis of music and speech twang Toolkit for Weighting and Analysis of Nonequivalent Groups tweedie Tweedie exponential family models twiddler Interactive manipulation of R expressions twitteR R based Twitter client two.stage.boot Two-stage cluster sample bootstrap algorithm twopartqtl QTL Mapping for Point-mass Mixtures twslm A two-way semilinear model for normalization and analysis of cDNA microarray data txtplot Text based plots USPS Unsupervised and Supervised methods of Propensity Score Adjustment for Bias UScensus2000 US Census 2000 Suite of R Packages UScensus2000add US Census 2000 Suite of R Packages: Demographic Add UScensus2000blkgrp US Census 2000 Block Group Shapefiles and Additional Demographic Data UScensus2000cdp US Census 2000 Designated Places Shapefiles and Additional Demographic Data UScensus2000tract US Census 2000 Tract Level Shapefiles and Additional Demographic Data Unicode Unicode data and utilities UsingR Data sets for the text "Using R for Introductory Statistics" ucminf General-purpose unconstrained non-linear optimization udunits2 udunits-2 bindings for R ump Uniformly Most Powerful Tests unbalhaar Function estimation via Unbalanced Haar wavelets uncompress Uncompress uniCox Univarate shrinkage prediction in the Cox model uniPlot Uniforms and customizes plots of packages ggplot2, graphics and lattice unknownR You didn't know you didn't know? unmarked Models for Data from Unmarked Animals untb ecological drift under the UNTB urca Unit root and cointegration tests for time series data urn Urn : Sampling Without Replacement VBmix Variational Bayesian mixture models VGAM Vector Generalized Linear and Additive Models VHDClassification Discrimination/Classification in very high dimension with linear and quadratic rules VIF VIF Regression: A Fast Regression Algorithm For Large Data VIM Visualization and Imputation of Missing Values VLMC VLMC – Variable Length Markov Chains VPdtw Variable Penalty Dynamic Time Warping VarianceGamma The Variance Gamma Distribution Vdgraph This package creates variance dispersion graphs for response surface designs VecStatGraphs2D Vector analysis using graphical and analytical methods in 2D VecStatGraphs3D Vector analysis using graphical and analytical methods in 3D VennDiagram Generate high-resolution Venn and Euler plots VhayuR Vhayu R Interface VisCov Visualizing of distributions of covariance matrices VizCompX Visualisation of Computer Models validator External and Internal Validation Indices varSelRF Variable selection using random forests varSelectIP Objective Bayes Model Selection varcompci VARCOMPCI: A Package for Computation of Confidence Intervals for Variance Components of Mixed Models in R vardiag A package for variogram diagnostics vars VAR Modelling vcd Visualizing Categorical Data vcdExtra vcd additions vegan Community Ecology Package vegclust Fuzzy clustering of vegetation data vegdata Functions to access vegetation databases (Turboveg and VegetWeb) and prepare data for analysis vegetarian Jost Diversity Measures for Community Data venneuler Venn and Euler Diagrams verification Forecast verification utilities vines Multivariate Dependence Modeling with Vines violinmplot Combination of violin plot with mean and standard deviation vioplot Violin plot viopoints 1-D Scatter Plots with Jitter Using Kernel Density Estimates visualizationTools Package contains a few functions to visualize statistical circumstances vmv Visualization of Missing Values voronoi Methods and applications related to Voronoi tessellations vowels Vowel Manipulation, Normalization, and Plotting vrmlgen Generate 3D visualizations for data exploration on the web vrtest Variance Ratio tests and other tests for Martigale Difference Hypothesis vwr Useful functions for visual word recognition research WDI World Development Indicators (World Bank) WGCNA Weighted Gene Co-Expression Network Analysis WINRPACK Read in WIN format data WMBrukerParser William and Mary Parser For Bruker-Ultraflex Mass Spec Data WMCapacity GUI implementing Bayesian working memory models WMTregions Exact Calculation of WMTR WWGbook Functions and datasets for WWGbook WaveCD Wavelet change point detection for array CGH data WaveletCo Wavelet Coherence Analysis WhatIf WhatIf: Software for Evaluating Counterfactuals WilcoxCV Wilcoxon-based variable selection in cross-validation WriteXLS Cross-platform Perl based R function to create Excel 2003 (XLS) files wSVM Weighted SVM with boosting algorithm for improving accuracy walkscoreAPI Walk Score and Transit Score API wasim Visualisation and analysis of output files of the hydrological model WASIM waterfall Waterfall Charts in R waveband Computes credible intervals for Bayesian wavelet shrinkage waveclock Time-frequency analysis of cycling cell luminescence data waved Wavelet Deconvolution wavelets A package of funtions for computing wavelet filters, wavelet transforms and multiresolution analyses wavemulcor Wavelet routine for multiple correlation waveslim Basic wavelet routines for one-, two- and three-dimensional signal processing wavethresh Wavelets statistics and transforms wccsom SOM networks for comparing patterns with peak shifts websockets HTML 5 Websocket Interface for R weights Weighting and Weighted Statistics weirs A Hydraulics Package to Compute Open-Channel Flow over Weirs wgaim Whole Genome Average Interval Mapping for QTL detection using mixed models wikibooks Functions and datasets of the german WikiBook "GNU R" wild1 R Tools for Wildlife Research and Management wle Weighted Likelihood Estimation wmtsa Insightful Wavelet Methods for Time Series Analysis wnominate WNOMINATE Roll Call Analysis Software wombsoft Wombling Computation wordcloud Word Clouds wordnet WordNet Interface wq Exploring water quality monitoring data write.snns Function for exporting data to SNNS pattern files wvioplot Weighted violin plot XLConnect Excel Connector for R XLConnectJars JAR dependencies for the XLConnect package XML Tools for parsing and generating XML within R and S-Plus x12 X12 - wrapper function and GUI xgobi Interface to the XGobi and XGvis programs for graphical data analysis xgrid Access Apple Xgrid using R xlsReadWrite Read and write Excel files (.xls) xlsx Read, write, format Excel 2007 and Excel 97/2000/XP/2003 files xlsxjars Package required jars for the xlsx package xpose4 Xpose 4 xpose4classic Xpose 4 Classic Menu System xpose4data Xpose 4 Data Functions Package xpose4generic Xpose 4 Generic Functions Package xpose4specific Xpose 4 Specific Functions Package xtable Export tables to LaTeX or HTML xterm256 Support for xterm256 escape sequences xtermStyle Basic text formatting using xterm escape sequences xts eXtensible Time Series YaleToolkit Data exploration tools from Yale University YieldCurve Modelling and estimation of the yield curve YjdnJlp Text Analysis by Yahoo! Japan Develper Network YourCast YourCast yaImpute yaImpute: An R Package for k-NN Imputation yacca Yet Another Canonical Correlation Analysis Package yaml Methods to convert R to YAML and back yest Gaussian Independence Models yhat Interpreting Regression Effects Zelig Everyone's Statistical Software zic Bayesian Inference for Zero-Inflated Count Models zipcode U.S. ZIP Code database zipfR Statistical models for word frequency distributions zoeppritz Zoeppritz Equations zoo S3 Infrastructure for Regular and Irregular Time Series (Z's ordered observations) zyp Zhang + Yue-Pilon trends package 評論 Post preview: Close preview or Sign in as Wikidot user (will not be published) - + Help: wiki text quick reference 授權 本網頁的作者、授權與引用方式 作者 陳鍾誠 (部分網頁改寫來源為：徐俊晓 「统计学与R读书笔记第五版」)，於金門大學資訊工程系，電子郵件：wt.ude.uqn|ccc#wt.ude.uqn|ccc，網站：http://ccckmit.wikidot.com。 授權 本文採用 GFDL 授權條款 (GNU Free Documentation License)。 引用方式 陳鍾誠, 「免費電子書：R 統計軟體」， (網站) 陳鍾誠的網站 (網頁標題) R 軟體的套件與用途，取自 http://ccckmit.wikidot.com/r:package ，網頁修改第 6 版 (02 Sep 2011 04:53)