More than 4700 packages are available in R. It keeps growing, whole bunch of functionalities are available, only thing is too choose correct package. R provides package to handle big data (ff), allow parallelism, plot graphs (ggplot2), analyze data through different algorithm available (ABCp2 etc etc..), develop GUI (shiny) and many more.

A3 | A3: Accurate, Adaptable, and Accessible Error Metrics for Predictive Models |

abc | Tools for Approximate Bayesian Computation (ABC) |

abcdeFBA | ABCDE_FBA: A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package |

ABCExtremes | ABC Extremes |

ABCp2 | Approximate Bayesian Computational model for estimating P2 |

abctools | Tools for ABC analyses |

abd | The Analysis of Biological Data |

abf2 | Load Axon ABF2 files (currently only in gap-free recording mode) |

abind | Combine multi-dimensional arrays |

aBioMarVsuit | A Biomarker Validation Suit for predicting Survival using gene signature |

abn | Data Modelling with Additive Bayesian Networks |

abundant | Abundant regression and high-dimensional principal fitted components |

accelerometry | Functions for processing uniaxial minute-to-minute accelerometer data |

AcceptanceSampling | Creation and evaluation of Acceptance Sampling Plans |

ACCLMA | ACC & LMA Graph Plotting |

ACD | Categorical data analisys with complete or missing responses |

Ace | Assay-based Cross-sectional Estimation of incidence rates |

acepack | ace() and avas() for selecting regression transformations |

acer | The ACER Method for Extreme Value Estimation |

aCGH.Spline | Robust spline interpolation for dual color array comparative genomic hybridisation data |

ACNE | Affymetrix SNP probe-summarization using non-negative matrix factorization |

acopula | Modelling dependence with multivariate Archimax (or any user-defined continuous) copulas |

aCRM | Convenience functions for analytical Customer Relationship Management |

acs | Download, manipulate, and present data from the US Census American Community Survey |

Actigraphy | Actigraphy Data Analysis |

actuar | Actuarial functions |

ActuDistns | Functions for actuarial scientists |

ada | ada: an R package for stochastic boosting |

adabag | Applies multiclass AdaBoost.M1, AdaBoost-SAMME and Bagging |

adagio | Discrete and Global Optimization Routines |

AdaptFit | Adaptive Semiparametic Regression |

AdaptFitOS | Adaptive Semiparametric Regression with Simultaneous Confidence Bands |

adaptivetau | Tau-leaping stochastic simulation |

adaptMCMC | Implementation of a generic adaptive Monte Carlo Markov Chain sampler |

adaptsmoFMRI | Adaptive Smoothing of FMRI Data |

adaptTest | Adaptive two-stage tests |

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 |

AdequacyModel | Adequacy of probabilistic models and generation of pseudo-random numbers |

ADGofTest | Anderson-Darling GoF test |

adimpro | Adaptive Smoothing of Digital Images |

adk | Anderson-Darling K-Sample Test and Combinations of Such Tests |

adlift | An adaptive lifting scheme algorithm |

ADM3 | An Interpretation of the ADM method – automated detection algorithm |

AdMit | Adaptive Mixture of Student-t distributions |

ads | Spatial point patterns analysis |

AER | Applied Econometrics with R |

afex | Analysis of Factorial Experiments |

aftgee | Accelerated Failure Time Model with Generalized Estimating Equations |

AGD | Analysis of Growth Data |

ageprior | Prior distributions for molecular dating |

aggrisk | Estimate individual level risk using individual case data and spatially aggregated control data |

agop | Aggregation Operators and Preordered Sets |

agRee | Various Methods for Measuring Agreement |

Agreement | Statistical Tools for Measuring Agreement |

agricolae | Statistical Procedures for Agricultural Research |

agridat | Agricultural datasets |

agrmt | Calculate agreement |

ahaz | Regularization for semiparametric additive hazards regression |

AICcmodavg | Model selection and multimodel inference based on (Q)AIC(c) |

AID | An R Package to Estimate Box-Cox Power Transformation Parameter |

AIM | AIM: adaptive index model |

akima | Interpolation of irregularly spaced data |

akmeans | Adaptive Kmeans algorithm based on threshold |

alabama | Constrained nonlinear optimization |

ALDqr | Quantile Regression Using Asymmetric Laplace Distribution |

AlgDesign | Algorithmic Experimental Design |

ALKr | Generate Age-Length Keys for fish populations |

allan | Automated Large Linear Analysis Node |

allanvar | Allan Variance Analysis |

allelematch | Identifying unique multilocus genotypes where genotyping error and missing data may be present |

AlleleRetain | Allele Retention, Inbreeding, and Demography |

allelic | A fast, unbiased and exact allelic exact test |

AllPossibleSpellings | Computes all of a word’s possible spellings |

alphahull | Generalization of the convex hull of a sample of points in the plane |

alphashape3d | Implementation of the 3D alpha-shape for the reconstruction of 3D sets from a point cloud |

alr3 | Data to accompany Applied Linear Regression 3rd edition |

alr4 | Data to accompany Applied Linear Regression 4rd edition |

ALS | multivariate curve resolution alternating least squares (MCR-ALS) |

amap | Another Multidimensional Analysis Package |

AMAP.Seq | Compare Gene Expressions from 2-Treatment RNA-Seq Experiments |

amei | Adaptive Management of Epidemiological Interventions |

Amelia | Amelia II: A Program for Missing Data |

amen | Additive and multiplicative effects modeling of networks and relational data |

AmericanCallOpt | This package includes pricing function for selected American call options with underlying assets that generate payouts |

AMGET | Post-processing tool for ADAPT 5 |

AMORE | A MORE flexible neural network package |

anacor | Simple and Canonical Correspondence Analysis |

anaglyph | 3D Anaglyph Plots |

analogue | Analogue and weighted averaging methods for palaeoecology |

AnalyzeFMRI | Functions for analysis of fMRI datasets stored in the ANALYZE or NIFTI format |

anametrix | Bidirectional connector to Anametrix API |

anapuce | Tools for microarray data analysis |

AncestryMapper | Ancestry Mapper |

AnDE | An extended Bayesian Learning Technique developed by Dr. Geoff Webb |

andrews | Andrews curves |

anesrake | ANES Raking Implementation |

Animal | Analyze time-coded animal behavior data |

animation | A gallery of animations in statistics and utilities to create animations |

ANN | Feedforward Artificial Neural Network optimized by Genetic Algorithm |

AnnotLists | AnnotLists: A tool to annotate multiple lists from a specific annotation file |

anoint | Analysis of interactions |

ant | Version of ant specific to R |

AnthropMMD | A GUI for Mean Measures of Divergence |

antitrust | Antitrust Library |

aod | Analysis of Overdispersed Data |

aods3 | Analysis of Overdispersed Data using S3 methods |

AOfamilies | Aranda-Ordaz (AO) transformation families |

apcluster | Affinity Propagation Clustering |

ape | Analyses of Phylogenetics and Evolution |

aplpack | Another Plot PACKage: stem.leaf, bagplot, faces, spin3R, and some slider functions |

appell | Compute Appell’s F1 hypergeometric function |

apple | Approximate Path for Penalized Likelihood Estimators |

AppliedPredictiveModeling | Functions and Data Sets for ‘Applied Predictive Modeling’ |

approximator | Bayesian prediction of complex computer codes |

APSIMBatch | Analysis the output of Apsim software |

apsrtable | apsrtable model-output formatter for social science |

apt | Asymmetric Price Transmission (apt) |

apTreeshape | Analyses of Phylogenetic Treeshape |

aqp | Algorithms for Quantitative Pedology |

aqr | Interface methods to use with an ActiveQuant Master Server |

AquaEnv | AquaEnv – an integrated development toolbox for aquatic chemical model generation |

ARAMIS | A R Adaptive Multiple Importance Sampling |

archetypes | Archetypal Analysis |

ArDec | Time series autoregressive-based decomposition |

arf3DS4 | Activated Region Fitting, fMRI data analysis (3D) |

arfima | Fractional ARIMA Time Series Modeling |

argosfilter | Argos locations filter |

argparse | Command line optional and positional argument parser |

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.* packages part of The Aroma Framework |

ArrayBin | Binarization of numeric data arrays |

arrayhelpers | Convenience functions for arrays |

ars | Adaptive Rejection Sampling |

ARTIVA | Infer a time-varying DBN network from time series data |

ARTP | Gene and Pathway p-values computed using the Adaptive Rank Truncated Product |

arules | Mining Association Rules and Frequent Itemsets |

arulesNBMiner | Mining NB-Frequent Itemsets and NB-Precise Rules |

arulesSequences | Mining frequent sequences |

arulesViz | Visualizing Association Rules and Frequent Itemsets |

asbio | A collection of statistical tools for biologists |

ascii | Export R objects to several markup languages |

ascrda | Augmented SCRDA |

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 |

assertive | Readable check functions to ensure code integrity |

AssetPricing | Optimal pricing of assets with fixed expiry date |

AssotesteR | Statistical Tests for Genetic Association Studies |

aster | Aster Models |

aster2 | Aster Models |

astro | Astronomy Functions, Tools and Routines |

astroFns | Astronomy: time and position functions, misc. utilities |

astsa | Applied Statistical Time Series Analysis |

asympTest | Asymptotic statistic |

asypow | Calculate Power Utilizing Asymptotic Likelihood Ratio Methods |

AtelieR | A GTK GUI for teaching basic concepts in statistical inference, and doing elementary bayesian tests |

AtmRay | Acoustic Traveltime Calculations for 1-D Atmospheric Models |

attfad | Evaluation and comparison of expression data and GRNs |

AUC | Threshold independent performance measures for probabilistic classifiers |

AUCRF | Variable Selection with Random Forest and the Area Under the Curve |

audio | Audio Interface for R |

audiolyzR | audiolyzR: Give your data a listen |

audit | Bounds for Accounting Populations |

automap | Automatic interpolation package |

autopls | pls regression with backward selection of predictors |

AutoSEARCH | General-to-Specific (GETS) Model Selection |

aws | Adaptive Weights Smoothing |

awsMethods | Class and Methods definitions for packages aws, adimpro, fmri, dwi |

AWS.tools | R package to use Amazon Web Services |

aylmer | A generalization of Fisher’s exact test |

B2Z | Bayesian Two-Zone Model |

b6e6rl | Adaptive differential evolution, b6e6rl variant |

BaBooN | Bayesian Bootstrap Predictive Mean Matching – Multiple and single imputation for discrete data |

BACCO | Bayesian Analysis of Computer Code Output (BACCO) |

backtest | Exploring portfolio-based conjectures about financial instruments |

BACprior | Sensitivity of the Bayesian Adjustment for Confounding (BAC) algorithm to the choice of hyperparameter omega |

BAEssd | Bayesian Average Error approach to Sample Size Determination |

bagRboostR | Ensemble bagging and boosting classifiers |

BaM | Functions and datasets for books by Jeff Gill |

bamdit | Bayesian Meta-Analysis of diagnostic test data |

bams | Breakpoint annotation model smoothing |

bandit | Functions for simple A/B split test and multi-armed bandit analysis |

barcode | Barcode distribution plots |

bark | Bayesian Additive Regresssion Kernels |

Barnard | Barnard’s Unconditional Test |

BAS | Bayesian Model Averaging using Bayesian Adaptive Sampling |

BaSAR | Bayesian Spectrum Analysis in R |

base64 | Base 64 encoder/decoder |

base64enc | Tools for base64 encoding |

baseline | Baseline Correction of Spectra |

basicspace | A Package to Recover a Basic Space from Issue Scales |

BaSTA | A package for estimating age-specific survival from incomplete capture-recapture/recovery data |

batade | HTML reports and so on |

batch | Batching Routines in Parallel and Passing Command-Line Arguments to R |

BatchExperiments | Statistical experiments on batch computing clusters |

BatchJobs | Batch computing with R |

batchmeans | Consistent Batch Means Estimation of Monte Carlo Standard Errors |

BayesBridge | Bridge Regression |

bayesclust | Tests/Searches for significant clusters in genetic data |

BayesComm | Bayesian community ecology analysis |

bayescount | Power calculations and Bayesian analysis of count distributions and FECRT data using MCMC |

BayesCR | Bayesian analysis of censored linear regression models with scale mixtures of normal (SMN) distributions |

BayesDA | Functions and Datasets for the book “Bayesian Data Analysis” |

bayesDem | Graphical User Interface for bayesTFR, bayesLife and bayesPop |

BayesFactor | Computation of Bayes factors for common designs |

bayesGARCH | Bayesian Estimation of the GARCH(1,1) Model with Student-t Innovations |

bayesGDS | Functions to implement Generalized Direct Sampling |

BayesLCA | Bayesian Latent Class Analysis |

bayesLife | Bayesian Projection of Life Expectancy |

BayesLogit | Logistic Regression |

bayesm | Bayesian Inference for Marketing/Micro-econometrics |

bayesMCClust | Mixtures-of-Experts Markov Chain Clustering and Dirichlet Multinomial Clustering |

bayesmix | Bayesian Mixture Models with JAGS |

BayesNI | BayesNI: Bayesian Testing Procedure for Noninferiority with Binary Endpoints |

bayesPop | Probabilistic Population Projection |

bayespref | Hierarchical Bayesian analysis of ecological count data |

bayesQR | Bayesian quantile regression |

BayesQTLBIC | Bayesian multi-locus QTL analysis based on the BIC criterion |

bayess | Bayesian Essentials with R |

BayesSingleSub | Computation of Bayes factors for interrupted time-series designs |

bayesSurv | Bayesian Survival Regression with Flexible Error and Random Effects Distributions |

bayesTFR | Bayesian Fertility Projection |

Bayesthresh | Bayesian thresholds mixed-effects models for categorical data |

BayesTree | Bayesian Methods for Tree Based Models |

BayesValidate | BayesValidate Package |

BayesVarSel | Bayesian Variable selection in Linear Models |

BayesX | R Utilities Accompanying the Software Package BayesX |

BayesXsrc | R Package Distribution of the BayesX C++ Sources |

BayHap | Bayesian analysis of haplotype association using Markov Chain Monte Carlo |

BayHaz | R Functions for Bayesian Hazard Rate Estimation |

BaylorEdPsych | R Package for Baylor University Educational Psychology Quantitative Courses |

BaySIC | Bayesian Analysis of Significantly Mutated Genes in Cancer |

BB | Solving and Optimizing Large-Scale Nonlinear Systems |

bbemkr | Bayesian bandwidth estimation for multivariate kernel regression with Gaussian error |

BBmisc | Miscellaneous helper functions for B. Bischl |

bbmle | Tools for general maximum likelihood estimation |

BBMM | Brownian bridge movement model |

bbo | Biogeography-Based Optimization |

bc3net | BC3NET |

BCA | Business and Customer Analytics |

BCBCSF | Bias-corrected Bayesian Classification with Selected Features |

BCDating | Business Cycle Dating and Plotting Tools – BCDating |

BcDiag | Diagnostics plots for Bicluster Data |

BCE | Bayesian composition estimator: estimating sample (taxonomic) composition from biomarker data |

BCEA | Bayesian Cost Effectiveness Analysis |

BCEs0 | Bayesian models for cost-effectiveness analysis in the presence of structural zero costs |

Bchron | Bayesian radiocarbon chronologies and relative sea level analysis |

Bclim | Bayesian Palaeoclimate Reconstruction from Pollen |

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 |

bcrm | Bayesian continuous reassessment method (CRM) designs for Phase I dose-finding trials |

bcv | Cross-Validation for the SVD (Bi-Cross-Validation) |

bda | Density Estimation for Binned/Weighted Data |

BDgraph | Graph determination based on birth-death MCMC |

bdoc | Bayesian Discrete Ordered Classification of DNA Barcodes |

bdpv | Inference and design for predictive values in binary diagnostic tests |

bdsmatrix | Routines for Block Diagonal Symmetric matrices |

bdynsys | Bayesian Dynamical System Model |

beadarrayFilter | Bead filtering for Illumina bead arrays |

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 |

BEDASSLE | Disentangles the effects of geographic and ecological isolation on genetic differentiation |

beeswarm | The bee swarm plot, an alternative to stripchart |

benchden | 28 benchmark densities from Berlinet/Devroye (1994) |

benchmark | Benchmark Experiments Toolbox |

Benchmarking | Benchmark and frontier analysis using DEA and SFA |

BenfordTests | Statistical Tests for Evaluating Conformity to Benford’s Law |

bentcableAR | Bent-Cable Regression for Independent Data or Autoregressive Time Series |

ber | Batch Effects Removal |

Bergm | Bayesian analysis for exponential random graph models |

BerkeleyEarth | Data Input for Berkeley Earth Surface Temperature |

Bessel | Bessel – Bessel Functions Computations and Approximations |

BEST | Bayesian Estimation Supersedes the t-Test |

bestglm | Best Subset GLM |

betafam | Detecting rare variants for quantitative traits using nuclear families |

betapart | Partitioning beta diversity into turnover and nestedness components |

betaper | Functions to incorporate taxonomic uncertainty on multivariate analyses of ecological data |

betareg | Beta Regression |

betategarch | Estimation and simulation of first-order Beta-t-EGARCH models |

bethel | Bethel’s algorithm |

bfa | Bayesian Factor Analysis |

bfast | Breaks For Additive Season and Trend (BFAST) |

bfp | Bayesian Fractional Polynomials |

bgeva | Binary Generalized Extreme Value Additive Models |

bgmm | Gaussian Mixture Modeling algorithms. Including the belief-based mixture modeling |

BGSIMD | Block Gibbs Sampler with Incomplete Multinomial Distribution |

BH | The Boost C++ Libraries |

Bhat | General likelihood exploration |

BHH2 | Useful Functions for Box, Hunter and Hunter II |

biasbetareg | Bias correction of the parameter estimates of the beta regression model |

BiasedUrn | Biased Urn model distributions |

bibtex | bibtex parser |

biclust | BiCluster Algorithms |

BiDimRegression | Calculates the bidimensional regression between two 2D configurations |

bifactorial | Inferences for bi- and trifactorial trial designs |

biganalytics | A library of utilities for big.matrix objects of package bigmemory |

bigdata | Big Data Analytics |

bigGP | Distributed Gaussian process calculations |

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 |

bigmemory.sri | A shared resource interface for Bigmemory Project packages |

bigml | R bindings for the BigML API |

bigrf | Big Random Forests: Classification and Regression Forests for Large Data Sets |

bigRR | Generalized Ridge Regression (with special advantage for p >> n cases) |

bigtabulate | table-, tapply-, and split-like functionality for matrix and big.matrix objects |

BigTSP | Top Scoring Pair based methods for classification |

bild | bild: a package for BInary Longitudinal Data |

bimetallic | Power for SNP analyses using silver standard cases |

binarySimCLF | Simulates Correlated Binary Data |

BINCO | Bootstrap Inference for Network COstruction |

bindata | Generation of Artificial Binary Data |

binGroup | Evaluation and experimental design for binomial group testing |

binMto | Asymptotic simultaneous confidence intervals for many-to-one comparisons of proportions |

BinNor | Simultaneous generation of multivariate binary and normal variates |

binom | Binomial Confidence Intervals For Several Parameterizations |

binomialcftp | Generates binomial random numbers via the coupling from the past algorithm |

binomlogit | Efficient MCMC for Binomial Logit Models |

binomTools | Performing diagnostics on binomial regression models |

binseqtest | Exact Binary Sequential Designs and Analysis |

Biodem | Biodemography functions |

BiodiversityR | GUI for biodiversity, suitability and community ecology analysis |

BioGeoBEARS | BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts |

Biograph | Explore life histories |

bio.infer | Predict environmental conditions from biological observations |

biom | An interface package (beta) for the BIOM file format |

BioMark | Find biomarkers in two-class discrimination problems |

BiomarkeR | Paired (pBI) and Unpaired Biomarker Identifier (uBI) including a method to infer networks |

biomod2 | Ensemble platform for species distribution modeling |

bionetdata | Biological and chemical data networks |

biopara | Self-contained parallel system for R |

BioPhysConnectoR | BioPhysConnectoR |

biOps | Image processing and analysis |

biOpsGUI | GUI for Basic image operations |

bios2mds | From BIOlogical Sequences to MultiDimensional Scaling |

BioStatR | Initiation à la Statistique avec R |

bipartite | Visualising bipartite networks and calculating some (ecological) indices |

BiplotGUI | Interactive Biplots in R |

birch | Dealing with very large datasets using BIRCH |

bisectr | Tools to find bad commits with git bisect |

bisoreg | Bayesian Isotonic Regression with Bernstein Polynomials |

bit | A class for vectors of 1-bit booleans |

bit64 | A S3 class for vectors of 64bit integers |

bitops | Bitwise Operations |

bivarRIpower | Sample size calculations for bivariate longitudinal data |

biwavelet | Conduct univariate and bivariate wavelet analyses |

biwt | Functions to compute the biweight mean vector and covariance & correlation matrices |

BlakerCI | Blaker’s binomial confidence limits |

BLCOP | Black-Litterman and copula-opinion pooling frameworks |

blender | Analyze biotic homogenization of landscapes |

blighty | United Kingdom coastlines |

blm | Binomial linear and linear-expit regression |

blme | Bayesian Linear Mixed-Effects models |

blockcluster | Co-Clustering package for Binary, Contingency and Continuous data-sets |

BlockMessage | Creates strings that show a text message in 8 by 8 block letters |

blockmodeling | An R package for Generalized and classical blockmodeling of valued networks |

blockrand | Randomization for block random clinical trials |

blockTools | Block, assign, and diagnose potential interference in randomized experiments |

BLR | Bayesian Linear Regression |

BMA | Bayesian Model Averaging |

bmd | Benchmark dose analysis for dose-response data |

bmem | Mediation analysis with missing data using bootstrap |

Bmix | Bayesian Sampling for Stick-breaking Mixtures |

bmk | MCMC diagnostics package |

BMN | The pseudo-likelihood method for pairwise binary markov networks |

bmp | Read Windows Bitmap (BMP) images |

bmrm | Bundle Methods for Regularized Risk Minimization Package |

BMS | Bayesian Model Averaging Library |

bnlearn | Bayesian network structure learning, parameter learning and inference |

BNPdensity | Ferguson-Klass type algorithm for posterior normalized random measures |

bnpmr | Bayesian monotonic nonparametric regression |

boa | Bayesian Output Analysis Program (BOA) for MCMC |

BOG | Bacterium and virus analysis of Orthologous Groups (BOG) is a package for identifying differentially regulated genes in the light of gene functions |

boilerpipeR | Interface to the boilerpipe Java library by Christian Kohlschutter (http://code.google.com/p/boilerpipe/) |

Bolstad | Bolstad functions |

Bolstad2 | Bolstad functions |

boolfun | Cryptographic Boolean Functions |

BoolNet | Generation, reconstruction, simulation and analysis of synchronous, asynchronous, and probabilistic Boolean networks |

boostSeq | Optimized GWAS cohort subset selection for resequencing studies |

boot | Bootstrap Functions (originally by Angelo Canty for S) |

bootES | Bootstrap Effect Sizes |

bootfs | Use multiple feature selection algorithms to derive robust feature sets for two class classification problems |

bootRes | Bootstrapped Response and Correlation Functions |

bootruin | A bootstrap test for the probability of ruin in the classical risk process |

bootspecdens | Testing equality of spectral densities |

bootStepAIC | Bootstrap stepAIC |

bootstrap | Functions for the Book “An Introduction to the Bootstrap” |

Boruta | A wrapper algorithm for all-relevant feature selection |

boss | Boosted One-Step Statistics: Fast and accurate approximations for GLM, GEE and Mixed models for use in GWAS |

BoSSA | a Bunch of Structure and Sequence Analysis |

boussinesq | Analytic Solutions for (ground-water) Boussinesq Equation |

bpca | Biplot of Multivariate Data Based on Principal Components Analysis |

bpcp | Beta Product Confidence Procedure for Right Censored Data |

bPeaks | bPeaks: a simple and intuitive approach for detection of basic peaks (bPeaks) from ChIP-seq data |

bpkde | Back-Projected Kernel Density Estimation |

bqtl | Bayesian QTL mapping toolkit |

BradleyTerry2 | Bradley-Terry Models |

BrailleR | Improved access for blind useRs |

brainwaver | Basic wavelet analysis of multivariate time series with a visualisation and parametrisation using graph theory |

branchLars | Cost-efficient Variable Selection |

breakage | SICM pipette tip geometry estimation |

bReeze | Functions for wind resource assessment |

brew | Templating Framework for Report Generation |

brglm | Bias reduction in binomial-response generalized linear models |

bride | Brier score decomposition of probabilistic forecasts for binary events |

brnn | brnn (Bayesian regularization for feed-forward neural networks) |

Brobdingnag | Very large numbers in R |

broman | Karl Broman’s R code |

Brq | Bayesian analysis of quantile regression models |

BRugs | R interface to the OpenBUGS MCMC software |

BSagri | Statistical methods for safety assessment in agricultural field trials |

bscr | Bayesian parametric and semi-parametric analyses for semi-competing risks data |

BSDA | Basic Statistics and Data Analysis |

BsMD | Bayes Screening and Model Discrimination |

bspec | Bayesian spectral inference |

bspmma | bspmma: Bayesian Semiparametric Models for Meta-Analysis |

BSquare | Bayesian Simultaneous Quantile Regression |

bst | Gradient Boosting |

bstats | Basic statistical functions for R |

BTSPAS | Bayesian Time-Strat. Population Analysis |

BTYD | Implementing Buy ‘Til You Die Models |

BurStFin | Burns Statistics Financial |

BurStMisc | Burns Statistics miscellaneous |

bursts | Markov model for bursty behavior in streams |

bvenn | A Simple alternative to proportional Venn diagrams |

bvls | The Stark-Parker algorithm for bounded-variable least squares |

bvpSolve | Solvers for boundary value problems of ordinary differential equations |

BVS | Bayesian Variant Selection: Bayesian Model Uncertainty Techniques for Genetic Association Studies |

c060 | Additional variable selection, model validation and parameter tuning functions for glmnet models |

c3net | Infering large-scale gene networks with C3NET |

C50 | C5.0 Decision Trees and Rule-Based Models |

ca | Simple, Multiple and Joint Correspondence Analysis |

cabootcrs | Bootstrap Confidence Regions for Correspondence Analysis |

cacher | Tools for caching and distributing statistical analyses |

cacheSweave | Tools for caching Sweave computations |

cacIRT | Classification accuracy and consistency under Item Response Theory |

CaDENCE | Conditional Density Estimation Network Construction and Evaluation |

CADFtest | This package performs the CADF unit root test proposed in Hansen (1995) |

caGUI | A Tcl/Tk GUI for the functions in the ca package |

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 |

cairoDevice | Cairo-based cross-platform antialiased graphics device driver |

CalciOMatic | Automatic Calcium Imaging Analysis |

calibrate | Calibration of Scatterplot and Biplot Axes |

calibrator | Bayesian calibration of complex computer codes |

CALINE3 | R interface to Fortran 77 implementation of CALINE3 |

calmate | CalMaTe – Improved allele-specific copy number of SNP arrays for downstream segmentation |

CAMAN | Finite Mixture Models and meta-analysis tools – based on C.A.MAN |

cancerTiming | Estimation of temporal ordering of cancer abnormalities |

candisc | Visualizing Generalized Canonical Discriminant and Canonical Correlation Analysis |

cape | Combined analysis of pleiotropy and epistasis |

caper | Comparative Analyses of Phylogenetics and Evolution in R |

capme | Covariate Adjusted Precision Matrix Estimation |

capushe | Capushe, data-driven slope estimation and dimension jump |

capwire | Estimates population size from non-invasive sampling |

car | Companion to Applied Regression |

CARBayes | Spatial areal unit modelling |

carcass | Estimation of the number of fatalities from carcass searches |

cardidates | Identification of cardinal dates in ecological time series |

care | High-Dimensional Regression and CAR Score Variable Selection |

CARE1 | Statistical package for population size estimation in capture-recapture models |

caret | Classification and Regression Training |

caribou | Estimation of caribou abundance based on large scale aggregations monitored by radio telemetry |

CARramps | Reparameterized and marginalized posterior sampling for conditional autoregressive models |

CAscaling | CA scaling in R |

caschrono | Séries temporelles avec R – Méthodes et cas |

cat | Analysis of categorical-variable datasets with missing values |

catdata | Categorical Data |

CatDyn | Fishery Stock Assessment by Catch Dynamic Models |

catenary | Fits a catenary to given points |

catIrt | An R Package for Simulating IRT-Based Computerized Adaptive Tests |

catnet | Categorical Bayesian Network Inference |

caTools | Tools: moving window statistics, GIF, Base64, ROC AUC, etc |

catR | Procedures to generate IRT adaptive tests (CAT) |

catspec | Special models for categorical variables |

CausalGAM | Estimation of Causal Effects with Generalized Additive Models |

causalsens | Selection Bias Approach to Sensitivity Analysis for Causal Effects |

Causata | Analysis utilities for binary classification and Causata users |

cba | Clustering for Business Analytics |

CBPS | R Package for Covariate Balancing Propensity Score |

CCA | Canonical correlation analysis |

CCAGFA | Bayesian canonical correlation analysis and group factor analysis |

ccaPP | (Robust) canonical correlation analysis via projection pursuit |

cccd | Class Cover Catch Digraphs |

ccChooser | Developing a core collections |

cccrm | CCC-RM |

ccgarch | Conditional Correlation GARCH models |

cclust | Convex Clustering Methods and Clustering Indexes |

CCM | Correlation classification method (CCM) |

CCP | Significance Tests for Canonical Correlation Analysis (CCA) |

cda | Coupled dipole approximation in electromagnetic scattering |

cdb | Reading and Writing Constant DataBases |

CDFt | Statistical downscaling through CDF-transform |

CDLasso | Coordinate Descent Algorithms for Lasso Penalized L1, L2, and Logistic Regression |

CDM | Cognitive Diagnosis Modeling |

CDNmoney | Components of Canadian Monetary and Credit Aggregates |

CDVine | Statistical inference of C- and D-vine copulas |

cec2005benchmark | Benchmark for the CEC 2005 Special Session on Real-Parameter Optimization |

cec2013 | Benchmark functions for the Special Session and Competition on Real-Parameter Single Objective Optimization at CEC-2013 |

celestial | Collection of common astronomical conversion routines |

CellularAutomaton | One-Dimensional Cellular Automata |

cellVolumeDist | Functions to fit cell volume distributions and thereby estimate cell growth rates and division times |

cem | Coarsened Exact Matching |

cems | Conditional expectation manifolds |

censReg | Censored Regression (Tobit) Models |

CensRegMod | Fitting Normal and Student-t censored regression model |

CePa | Centrality-based pathway enrichment |

cepp | Context Driven Exploratory Projection Pursuit |

cfa | Analysis of configuration frequencies (CFA) |

CfEstimateQuantiles | Estimate quantiles using any order Cornish-Fisher expansion |

CFL | Compensatory Fuzzy Logic |

cg | Comparison of groups |

cgAUC | Calculate AUC-type measure when gold standard is continuous and the corresponding optimal linear combination of variables with respect to it |

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 |

CGP | Composite Gaussian process models |

ChainLadder | Statistical methods for the calculation of outstanding claims reserves in general insurance |

ChangeAnomalyDetection | Change Anomaly Detection |

changeLOS | Change in LOS |

changepoint | An R package for changepoint analysis |

charlson | Converts listwise icd9 data into comorbidity count and Charlson Index |

CHCN | Canadian Historical Climate Network |

cheb | Discrete Linear Chebyshev Approximation |

chebpol | Multivariate Chebyshev interpolation |

CheckDigit | Calculate and verify check digits |

cheddar | Analysis and visualisation of ecological communities |

chemCal | Calibration functions for analytical chemistry |

chemometrics | Multivariate Statistical Analysis in Chemometrics |

ChemometricsWithR | Chemometrics with R – Multivariate Data Analysis in the Natural Sciences and Life Sciences |

ChemometricsWithRData | Data for package ChemometricsWithR |

ChemoSpec | Exploratory Chemometrics for Spectroscopy |

cherry | Multiple testing methods for exploratory research |

chillR | Statistical methods for phenology analysis in temperate fruit trees |

CHNOSZ | Chemical Thermodynamics and Activity Diagrams |

ChoiceModelR | Choice Modeling in R |

choplump | Choplump tests |

chords | Estimation in respondent driven samples |

chron | Chronological objects which can handle dates and times |

CHsharp | Choi and Hall Clustering in 3d |

cimis | R package for retrieving data from CIMIS |

cin | Causal Inference for Neuroscience |

circlize | Circular layout in R |

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) |

circular | Circular Statistics |

cit | Causal Inference Test |

CITAN | CITation ANalysis toolpack |

citbcmst | Assigning tumor samples to CIT Breast Cancer Molecular Subtypes from gene expression data |

citccmst | CIT Colon Cancer Molecular SubTypes Prediction |

CityPlot | Visualization of structure and contents of a database |

Ckmeans.1d.dp | Optimal distance-based clustering for one-dimensional data |

cladoRcpp | C++ implementations of phylogenetic calculations |

CLAG | CLAG: an unsupervised non hierarchical clustering algorithm handling biological data |

class | Functions for Classification |

classGraph | Construct Graphs of S4 Class Hierarchies |

classifly | Explore classification models in high dimensions |

classify | Classification Accuracy and Consistency under IRT models |

classInt | Choose univariate class intervals |

cldr | Language Identifier based on CLD library |

clhs | Conditioned Latin Hypercube Sampling |

climatol | Some Tools for Climatology: series homogenization, plus windrose and Walter&Lieth diagrams |

climdex.pcic | PCIC implementation of Climdex routines |

clime | Constrained L1-minimization for Inverse (covariance) Matrix Estimation |

clinfun | Clinical Trial Design and Data Analysis Functions |

ClinicalRobustPriors | Robust Bayesian Priors in Clinical Trials: An R Package for Practitioners |

clinsig | Clinical significance functions |

clinUtiDNA | Clinical Utility of DNA Testing |

clogitL1 | Fitting exact conditional logistic regression with lasso and elastic net penalties |

cloudUtil | Cloud Util Plots |

clpAPI | R Interface to C API of COIN-OR Clp |

CLSOCP | A smoothing Newton method SOCP solver |

clue | Cluster ensembles |

clues | Clustering Method Based on Local Shrinking |

cluster | Cluster Analysis Extended Rousseeuw et al |

clusterCrit | Clustering Indices |

clustergas | A hierarchical clustering method based on genetic algorithms |

clusterGeneration | random cluster generation (with specified degree of separation) |

clusterGenomics | Identifying clusters in genomics data by recursive partitioning |

clusterPower | Power calculations for cluster-randomized and cluster-randomized crossover trials |

clusterRepro | Reproducibility of gene expression clusters |

clusterSim | Searching for optimal clustering procedure for a data set |

clusteval | Evaluation of Clustering Algorithms |

clusthaplo | Clustering of haplotypes |

ClustOfVar | Clustering of variables |

clustsig | Significant Cluster Analysis |

clv | Cluster Validation Techniques |

clValid | Validation of Clustering Results |

cmaes | Covariance Matrix Adapting Evolutionary Strategy |

CMC | Cronbach-Mesbah Curve |

cmm | Categorical Marginal Models |

cmprsk | Subdistribution Analysis of Competing Risks |

cmrutils | Misc Functions of the Center for the Mathematical Research |

cncaGUI | Canonical Non-symmetrical Correspondence Analysis in R |

CNprep | pre-process DNA copy number (CN) data for detection of CN events |

CNVassoc | Association analysis of CNV data |

coalescentMCMC | MCMC Algorithms for the Coalescent |

coarseDataTools | A collection of functions to help with analysis of coarsely observed data |

COBRA | Nonlinear Aggregation of Predictors |

cobs | COBS – Constrained B-splines (Sparse matrix based) |

cobs99 | Constrained B-splines – outdated 1999 version |

CoClust | Copula based cluster analysis |

cocor | Comparing correlations |

cocorresp | Co-correspondence analysis methods |

cocron | Statistical comparisons of two or more alpha coefficients |

coda | Output analysis and diagnostics for MCMC |

codep | Multiscale Codependence Analysis |

codetools | Code Analysis Tools for R |

coefficientalpha | Robust Cronbach’s alpha with missing and non-normal data |

coefplot | Plots Coefficients from Fitted Models |

coexist | Species coexistence modeling and analysis |

coin | Conditional Inference Procedures in a Permutation Test Framework |

CoinMinD | Simultaneous Confidence Interval for Multinomial Proportion |

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 |

cold | cold: a package for Count Longitudinal Data |

CollocInfer | Collocation Inference for Dynamic Systems |

coloc | Colocalisation tests of two genetic traits |

colorfulVennPlot | Plot and add custom coloring to Venn diagrams for 2-dimensional, 3-dimensional and 4-dimensional data |

colorRamps | Builds color tables |

colorspace | Color Space Manipulation |

colortools | Tools for colors in an HSV color model |

combinat | combinatorics utilities |

CombMSC | Combined Model Selection Criteria |

commandr | Command pattern in R |

CommonJavaJars | Useful libraries for building a Java based GUI under R |

CommonTrend | Extract and plot common trends from a cointegration system. Calculate P-value for Johansen Statistics |

comorbidities | Categorizes ICD-9-CM codes based on published comorbidity indices |

Comp2ROC | Compare two ROC curves that intersect |

compactr | Creates empty plots with compact axis notation |

compare | Comparing Objects for Differences |

compareGroups | Descriptive analysis by groups |

compareODM | comparison of medical forms in CDISC ODM format |

CompareTests | Estimate diagnostic accuracy (sensitivity, specificity, etc) and agreement statistics when one test is conducted on only a subsample of specimens |

comparison | Multivariate likelihood ratio calculation and evaluation |

compeir | Event-specific incidence rates for competing risks data |

compHclust | Complementary Hierarchical Clustering |

complex.surv.dat.sim | Simulation of complex survival data |

CompLognormal | Functions for actuarial scientists |

compoisson | Conway-Maxwell-Poisson Distribution |

COMPoissonReg | Conway-Maxwell Poisson (COM-Poisson) Regression |

compositions | Compositional Data Analysis |

compositionsGUI | Graphical User Environment for Compositional Data Analysis |

compound.Cox | Regression estimation based on the compound shrinkage method under the Cox proportional hazard model |

Compounding | Computing Continuous Distributions |

CompQuadForm | Distribution function of quadratic forms in normal variables |

CompRandFld | Composite-likelihood based Analysis of Random Fields |

compute.es | Compute Effect Sizes |

ConConPiWiFun | This package contains an implementation of continuous convex piecewise (linear and quadratic) functions |

concor | Concordance |

concreg | Concordance regression |

condGEE | Parameter estimation in conditional GEE for recurrent event gap times |

condmixt | Conditional Density Estimation with Neural Network Conditional Mixtures |

CondReg | Condition Number Regularized Covariance Estimation |

coneproj | Primal or Dual Cone Projections with Routines for Shape-restricted Regression |

conf.design | Construction of factorial designs |

confReg | Confidence Estimators for Individual Regression Predictions |

conics | Plot Conics |

conjoint | Conjoint analysis package |

ConjointChecks | A package to check the cancellation axioms of conjoint measurement |

CONOR | CONOR |

CONORData | CONORData |

constrainedKriging | Constrained, covariance-matching constrained and universal point or block kriging |

contfrac | Continued fractions |

conting | Bayesian analysis of contingency tables |

contrast | A collection of contrast methods |

ConvCalendar | Converts dates between calendars |

ConvergenceConcepts | Seeing convergence concepts in action |

convexHaz | Nonparametric MLE/LSE of convex hazard |

COP | Variables selection for index models via correlation pursuit |

copas | Statistical methods to model and adjust for bias in meta-analysis |

copBasic | Basic Theoretical Copula, Empirical Copula, and Various Utility Functions |

copula | Multivariate Dependence with Copulas |

copulaedas | Estimation of Distribution Algorithms Based on Copulas |

CopulaRegression | Bivariate Copula Based Regression Models |

CopyDetect | An R Package for Computing Statistical Indices to Detect Answer Copying on Multiple-Choice Tests |

corcounts | Generate correlated count random variables |

CORE | Cores of Recurrent Events |

CORElearn | CORElearn – classification, regression, feature evaluation and ordinal evaluation |

corHMM | Analysis of binary character evolution |

corpcor | Efficient Estimation of Covariance and (Partial) Correlation |

corpora | Statistics and data sets for corpus frequency data |

CorrBin | Nonparametrics with clustered binary data |

corrgram | Plot a correlogram |

corrperm | Permutation Tests of Correlation with Repeated Measurements |

corrplot | Visualization of a correlation matrix |

corrsieve | CorrSieve |

COSINE | COndition SpecIfic sub-NEtwork |

cosmoFns | Functions for cosmological distances, times, luminosities, etc |

cosso | Fit Regularized Nonparametric Regression Models Using COSSO Penalty |

costat | Time series costationarity determination |

cotrend | Consistant Cotrend Rank Selection |

COUNT | Functions, data and code for count data |

countrycode | Convert country names and country codes |

CountsEPPM | Mean and variance modeling of count data |

covLCA | Latent Class Models with Covariate Effects on Underlying and Measured Variables |

covRobust | Robust Covariance Estimation via Nearest Neighbor Cleaning |

covTest | Computes covariance test for adaptive linear modelling |

CoxBoost | Cox models by likelihood based boosting for a single survival endpoint or competing risks |

coxme | Mixed Effects Cox Models |

coxphf | Cox regression with Firth’s penalized likelihood |

coxphw | Weighted Cox regression |

CoxRidge | Cox models with dynamic ridge penalties |

coxrobust | Robust Estimation in Cox Model |

CPE | Concordance Probability Estimates in Survival Analysis |

CpGassoc | Association between Methylation and a phenotype of interest |

CPHshape | Find the maximum likelihood estimator of the shape constrained hazard baseline and the effect parameters in the Cox proportional hazards model |

cpk | Clinical Pharmacokinetics |

cplexAPI | R Interface to C API of IBM ILOG CPLEX |

cplm | Compound Poisson linear models |

cpm | Sequential Parametric and Nonparametric Change Detection |

CPMCGLM | Correction of the pvalue after multiple coding |

Cprob | Conditional probability function of a competing event |

CR | Power Calculation for Weighted Log-Rank Tests in Cure Rate 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 to animal movement data |

crblocks | Categorical Randomized Block Data Analysis |

CreditMetrics | Functions for calculating the CreditMetrics risk model |

crimCV | Group-Based Modelling of Longitudinal Data |

CRM | Continual Reassessment Method (CRM) for Phase I Clinical Trials |

crmn | CCMN and other noRMalizatioN methods for metabolomics data |

crn | Downloads and Builds datasets for Climate Reference Network |

crossdes | Construction of Crossover Designs |

crossmatch | The Cross-match Test |

crp.CSFP | CreditRisk+ portfolio model |

crrSC | Competing risks regression for Stratified and Clustered data |

crrstep | Stepwise covariate selection for the Fine & Gray competing risks regression model |

crs | Categorical Regression Splines |

CRTSize | Sample Size Estimation Functions for Cluster Randomized Trials |

CrypticIBDcheck | Identifying cryptic relatedness in genetic association studies |

cshapes | CShapes Dataset and Utilities |

cslogistic | Conditionally Specified Logistic Regression |

csound | Accessing Csound functionality through R |

CSS | Extract information from an html document with CSS selectors |

csSAM | csSAM – cell-specific Significance Analysis of Microarrays |

cts | Continuous Time Autoregressive Models |

CTT | Classical Test Theory Functions |

ctv | CRAN Task Views |

cubature | Adaptive multivariate integration over hypercubes |

Cubist | Rule- and Instance-Based Regression Modeling |

cudaBayesreg | CUDA Parallel Implementation of a Bayesian Multilevel Model for fMRI Data Analysis |

cudaBayesregData | Data sets for the examples used in the package “cudaBayesreg” |

cudia | CUDIA Cross-level Imputation |

CUMP | Analyze Multivariate Phenotypes by Combining Univariate results |

cumplyr | Extends ddply to allow calculation of cumulative quantities |

cumSeg | Change point detection in genomic sequences |

currentSurvival | Estimation of CCI and CLFS Functions |

curvetest | The package will formally test two curves represented by discrete data sets to be statistically equal or not when the errors of the two curves were assumed either equal or not using the tube formula to calculate the tail probabilities |

curvHDR | curvHDR filtering of flow cytometry samples |

cusp | Cusp Catastrophe Model Fitting Using Maximum Likelihood |

cvAUC | Cross-Validated Area Under the ROC Curve Confidence Intervals |

CvM2SL1Test | L1-version of Cramer-von Mises Two Sample Tests |

CvM2SL2Test | Cramer-von Mises Two Sample Tests |

cvplogistic | Penalized Logistic Regression Model using Majorization Minimization by Coordinate Descent (MMCD) Algorithm |

cvq2 | Calculate the predictive squared correlation coefficient |

CVST | Fast Cross-Validation via Sequential Testing |

CVThresh | Level-Dependent Cross-Validation Thresholding |

cvTools | Cross-validation tools for regression models |

cvxclustr | Splitting methods for convex clustering |

cwhmisc | Miscellaneous Functions for math, plotting, printing, statistics, strings, and tools |

cwm | Cluster Weighted Models by EM algorithm |

cxxfunplus | extend cxxfunction by saving the dynamic shared objects |

cyphid | Cycle and Phase Identification for mastication data |

cytoDiv | Cytometric diversity indices |

d3Network | Tools for creating D3 JavaScript network and tree graphs from R |

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 |

dae | Functions useful in the design and ANOVA of experiments |

daewr | Design and Analysis of Experiments with R |

dafs | Data analysis for forensic scientists |

DAGGER | Consensus genetic maps |

dagR | R functions for directed acyclic graphs |

DAKS | Data Analysis and Knowledge Spaces |

DALY | DALY Calculator – A GUI for stochastic DALY calculation in R |

DAMisc | Dave Armstrong’s Miscellaneous Functions |

DandEFA | Dandelion Plot for R-mode Exploratory Factor Analysis |

darts | Statistical Tools to Analyze Your Darts Game |

DatABEL | file-based access to large matrices stored on HDD in binary format |

datacheck | Tools for checking data consistency |

DataCombine | R tools for making it easier to combine and clean data sets |

DataFrameConstr | Constrained data frames and homogenous list classes |

dataframes2xls | dataframes2xls writes data frames to xls files |

datamap | A system for mapping foreign objects to R variables and environments |

datamart | Unified access to your data sources |

datamerge | Merging of overlapping and inconsistent data |

dataone | DataONE R Client |

dataonelibs | DataONE R Client Libraries |

data.table | Extension of data.frame for fast indexing, fast ordered joins, fast assignment, fast grouping and list columns |

datautils | Support functions for packages VBmix, semisupKernelPCA, and patchPlot |

dataview | Human readable data presentation |

date | Functions for handling dates |

DATforDCEMRI | Deconvolution Analysis Tool for Dynamic Contrast Enhanced MRI |

dave | Functions for “Data Analysis in Vegetation Ecology” |

Davies | The Davies quantile function |

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 |

dbEmpLikeNorm | Test for joint assessment of normality |

DBGSA | methods of distance-based gene set functional enrichment analysis |

DBI | R Database Interface |

DBKGrad | Discrete Beta Kernel Graduation of mortality data |

dblcens | Compute the NPMLE of distribution from doubly censored data |

dbmss | Distance-based measures of spatial structures |

dbstats | Distance-based statistics (dbstats) |

dcemriS4 | A Package for Medical Image Analysis (S4 implementation) |

DCGL | Differential Co-expression Analysis and Differential Regulation Analysis of Gene Expression Microarray Data |

dclone | Data Cloning and MCMC Tools for Maximum Likelihood Methods |

DCluster | Functions for the detection of spatial clusters of diseases |

dcmle | Hierarchical Models Made Easy with Data Cloning |

dcv | Conventional Cross-validation statistics for climate-growth model |

ddalpha | DDalpha-Classifier |

DDD | Diversity-dependent diversification |

ddepn | Dynamic Deterministic Effects Propagation Networks: Infer signalling networks for timecourse RPPA data |

ddst | Data driven smooth test |

deal | Learning Bayesian Networks with Mixed Variables |

deamer | Deconvolution density estimation with adaptive methods for a variable prone to measurement error |

debug | MVB’s debugger for R |

decctools | Get energy data from the UK Dept of Energy and Climate Change |

DECIDE | DEComposition of Indirect and Direct Effects |

decon | Deconvolution Estimation in Measurement Error Models |

Deducer | Deducer |

DeducerExtras | Additional dialogs and functions for Deducer |

DeducerPlugInExample | Deducer Plug-in Example |

DeducerPlugInScaling | Reliability and factor analysis plugin |

DeducerSpatial | Deducer for spatial data analysis |

DeducerSurvival | Add Survival Dialogue to Deducer |

DeducerText | Deducer GUI for Text Data |

deducorrect | deducorrect: Deductive correction, deductive imputation, and deterministic correction |

Defaults | Create Global Function Defaults |

degenes | Detection of differentially expressed genes |

degreenet | Models for Skewed Count Distributions Relevant to Networks |

Delaporte | Statistical functions for the Delaporte distribution |

deldir | Delaunay Triangulation and Dirichlet (Voronoi) Tessellation |

deltaPlotR | Identification of dichotomous differential item functioning (DIF) using Angoff’s Delta Plot method |

Demerelate | Functions to calculate relatedness on diploid genetic data |

DEMEtics | Evaluating the genetic differentiation between populations based on Gst and D values |

demi | Differential Expression from Multiple Indicators |

demography | Forecasting mortality, fertility, migration and population data |

dendroextras | Extra functions to cut, label and colour dendrogram clusters |

DendSer | Dendrogram seriation: ordering for visualisation |

denstrip | Density strips and other methods for compactly illustrating distributions |

DEoptim | Global optimization by Differential Evolution |

depend.truncation | Inference for parametric and semiparametric models based on dependent truncation data |

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 |

DescribeDisplay | R interface to DescribeDisplay (GGobi plugin) |

deseasonalize | Optimal deseasonalization for geophysical time series using AR fitting |

designGG | Computational tool for designing genetical genomics experiments |

DesignPatterns | Design Patterns in R to build reusable object-oriented software |

desirability | Desirabiliy Function Optimization and Ranking |

desire | Desirability functions in R |

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) |

detect | Analyzing Wildlife Data with Detection Error |

deTestSet | Testset for differential equations |

detrendeR | Start the detrendeR Graphical User Interface (GUI) |

DetSel | A computer program to detect markers responding to selection |

devEMF | EMF graphics output device |

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)” |

devtools | Tools to make developing R code easier |

df2json | Convert a dataframe to JSON |

dfcrm | Dose-finding by the continual reassessment method |

dfoptim | Derivative-free Optimization |

dglars | Differential Geometric LARS (dgLARS) method |

dglm | Double generalized linear models |

dgmb | dgmb Simulating data for PLS structural models |

dgof | Discrete Goodness-of-Fit Tests |

dhglm | Double Hierarchical Generalized Linear Models |

diagram | Functions for visualising simple graphs (networks), plotting flow diagrams |

DiagTest3Grp | Diagnostic test summary measures for three ordinal groups |

dice | Calculate probabilities of various dice-rolling events |

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 |

dichromat | Color Schemes for Dichromats |

dicionariosIBGE | Dictionaries for reading microdata surveys from IBGE |

dielectric | Defines some physical constants and dielectric functions commonly used in optics, plasmonics |

DierckxSpline | R companion to “Curve and Surface Fitting with Splines” |

diffdepprop | Calculates Confidence Intervals for two Dependent Proportions |

diffEq | Functions from the book Solving Differential Equations in R |

diffractometry | Baseline identification and peak decomposition for x-ray diffractograms |

diffusionMap | Diffusion map |

difR | Collection of methods to detect dichotomous differential item functioning (DIF) in psychometrics |

digest | Create cryptographic hash digests of R objects |

Digiroo2 | An application programming interface for generating null models of social contacts based on individuals’ space use |

DIME | DIME (Differential Identification using Mixture Ensemble) |

dinamic | DiNAMIC A Method To Analyze Recurrent DNA Copy Number Aberrations in Tumors |

diptest | Hartigan’s dip test statistic for unimodality – corrected code |

DIRECT | Bayesian Clustering of Multivariate Data Under the Dirichlet-Process Prior |

directlabels | Direct labels for multicolor plots in lattice or ggplot2 |

DirichletReg | Dirichlet Regression in R |

dirmult | Estimation in Dirichlet-Multinomial distribution |

disclap | Discrete Laplace Exponential Family |

disclapmix | Discrete Laplace mixture inference using the EM algorithm |

DiscreteInverseWeibull | Discrete inverse Weibull distribution |

DiscreteLaplace | Discrete Laplace distribution |

discreteMTP | Multiple testing procedures for discrete test statistics |

discreteRV | Functions to create and manipulate discrete random variables |

DiscreteWeibull | Discrete Weibull distribution |

discretization | Data preprocessing, discretization for classification |

discrimARTs | Discrimination of Alternative Reproductive Tactics (ARTs) |

DiscriMiner | Tools of the Trade for Discriminant Analysis |

diseasemapping | Calculate observed and expected disease incidence counts from a case file and population data |

dismo | Species distribution modeling |

disp2D | 2D Hausdorff and Simplex Dispersion Orderings |

displayHTS | displayHTS |

dispmod | Dispersion models |

Distance | A simple way to fit detection functions to distance sampling data and calculate abundance/density for biological populations |

DistatisR | DiSTATIS Three Way Metric Multidimensional Scaling |

distfree.cr | Distribution-free confidence region (distfree.cr) |

distillery | Method Functions for Confidence Intervals and to Distill Information from an Object |

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 |

DistributionUtils | Distribution Utilities |

distrMod | Object oriented implementation of probability models |

distrRmetrics | Package distr classes for distributions from Rmetrics |

distrSim | Simulation classes based on package distr |

distrTeach | Extensions of package distr for teaching Stochastics/Statistics in secondary school |

distrTEst | Estimation and Testing classes based on package distr |

divagis | Provides tools for quality checks of georeferenced plant species accessions |

diveMove | Dive analysis and calibration |

diversitree | diversitree: comparative phylogenetic analyses of diversification |

diveRsity | Genetic diversity partition statistics and Informative locus selection using Fst, Gst, Dest(Jost Chao) G’st and In |

DiversitySampler | Functions for re-sampling a community matrix to compute diversity indices at different sampling levels |

DivMelt | HRM Diversity Assay Analysis Tool |

dixon | Nearest Neighbour Contingency Table Analysis |

dkDNA | Diffusion kernels on a set of genotypes |

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 |

dma | Dynamic model averaging |

DMR | Delete or Merge Regressors for linear model selection |

dmt | Dependency Modeling Toolkit |

DMwR | Functions and data for “Data Mining with R” |

dna | Differential Network Analysis |

DNAtools | Tools for analysing forensic genetic DNA data |

DnE | DnE(Distribution and Equation) |

DOBAD | Analysis of Discretely Observed linear Birth-And-Death(-and-immigration) Markov Chains |

doBy | doBy – Groupwise summary statistics, general linear contrasts, population means (least-squares-means), and other utilities |

Dodge | Functions for Acceptance Sampling Ideas originated by H.F. Dodge |

DoE.base | Full factorials, orthogonal arrays and base utilities for DoE packages |

DoE.wrapper | Wrapper package for design of experiments functionality |

doMC | Foreach parallel adaptor for the multicore package |

Dominance | ADI (average dominance index) and social network graphs with dual directions |

doMPI | Foreach parallel adaptor for the Rmpi package |

doParallel | Foreach parallel adaptor for the parallel package |

doRedis | Foreach parallel adapter for the rredis package |

doRNG | Generic Reproducible Parallel Backend for foreach Loops |

DoseFinding | Planning and Analyzing Dose Finding experiments |

doSNOW | Foreach parallel adaptor for the snow package |

dostats | Compute statistics helper functions |

downloader | A package for downloading files over http and https |

dpa | Dynamic Path Approach |

dpglasso | Primal Graphical Lasso |

dplR | Dendrochronology Program Library in R |

DPM.GGM | Dirichlet Process Mixtures (DPM) and related models using Gaussian Graphical Models (GGM) for Sparse covariance estimation in heterogeneous samples |

dpmixsim | Dirichlet Process Mixture model simulation for clustering and image segmentation |

DPpackage | Bayesian nonparametric modeling in R |

DPw | Semiparametric Bayesian procedure for selecting a subset containing the weakest species with an acceptably high probability |

dr | Methods for dimension reduction for regression |

drawExpression | Visualising R syntax through graphics |

drc | Analysis of dose-response curves |

drfit | Dose-response data evaluation |

DRI | DR-Integrator |

driftsel | Distinguishing drift and natural selection as causes of phenotypic differentiation |

drm | Regression and association models for repeated categorical data |

ds | Descriptive Statistics |

dsample | Discretization-based Direct Random Sample Generation |

dse | Dynamic Systems Estimation (time series package) |

dse1 | DSE (unbundled transition package) |

dse2 | DSE (unbundled transition package) |

DSL | Distributed Storage and List |

dsm | Density surface modelling of distance sampling data |

DSpat | Spatial modelling for distance sampling data |

DTComPair | Comparison of Binary Diagnostic Tests in a Paired Study Design |

DTDA | Doubly truncated data analysis |

dti | Analysis of diffusion weighted imaging (DWI) data |

DTK | Dunnett-Tukey-Kramer Pairwise Multiple Comparison Test Adjusted for Unequal Variances and Unequal Sample Sizes |

DTMCPack | Suite of functions related to discrete-time discrete-state Markov Chains |

DTR | Estimation and comparison of dynamic treatment regimes |

dtw | Dynamic time warping algorithms |

dummies | Create dummy/indicator variables flexibly and efficiently |

dupiR | Bayesian inference from count data using discrete uniform priors |

dvfBm | Discrete variations of a fractional Brownian motion |

dvn | Access to The Dataverse Network API |

DWD | DWD implementation based on A IPM SOCP solver |

dyn | Time Series Regression |

dynamicGraph | dynamicGraph |

dynamicTreeCut | Methods for detection of clusters in hierarchical clustering dendrograms |

dynaTree | Dynamic trees for learning and design |

DynClust | non-parametric denoising and clustering method of noisy images both indexed by time and space |

dynCorr | Dynamic Correlation Package |

dynlm | Dynamic Linear Regression |

dynpred | Companion package to “Dynamic Prediction in Clinical Survival Analysis” |

dynsurv | Dynamic models for survival data |

e1071 | Misc Functions of the Department of Statistics (e1071), TU Wien |

eaf | Plots of the Empirical Attainment Function |

earlywarnings | Early Warning Signals Toolbox for Detecting Critical Transitions in Timeseries |

earth | Multivariate Adaptive Regression Spline Models |

easi | EASI Demand System Estimation |

EasyABC | EasyABC: performing efficient approximate Bayesian computation sampling schemes |

easyanova | Analysis of variance and other important complementary analyzes |

EasyHTMLReport | Easy to send HTML reports |

easystab | Clustering Perturbation Stability Analysis |

EasyUpliftTree | Easy Uplift Tree Model |

eba | Elimination-by-Aspects (EBA) Models |

ebal | Entropy reweighting to create balanced samples |

EbayesThresh | Empirical Bayes Thresholding and Related Methods |

ebdbNet | Empirical Bayes Estimation of Dynamic Bayesian Networks |

EBMAforecast | Ensemble BMA Forecasting |

EBS | Exact Bayesian Segmentation |

Ecdat | Data sets for econometrics |

ecespa | Functions for spatial point pattern analysis |

eco | R Package for Ecological Inference in 2×2 Tables |

ecodist | Dissimilarity-based functions for ecological analysis |

EcoHydRology | A community modeling foundation for Eco-Hydrology |

ecolMod | “A practical guide to ecological modelling – using R as a simulation platform” |

ecoreg | Ecological regression using aggregate and individual data |

ecosim | Toolbox for Aquatic Ecosystem Modeling |

EcoTroph | EcoTroph modelling support |

ecp | Nonparametric Multiple Change Point Analysis of Multivariate Data |

EDanalysis | A R Package For Gene Enrichment Disequilibrium Analysis |

edcc | Economic Design of Control Charts |

EDISON | Software for network reconstruction and changepoint detection |

editrules | R package for parsing, applying, and manipulating data cleaning rules |

EDR | Estimation of the effective dimension reduction (EDR) space |

edrGraphicalTools | Provides tools for dimension reduction methods |

eeptools | Convenience functions for education data |

effects | Effect Displays for Linear, Generalized Linear, Multinomial-Logit, Proportional-Odds Logit Models and Mixed-Effects Models |

EffectStars | Visualization of Categorical Response Models |

effsize | Functions for computing effect sizes |

egonet | Tool for ego-centric measures in Social Network Analysis |

eha | Event History Analysis |

eHOF | Extended and enhanced Hierarchical Logistic Regression models (so called Huisman-Olff-Fresco models) |

eigendog | EigenDog |

eigeninv | Generates (dense) matrices that have a given set of eigenvalues |

eigenmodel | Semiparametric factor and regression models for symmetric relational data |

eigenprcomp | Computes confidence intervals for principal components |

eiPack | eiPack: Ecological Inference and Higher-Dimension Data Management |

eive | An algorithm for reducing errors-in-variable bias in simple linear regression |

EL | Two-sample Empirical Likelihood |

elasticnet | Elastic-Net for Sparse Estimation and Sparse PCA |

el.convex | empirical likelihood ratio tests for means |

elec | Collection of functions for statistical election audits |

elec.strat | Functions for election audits using stratified random samples |

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 |

ellipse | Functions for drawing ellipses and ellipse-like confidence regions |

elliptic | elliptic functions |

elmNN | Implementation of ELM (Extreme Learning Machine ) algorithm for SLFN ( Single Hidden Layer Feedforward Neural Networks ) |

EMA | Easy Microarray data Analysis |

EMC | Evolutionary Monte Carlo (EMC) algorithm |

EMCC | Evolutionary Monte Carlo (EMC) methods for clustering |

EMCluster | EM Algorithm for Model-Based Clustering of Finite Mixture Gaussian Distribution |

EMD | Empirical Mode Decomposition and Hilbert Spectral Analysis |

emdbook | Ecological models and data (book support) |

emdist | Earth Mover’s Distance |

emg | Exponentially Modified Gaussian (EMG) Distribution |

EMJumpDiffusion | EM-Algorithm for Jump Diffusion processes |

emma | Evolutionary model-based multiresponse approach |

EMMAgeo | End-member modelling algorithm and supporting functions for grain-size analysis |

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) |

EMT | Exact Multinomial Test: Goodness-of-Fit Test for Discrete Multivariate data |

emulator | Bayesian emulation of computer programs |

ENA | Ensemble Network Aggregation |

enaR | Tools for ecological network analysis (ena) in R |

endogMNP | R Package for Fitting Multinomial Probit Models with Endogenous Selection |

endorse | R Package for Analyzing Endorsement Experiments |

energy | E-statistics (energy statistics) |

english | Translate integers into English |

EngrExpt | Data sets from “Introductory Statistics for Engineering Experimentation” |

ENmisc | Neuwirth miscellaneous |

EnQuireR | A package dedicated to questionnaires |

enRich | An R package for analysis of multiple ChIP-seq data |

enrichvs | Enrichment assessment of virtual screening approaches |

ensembleBMA | Probabilistic Forecasting using Ensembles and Bayesian Model Averaging |

ensembleMOS | Ensemble Model Output Statistics |

entropy | Estimation of Entropy, Mutual Information and Related Quantities |

enviPat | Isotope pattern, profile and centroid calculation |

EnvNicheR | Environmental niche |

epade | Easy Plots |

Epi | A package for statistical analysis in epidemiology |

epibase | basic tools for the analysis of disease outbreaks |

epibasix | Elementary Epidemiological Functions for Epidemiology and Biostatistics |

epicalc | Epidemiological calculator |

EpiContactTrace | Epidemiological tool for contact tracing |

EpiEstim | EpiEstim: a package to estimate time varying reproduction numbers from epidemic curves |

EpiModel | Mathematical Modeling of Infectious Disease |

epiR | An R package for the analysis of epidemiological data |

epitools | Epidemiology Tools |

epoc | EPoC (Endogenous Perturbation analysis of Cancer) |

epr | Easy polynomial regression |

EQL | Extended-Quasi-Likelihood-Function (EQL) |

eqs2lavaan | EQS Output Conversion to lavaan Functions |

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 |

equateIRT | Direct, chain and average equating coefficients with standard errors using IRT methods |

EquiNorm | Normalize expression data using equivalently expressed genes |

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.count | Fit, Simulate and Diagnose Exponential-Family Models for Networks with Count Edges |

ergmharris | Local Health Department network data set |

ergm.userterms | User-specified terms for the statnet suite of packages |

eRm | Extended Rasch Modeling |

ESG | ESG – A package for asset projection |

esotericR | esotericR articles from lemnica.com |

ESPRESSO | Power Analysis and Sample Size Calculation |

EstCRM | Calibrating Parameters for the Samejima’s Continuous IRT Model |

estout | Estimates Output |

EstSimPDMP | Estimation of the jump rate and simulation for piecewise-deterministic Markov processes |

etable | Easy Table |

ETAS | Modeling earthquake data using Epidemic Type Aftershock Sequence model |

ETC | Equivalence to control |

ETLUtils | Utility functions to execute standard ETL operations (using package ff) on large data |

etm | Empirical Transition Matrix |

EvalEst | Dynamic Systems Estimation – extensions |

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 |

eVenn | eVenn: A powerful tool to compare lists and draw Venn diagrams |

events | Store and manipulate event data |

eventstudies | Event study and extreme event analysis |

EVER | Estimation of Variance by Efficient Replication |

evir | Extreme Values in R |

evmix | Extreme Value Mixture Modelling and Threshold Estimation |

evora | Epigenetic Variable Outliers for Risk prediction Analysis |

evtree | Evolutionary Learning of Globally Optimal Trees |

Exact | Unconditional Exact Test |

exact2x2 | Exact Conditional Tests and Confidence Intervals for 2×2 tables |

exactci | Exact P-values and Matching Confidence Intervals for simple Discrete Parametric Cases |

ExactCIdiff | Inductive Confidence Intervals for the difference between two proportions |

exactLoglinTest | Monte Carlo Exact Tests for Log-linear models |

ExactNumCI | Exact Confidence Interval for binomial proportions |

ExactPath | Exact solution paths for regularized LASSO regressions with L_1 penalty |

exactRankTests | Exact Distributions for Rank and Permutation Tests |

ExactSampling | ExactSampling: risk evaluation using exact resampling methods for the k Nearest Neighbor algorithm |

exams | Automatic Generation of Exams in R |

ExceedanceTools | Confidence Regions for Exceedance Regions and Contour Lines |

excel.link | Convenient way to work with data in Microsoft Excel |

ExomeDepth | Calls CNV from exome sequence data |

ExpDes | Experimental Designs package |

ExpDes.pt | Pacote Experimental Designs (Portuguese) |

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 |

expoRkit | Expokit in R |

ExPosition | Exploratory analysis with the singular value decomposition |

expoTree | Calculate density dependent likelihood of a phylogenetic tree |

expsmooth | Data sets from “Forecasting with exponential smoothing” |

exptest | Tests for Exponentiality |

exsic | Convenience functions for botanist to create exsiccatae indices |

extraBinomial | Extra-binomial approach for pooled sequencing data |

extracat | Categorical Data Analysis and Visualization |

extrafont | Tools for using fonts |

extrafontdb | Package for holding the database for the extrafont package |

extraTrees | ExtraTrees method |

extRemes | Extreme value toolkit |

extremevalues | Univariate outlier detection |

eyetracking | Eyetracking Helper Functions |

ez | Easy analysis and visualization of factorial experiments |

ezglm | selects significant non-additive interaction between two variables using fast GLM implementation |

ezsim | provide an easy to use framework to conduct simulation |

FacPad | Bayesian Sparse Factor Analysis model for the inference of pathways responsive to drug treatment |

factas | Data Mining Methods |

FactMixtAnalysis | Factor Mixture Analysis with covariates |

FactoClass | Combination of Factorial Methods and Cluster Analysis |

FactoMineR | Multivariate Exploratory Data Analysis and Data Mining with R |

factorQR | Bayesian quantile regression factor models |

factualR | thin wrapper for the Factual.com server API |

FAdist | Distributions that are sometimes used in hydrology |

Fahrmeir | Data from the book “Multivariate Statistical Modelling Based on Generalized Linear Models”, first edition, by Ludwig Fahrmeir and Gerhard Tutz |

fail | File Abstraction Interface Layer (FAIL) mimicking a key-value store |

FAiR | Factor Analysis in R |

faisalconjoint | Faisal Conjoint Model: A New Approach to Conjoint Analysis |

fame | Interface for FAME time series database |

Familias | Probabilities for Pedigrees given DNA data |

FAMT | Factor Analysis for Multiple Testing (FAMT) : simultaneous tests under dependence in high-dimensional data |

fanc | Penalized likelihood factor analysis via nonconvex penalty |

fANCOVA | Nonparametric Analysis of Covariance |

fanovaGraph | Building Kriging models from FANOVA graphs |

fanplot | Visualisation of sequential probability distributions using fan charts |

FAOSTAT | A complementary package to the FAOSTAT database and the Statistical Yearbook of the Food and Agricultural Organization of the United Nations |

faoutlier | Influential case detection methods for factor analysis and SEM |

far | Modelization for Functional AutoRegressive processes |

faraway | Functions and datasets for books by Julian Faraway |

fArma | ARMA Time Series Modelling |

farsi | Translate integers into persian |

fAsianOptions | EBM and Asian Option Valuation |

fAssets | Rmetrics – Assets Selection and Modelling |

fast | Implementation of the Fourier Amplitude Sensitivity Test (FAST) |

fastclime | A fast solver for parameterized lp problems and constrained l1 minimization approach to sparse precision matrix estimation |

fastcluster | Fast hierarchical clustering routines for R and Python |

fastcox | Lasso and elastic-net penalized Cox’s regression in high dimensions models using the cocktail algorithm |

fastGHQuad | Fast Rcpp implementation of Gauss-Hermite quadrature |

fastICA | FastICA Algorithms to perform ICA and Projection Pursuit |

FastImputation | Learn from training data then quickly fill in missing data |

fastmatch | Fast match() function |

FastPCS | R package to compute the FastPCS outlyingness index |

fastR | Data sets and utilities for Foundations and Applications of Statistics by R Pruim |

FastRCS | R package to compute the FastRCS Algorithm |

FastRWeb | Fast Interactive Framework for Web Scripting Using R |

fastSOM | Fast Calculation of Spillover Measures |

FAwR | Functions and Datasets for “Forest Analytics with R” |

fBasics | Rmetrics – Markets and Basic Statistics |

fbati | Gene by Environment Interaction and Conditional Gene Tests for Nuclear Families |

FBFsearch | Algorithm for searching the space of Gaussian directed acyclic graphical models through moment fractional Bayes factors |

FBN | FISH Based Normalization and Copy Number inference of SNP microarray data |

fBonds | Bonds and Interest Rate Models |

fbRanks | Association Football (Soccer) Ranking via Poisson Regression |

fCertificates | fCertificates – Basics of Certificates and Structured Products Valuation |

fclust | Fuzzy clustering |

fCopulae | Rmetrics – Dependence Structures with Copulas |

fcros | FCROS for detecting differentially expressed genes |

FD | Measuring functional diversity (FD) from multiple traits, and other tools for functional ecology |

fda | Functional Data Analysis |

fdakma | Clustering and alignment of a functional dataset |

fdaMixed | Functional data analysis in a mixed model framework |

fdasrvf | Elastic Functional Data Analysis |

fdatest | Interval Testing Procedure for functional data |

fda.usc | Functional Data Analysis and Utilities for Statistical Computing (fda.usc) |

fdrci | Permutation-based FDR Point and Confidence Interval Estimation |

fdrtool | Estimation of (Local) False Discovery Rates and Higher Criticism |

fds | Functional data sets |

FeaLect | Scores features for Feature seLection |

feature | Feature significance for multivariate kernel density estimation |

features | Feature Extraction for Discretely-Sampled Functional Data |

fechner | Fechnerian Scaling of Discrete Object Sets |

fExoticOptions | Exotic Option Valuation |

fExtremes | Rmetrics – Extreme Financial Market Data |

ff | memory-efficient storage of large data on disk and fast access functions |

ffbase | Basic statistical functions for package ff |

FFD | Freedom From Disease |

FField | Force field simulation for a set of points |

ffmanova | Fifty-fifty MANOVA |

fftw | Fast FFT and DCT based on FFTW |

fftwtools | Wrapper for fftw3: includes 1-D, univariate and multivariate, and 2-D transform |

fgac | Generalized Archimedean Copula |

FGalgorithm | Flury and Gautschi algorithms |

fGarch | Rmetrics – Autoregressive Conditional Heteroskedastic Modelling |

FGN | Fractional Gaussian Noise and hyperbolic decay time series model fitting |

fgof | Fast Goodness-of-fit Test |

fgui | Function GUI |

FHtest | Tests for right and interval-censored survival data based on the Fleming-Harrington class |

FI | Provide functions for forest inventory calculations |

fields | Tools for spatial data |

FieldSim | Random fields simulations |

filehash | Simple key-value database |

filehashSQLite | Simple key-value database using SQLite |

fImport | Rmetrics – Economic and Financial Data Import |

FinancialInstrument | Financial Instrument Model Infrastructure for R |

FinAsym | Classifies implicit trading activity from market quotes and computes the probability of informed trading |

FinCal | Time Value of Money Calculation and Computational Finance |

FindAllRoots | Find all root(s) of the equation and Find root(s) of the equation by dichotomy |

FindIt | R Package for Finding Heterogeneous Treatment Effects |

fingerprint | Functions to operate on binary fingerprint data |

FinTS | Companion to Tsay (2005) Analysis of Financial Time Series |

FisherEM | The Fisher-EM algorithm |

fisheyeR | Fisheye and Hyperbolic-space-alike Interactive Visualization Tools in R |

fishmethods | Fishery Science Methods and Models in R |

fishmove | Prediction of Fish Movement Parameters |

fit4NM | NONMEM platform |

FitAR | Subset AR Model Fitting |

FitARMA | FitARMA: Fit ARMA or ARIMA using fast MLE algorithm |

fitdistrplus | Help to fit of a parametric distribution to non-censored or censored data |

fit.models | fit.models |

FITSio | FITS (Flexible Image Transport System) utilities |

fitTetra | fitTetra is an R package for assigning tetraploid genotype scores |

FKF | Fast Kalman Filter |

flare | Family of Lasso Regression |

flashClust | Implementation of optimal hierarchical clustering |

flexclust | Flexible Cluster Algorithms |

flexCWM | Flexible Cluster-Weighted Modeling |

flexmix | Flexible Mixture Modeling |

FlexParamCurve | Tools to Fit Flexible Parametric Curves |

flexsurv | Flexible parametric survival models |

flip | Multivariate Permutation Tests |

FLLat | Fused Lasso Latent Feature Model |

flora | flora: taxonomical information on flowering species that occur in Brazil |

flsa | Path algorithm for the general Fused Lasso Signal Approximator |

flubase | Baseline of mortality free of influenza epidemics |

FluOMatic | Estimation of background-subtracted fluorescence data |

Flury | Data Sets from Flury, 1997 |

flux | Flux rate calculation from dynamic closed chamber measurements |

fma | Data sets from “Forecasting: methods and applications” by Makridakis, Wheelwright & Hyndman (1998) |

FME | A Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability, Monte Carlo Analysis |

fmri | Analysis of fMRI experiments |

fmsb | Functions for medical statistics book with some demographic data |

FMStable | Finite Moment Stable Distributions |

fmt | Variance estimation of FMT method (Fully Moderated t-statistic) |

fMultivar | Multivariate Market Analysis |

FNN | Fast Nearest Neighbor Search Algorithms and Applications |

fNonlinear | Nonlinear and Chaotic Time Series Modelling |

foba | greedy variable selection |

fontcm | Computer Modern font for use with extrafont package |

foodweb | visualisation and analysis of food web networks |

fOptions | Basics of Option Valuation |

forams | Foraminifera and Community Ecology Analyses |

foreach | Foreach looping construct for R |

ForeCA | ForeCA – Forecastable Component Analysis |

forecast | Forecasting functions for time series and linear models |

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 |

ForImp | Imputation of missing values through a forward imputation algorithm |

fork | R functions for handling multiple processes |

FormalSeries | Elementary arithemtic in formal series rings |

formatR | Format R Code Automatically |

Formula | Extended Model Formulas |

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 |

FourScores | FourScores – A game for two players |

fpc | Flexible procedures for clustering |

fpca | Restricted MLE for Functional Principal Components Analysis |

fPortfolio | Rmetrics – Portfolio Selection and Optimization – ebook available at http://www.rmetrics.org |

fpow | Computing the noncentrality parameter of the noncentral F distribution |

fpp | Data for “Forecasting: principles and practice” |

fptdApprox | Approximation of first-passage-time densities for diffusion processes |

fracdiff | Fractionally differenced ARIMA aka ARFIMA(p,d,q) models |

fracprolif | Fraction Proliferation via a quiescent growth model |

fractaldim | Estimation of fractal dimensions |

fractalrock | Generate fractal time series with non-normal returns distribution |

FRACTION | Numeric number into fraction |

frailtyHL | Frailty Models via H-likelihood |

frailtypack | General Frailty models: shared, joint and nested frailty models with prediction |

FRAPO | Financial Risk Modelling and Portfolio Optimisation with R |

FRB | Fast and Robust Bootstrap |

FRBData | Download interest rate data from FRB’s website |

frbs | Fuzzy Rule-based Systems for Classification and Regression Tasks |

FRCC | Fast Regularized Canonical Correlation Analysis |

freeknotsplines | Free-Knot Splines |

fRegression | Regression Based Decision and Prediction |

freqMAP | Frequency Moving Average Plots (MAP) of Multinomial Data by a Continuous Covariate |

FrF2 | Fractional Factorial designs with 2-level factors |

FrF2.catlg128 | Catalogues of resolution IV 128 run 2-level fractional factorials up to 33 factors that do have 5-letter words |

frmqa | The Generalized Hyperbolic Distribution, Related Distributions and Their Applications in Finance |

frontier | Stochastic Frontier Analysis |

frontiles | Partial frontier efficiency analysis |

frt | Full Randomization Test |

fscaret | Automated caret feature selection |

FSelector | Selecting attributes |

fso | Fuzzy Set Ordination |

FTICRMS | Programs for Analyzing Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry Data |

ftnonpar | Features and Strings for Nonparametric Regression |

fTrading | Technical Trading Analysis |

fts | R interface to tslib (a time series library in c++) |

ftsa | Functional time series analysis |

fugeR | FUzzy GEnetic, a machine learning algorithm to construct prediction model based on fuzzy logic |

fume | FUME package |

fun | Use R for Fun |

FunCluster | Functional Profiling of Microarray Expression Data |

FuncMap | Hive Plots of R Package Function Calls |

functional | Curry, Compose, and other higher-order functions |

fUnitRoots | Trends and Unit Roots |

FunNet | Integrative Functional Analysis of Transcriptional Networks |

futile.any | Futile library to provide some polymorphic operations |

futile.logger | A logging library for R |

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 |

FuzzyNumbers | Tools to deal with fuzzy numbers |

fuzzyRankTests | Fuzzy Rank Tests and Confidence Intervals |

FuzzyStatProb | Fuzzy stationary probabilities from a sequence of observations of an unknown Markov chain |

FuzzyToolkitUoN | Type 1 Fuzzy Logic Toolkit |

fwdmsa | Forward search for Mokken scale analysis |

FWDselect | Selecting variables in regression models |

fwi.fbp | Fire Weather Index System and Fire Behaviour Prediction System Calculations |

fwsim | Fisher-Wright Population Simulation |

fxregime | Exchange Rate Regime Analysis |

G1DBN | A package performing Dynamic Bayesian Network inference |

G2Sd | Grain-size Statistics and Description of Sediment |

GA | Genetic Algorithms |

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 |

gains | Gains Table Package |

GAIPE | Graphical Extension with Accuracy in Parameter Estimation (GAIPE) |

galts | Genetic algorithms and C-steps based LTS (Least Trimmed Squares) estimation |

gam | Generalized Additive Models |

gamair | Data for “GAMs: An Introduction with R” |

GAMBoost | Generalized linear and additive models by likelihood based boosting |

gamboostLSS | Boosting Methods for GAMLSS Models |

gamclass | Functions and data for a course on modern regression and classification |

games | Statistical Estimation of Game-Theoretic Models |

gamesNws | Playing games using a NWS Server |

gamlr | Gamma Lasso Regression |

gamlss | Generalised 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 |

gammSlice | Generalized additive mixed model analysis via slice sampling |

GANPA | Gene Association Network-based Pathway Analysis |

GANPAdata | The GANPA Datasets Package |

gaoptim | Genetic Algorithm optimization for real-based and permutation-based problems |

gap | Genetic analysis package |

gaussDiff | Difference measures for multivariate Gaussian probability density functions |

gaussquad | Collection of functions for Gaussian quadrature |

gazetools | Gaze Tools |

gb | Generalize Lambda Distribution and Generalized Bootstrapping |

GB2 | Generalized Beta Distribution of the Second Kind: properties, likelihood, estimation |

gbm | Generalized Boosted Regression Models |

gbRd | Utilities for processing Rd objects and files |

gbs | Package for Generalized Birnbaum-Saunders Distributions |

gcbd | GPU/CPU Benchmarking in Debian-based systems |

gcdnet | A generalized coordinate descent (GCD) algorithm for computing the solution path of the hybrid Huberized support vector machine (HHSVM) and its generalization |

gcExplorer | Graphical Cluster Explorer |

gclus | Clustering Graphics |

gcmr | Gaussian Copula Marginal Regression |

gcookbook | Data for “R Graphics Cookbook” |

gdata | Various R programming tools for data manipulation |

g.data | Delayed-Data Packages |

gdimap | Generalized Diffusion Magnetic Resonance Imaging |

gdistance | distances and routes on geographical grids |

gdsfmt | CoreArray Genomic Data Structure (GDS) R Interface |

gearman | R interface to the Gearman Job Server |

gee | Generalized Estimation Equation solver |

geeM | Fit Generalized Estimating Equations |

geepack | Generalized Estimating Equation Package |

geigen | Calculate generalized eigenvalues of a matrix pair |

geiger | Analysis of evolutionary diversification |

gems | Generalized multistate simulation model |

gemtc | GeMTC network meta-analysis |

gemtc.jar | GeMTC Java binary |

GenABEL | genome-wide SNP association analysis |

genalg | R Based Genetic Algorithm |

GENEAread | Package For Reading Binary files |

GeneCycle | Identification of Periodically Expressed Genes |

GeneF | Package for Generalized F-statistics |

Geneland | Detection of structure from multilocus genetic data |

geneListPie | Profiling a gene list into GOslim or KEGG function pie |

GeneNet | Modeling and Inferring Gene Networks |

genepi | Genetic Epidemiology Design and Inference |

GeneralizedHyperbolic | The Generalized Hyperbolic Distribution |

GeneReg | Construct time delay gene regulatory network |

geneSignatureFinder | A Gene-signatures finder tools |

genetics | Population Genetics |

GeneticTools | Collection of Genetic Data Analysis Tools |

GenKern | Functions for generating and manipulating binned kernel density estimates |

genlasso | Path algorithm for generalized lasso problems |

genMOSS | An implementation of the MOSS algorithm for the analysis of GWAS data |

genomicper | Circular Genomic Permutation using GWAS p-values of association |

genoPlotR | Plot publication-grade gene and genome maps |

GenOrd | Simulation of ordinal and discrete variables with given correlation matrix and marginal distributions |

genridge | Generalized ridge trace plots for ridge regression |

GenSA | R functions for Generalized Simulated Annealing |

gensemble | generalized ensemble methods |

genSurv | Generating multi-state survival data |

GeoLight | Analysis of light based geolocator data |

GEOmap | Topographic and Geologic Mapping |

geomapdata | Data for topographic and Geologic Mapping |

geometry | Mesh generation and surface tesselation |

geomorph | Geometric morphometric analysis of 2d/3d landmark data |

geonames | Interface to http://www.geonames.org web service |

geophys | Geophysics, Continuum Mechanics, Mogi Model |

geoPlot | Geocodes street or ip addresses and plots them on a map |

geoR | Analysis of geostatistical data |

geoRglm | geoRglm – a package for generalised linear spatial models |

georob | Robust Geostatistical Analysis of Spatial Data |

geoscale | Geological timescale plot |

geospacom | Helper package to facilitate the generation of distance matrices used in the package spacom |

geosphere | Spherical Trigonometry |

geospt | Spatial geostatistics; some geostatistical and radial basis functions, prediction and cross validation; design of optimal spatial sampling networks based on geostatistical modelling |

geostatsp | Geostatistics using SpatialPoints and rasters |

geotools | Geo tools |

geotopbricks | geotopbricks: Analyzes raster maps as input/output files from the Hydrological Distributed Model GEOtop |

GeoXp | Interactive exploratory spatial data analysis |

geozoo | Zoo of Geometric Objects |

GESTr | Gene Expression State Transformation |

getopt | C-like getopt behavior |

GetR | GetR: Calculate Guttman error trees in R |

GEVcdn | GEV conditional density estimation network |

GExMap | A visual, intuitive, easy to use software giving access to a new type of information buried into your microarray data |

GGally | Extension to ggplot2 |

ggdendro | Tools for extracting dendrogram and tree diagram plot data for use with ggplot |

GGEBiplotGUI | GGEBiplotGUI: Interactive GGE Biplots in R |

GGIR | GGIR |

gglasso | Group Lasso Penalized Learning Using A Unified BMD Algorithm |

ggm | A package for Graphical Markov Models |

ggmap | A package for spatial visualization with Google Maps and OpenStreetMap |

ggmcmc | Graphical tools for analyzing Markov Chain Monte Carlo simulations from Bayesian inference |

GGMselect | Gaussian Graphs Models selection |

ggparallel | Variations of Parallel Coordinate Plots for Categorical Data |

ggplot2 | An implementation of the Grammar of Graphics |

ggROC | package for roc curve plot with ggplot2 |

ggsubplot | Explore complex data by embedding subplots within plots |

ggthemes | Extra themes, scales and geoms for ggplot |

GhcnDaily | Downloads and processes GHCN daily |

ghyp | A package on the generalized hyperbolic distribution and its special cases |

GibbsACOV | Gibbs Sampler for One-Way Mixed-Effects ANOVA and ANCOVA Models |

gibbs.met | Naive Gibbs Sampling with Metropolis Steps |

GIGrvg | Random variate generator for the GIG distribution |

GillespieSSA | Gillespie’s Stochastic Simulation Algorithm (SSA) |

gIPFrm | Generalized Iterative Proportional Fitting for Relational Models |

giRaph | The giRaph package for graph representation in R |

GISTools | Some further GIS capabilities for R |

gitter | Robust gridding and quantifying of pinned genetic screens |

Giza | Constructing panels of population pyramid plots based on lattice |

glasso | Graphical lasso- estimation of Gaussian graphical models |

glassomix | High dimensional Mixture Graph Models selection |

gld | Estimation and use of the generalised (Tukey) lambda distribution |

GLDEX | Fitting Single and Mixture of Generalised Lambda Distributions (RS and FMKL) using Various Methods |

gldist | An Asymmetry-Steepness Parameterization of the Generalized Lambda Distribution |

glm2 | Fitting Generalized Linear Models |

glmc | Fitting Generalized Linear Models Subject to Constraints |

glmdm | R Code for Simulation of GLMDM |

glmlep | Fit GLM with LEP-based penalized maximum likelihood |

glmmAK | Generalized Linear Mixed Models |

glmmBUGS | Generalised Linear Mixed Models and Spatial Models with WinBUGS, BRugs, or OpenBUGS |

glmmGS | Gauss-Seidel Generalized Linear Mixed Model solver |

glmmLasso | Variable selection for generalized linear mixed models by L1-penalized estimation |

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 | Model selection and multimodel inference made easy |

globalboosttest | Testing the additional predictive value of high-dimensional data |

glogis | Fitting and Testing Generalized Logistic Distributions |

glpkAPI | R Interface to C API of GLPK |

glrt | Generalized Logrank Tests for Interval-censored Failure Time Data |

gMCP | Graph Based Multiple Comparison Procedures |

GMD | Generalized Minimum Distance of distributions |

gmm | Generalized Method of Moments and Generalized Empirical Likelihood |

GMMBoost | Likelihood-based Boosting for Generalized mixed models |

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 |

gMWT | Generalized Mann-Whitney Type Tests |

gnm | Generalized Nonlinear Models |

gnmf | Generalized Non-negative Matrix Factorization |

gnumeric | Read data from files readable by gnumeric |

goalprog | Weighted and lexicographical goal programming and optimization |

gof | Model-diagnostics based on cumulative residuals |

GoFKernel | GoFKernel: Testing Goodness-of-fit with the Kernel Density Estimator |

GOFSN | Goodness-of-fit tests for the family of skew-normal models |

GOGANPA | GO-Functional-Network-based Gene-Set-Analysis |

gogarch | Generalized Orthogonal GARCH (GO-GARCH) models |

googlePublicData | An R library to build Google’s Public Data Explorer DSPL Metadata files |

googleVis | Interface between R and the Google Chart Tools |

gooJSON | Google JSON Data Interpreter for R |

goric | Generalized Order-Restricted Information Criterion |

GOSim | Computation of functional similarities between GO terms and gene products; GO enrichment analysis |

GOsummaries | Word cloud summaries of GO enrichment analysis |

govdat | Interface to API methods for government data |

govStatJPN | functions to get public survey data in Japan |

gpairs | gpairs: The Generalized Pairs Plot |

GPArotation | GPA Factor Rotation |

gPCA | Batch Effect Detection via Guided Principal Components Analysis |

gpclib | General Polygon Clipping Library for R |

gPdtest | Bootstrap goodness-of-fit test for the generalized Pareto distribution |

GPfit | Gaussian Process Modeling |

gpk | 100 Data Sets for Statistics Education |

gplm | Generalized partial linear models (GPLM) |

gplots | Various R programming tools for plotting data |

gppois | Gaussian Processes for Poisson-noised Data |

gProfileR | g:ProfileR |

GPseq | gpseq: Using the generalized Poisson distribution to model sequence read counts from high throughput sequencing experiments |

gptk | Gaussian Processes Tool-Kit |

gputools | A few GPU enabled functions |

GPvam | Maximum Likelihood Estimation of the Multiple Membership Mixed Models Used in Value-Added Modeling |

grade | Provides functions for matching student-answers to teacher answers for a variety of data types |

GRaF | Species distribution modelling using latent Gaussian random fields |

gRain | Graphical Independence Networks |

granova | Graphical Analysis of Variance |

granovaGG | Graphical Analysis of Variance Using ggplot2 |

gRapHD | Efficient selection of undirected graphical models for high-dimensional datasets |

GrapheR | A multi-platform GUI for drawing customizable graphs in R |

graphicsQC | Quality Control for Graphics in R |

GrassmannOptim | Grassmann Manifold Optimization |

gRbase | A package for graphical modelling in R |

gRc | Inference in Graphical Gaussian Models with Edge and Vertex Symmetries |

gregmisc | Greg’s Miscellaneous Functions |

Grid2Polygons | Convert Spatial Grids to Polygons |

gridBase | Integration of base and grid graphics |

gridDebug | Debugging Grid Graphics |

gridExtra | functions in Grid graphics |

gridGraphviz | Drawing Graphs with Grid |

GridR | Executes functions on remote hosts, clusters or grids |

gridSVG | Export grid graphics as SVG |

GriegSmith | Uses Grieg-Smith method on 2 dimentional spatial data |

gRim | Graphical Interaction Models |

grImport | Importing Vector Graphics |

grnn | General regression neural network |

grofit | The package was developed to fit fit many growth curves obtained under different conditions |

grouped | Regression Analysis of Grouped and Coarse Data |

GroupSeq | Performing computations related to group sequential designs |

growcurves | Bayesian semi and nonparametric growth curve models that additionally include multiple membership random effects |

growthrate | Bayesian reconstruction of growth velocity |

grplasso | Fitting user specified models with Group Lasso penalty |

grpreg | Regularization paths for regression models with grouped covariates |

GRRGI | Gauge R and R Confidence Intervals |

grt | General Recognition Theory |

GRTo | Tools for the analysis of Gutenberg-Richter distributions of earthquake magnitudes |

GSA | Gene set analysis |

gsalib | Utility functions for GATK |

gsarima | Two functions for Generalized SARIMA time series simulation |

gsbDesign | Group Sequential Bayes Design |

gsDesign | Group Sequential Design |

GSE | Robust Estimation of Multivariate Location and Scatter in the Presence of Missing Data |

gsg | Calculation of selection coefficients |

GSIF | Global Soil Information Facilities |

gsl | wrapper for the Gnu Scientific Library |

GSM | Gamma Shape Mixture |

gsmaRt | Gene Set Microarray Testing |

gsmoothr | Smoothing tools |

gss | General Smoothing Splines |

gstat | spatial and spatio-temporal geostatistical modelling, prediction and simulation |

gstudio | Spatial utility functions from the Dyer laboratory |

gsubfn | Utilities for strings and function arguments |

gtable | Arrange grobs in tables |

gtcorr | Calculate efficiencies of group testing algorithms with correlated responses |

gte | Generalized Turnbull’s estimator |

gtools | Various R programming tools |

gtx | Genetics ToolboX |

GuardianR | Guardian API Wrapper |

Guerry | Maps, data and methods related to Guerry (1833) “Moral Statistics of France” |

GUIDE | GUI for DErivatives in R |

gumbel | Gumbel copula |

GUniFrac | Generalized UniFrac distances |

GUTS | GUTS: Fast Calculation of the Likelihood of a Stochastic Survival Model |

gvcm.cat | Regularized Categorial Effects/Categorial Effect Modifiers/Continuous/Smooth effects in GLMs |

gvlma | Global Validation of Linear Models Assumptions |

GWAF | Genome-wide association/interaction analysis and rare variant analysis with family data |

GWASExactHW | Exact Hardy-Weinburg testing for Genome Wide Association Studies |

GWAtoolbox | GWAS Quality Control |

gwerAM | Controlling the genome-wide type I error rate in association mapping experiments |

GWG | Calculation of probabilities for inadequate and excessive gestational weight gain |

gWidgets | gWidgets API for building toolkit-independent, interactive GUIs |

gWidgetsRGtk2 | Toolkit implementation of gWidgets for RGtk2 |

gWidgetstcltk | Toolkit implementation of gWidgets for tcltk package |

gWidgetsWWW | Toolkit implementation of the gWidgets API for use with web pages |

GWmodel | Geographically weighted models |

GWRM | GWRM |

gwrr | Fits geographically weighted regression models with diagnostic tools |

h5r | Interface to HDF5 Files |

haarfisz | Software to perform Haar Fisz transforms |

HAC | Estimation, simulation and visualization of Hierarchical Archimedean Copulae (HAC) |

HadoopStreaming | Utilities for using R scripts in Hadoop streaming |

HandTill2001 | Multiple Class Area under ROC Curve |

hapassoc | Inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm |

HapEstXXR | Multi-locus stepwise regression (MSR) |

HAPim | HapIM |

Haplin | Analyzing case-parent triad and/or case-control data with SNP haplotypes |

haplo.ccs | Estimate Haplotype Relative Risks in Case-Control Data |

HaploSim | HaploSim |

haplo.stats | Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous |

HAP.ROR | Recursive Organizer (ROR) |

hapsim | Haplotype Data Simulation |

HardyWeinberg | Graphical tests for Hardy-Weinberg equilibrium |

harvestr | A Parallel Simulation Framework |

hash | Full feature implementation of hash/associated arrays/dictionaries |

hashFunction | A collection of non-cryptographic hash functions |

hbim | Hill/Bliss Independence Model for Combination Vaccines |

hbmem | Hierarchical Bayesian Analysis of Recognition Memory |

hbsae | Hierarchical Bayesian Small Area Estimation |

hcc | Hidden correlation check |

hda | Heteroscedastic Discriminant Analysis |

HDclassif | High Dimensional Supervised Classification and Clustering |

hddplot | Use known groups in high-dimensional data to derive scores for plots |

hdeco | Hierarchical DECOmposition of Entropy for Categorical Map Comparisons |

hdlm | Fitting High Dimensional Linear Models |

HDMD | Statistical Analysis Tools for High Dimension Molecular Data (HDMD) |

hdrcde | Highest density regions and conditional density estimation |

HEAT | Health Effects of Air Pollution and Temperature (HEAT) |

heatex | Heat exchange calculations during physical activity |

heatmapFit | Heatmap Fit Statistic For Binary Dependent Variable Models |

heatmap.plus | Heatmap with more sensible behavior |

heavy | Package for outliers accommodation using heavy-tailed distributions |

helloJavaWorld | Hello Java World |

heplots | Visualizing Hypothesis Tests in Multivariate Linear Models |

hergm | Hierarchical Exponential-Family Random Graph Models with Local Dependence |

hett | Heteroscedastic t-regression |

het.test | White’s Test for Heteroskedasticity |

hexbin | Hexagonal Binning Routines |

hexView | Viewing Binary Files |

hgam | High-dimensional Additive Modelling |

hglm | Hierarchical Generalized Linear Models |

HGLMMM | Hierarchical Generalized Linear Models |

HGNChelper | Handy functions for working with HGNC gene symbols and Affymetrix probeset identifiers |

HH | Statistical Analysis and Data Display: Heiberger and Holland |

HHG | Heller-Heller-Gorfine Tests of Independence |

hht | The Hilbert-Huang Transform: Tools and Methods |

HI | Simulation from distributions supported by nested hyperplanes |

HIBAG | HIBAG – HLA Genotype Imputation with Attribute Bagging |

HiddenMarkov | Hidden Markov Models |

HiDimDA | High Dimensional Discriminant Analysis |

hierarchicalDS | Functions for performing hierarchical analysis of distance sampling data |

hierfstat | Estimation and tests of hierarchical F-statistics |

hierNet | A Lasso for Hierarchical Interactions |

hier.part | Hierarchical Partitioning |

HIest | Hybrid index estimation |

highfrequency | highfrequency |

highlight | Syntax highlighter |

highr | Syntax highlighting for R |

highriskzone | Determining and evaluating high-risk zones |

hint | Tools for hypothesis testing based on Hypergeometric Intersection distributions |

hints | Provide hints on what to do next |

HiPLARM | High Performance Linear Algebra in R |

hiPOD | hierarchical Pooled Optimal Design |

hisemi | Hierarchical Semiparametric Regression of Test Statistics |

HistData | Data sets from the history of statistics and data visualization |

histogram | Construction of regular and irregular histograms with different options for automatic choice of bins |

hitandrun | “Hit and Run” method for sampling uniformly from convex shapes |

hive | Hadoop InteractiVE |

HiveR | 2D and 3D Hive Plots for R |

HLMdiag | Diagnostic tools for hierarchical (multilevel) linear models |

hlr | Hidden Logistic Regression |

hmeasure | The H-measure and other scalar classification performance metrics |

Hmisc | Harrell Miscellaneous |

HMM | HMM – Hidden Markov Models |

hmm.discnp | Hidden Markov models with discrete non-parametric observation distributions |

hmmm | hierarchical multinomial marginal models |

HMMmix | The HMMmixture package |

HMP | Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP |

HMPTrees | Statistical Object Oriented Data Analysis of RDP-based Taxonomic trees from Human Microbiome Data: Modeling, Visualization, and Two-Group Comparison |

HMR | Flux estimation with static chamber data |

hof | More higher order functions for R |

holdem | Texas Holdem simulator |

Holidays | Holiday and halfday data, for use with the TimeWarp package |

homals | Gifi Methods for Optimal Scaling |

homeR | Functions useful for building physics |

homtest | Homogeneity tests for Regional Frequency Analysis |

Hotelling | Hotelling’s T-squared test and variants |

hotspots | Hot spots |

howmany | A lower bound for the number of correct rejections |

HPbayes | Heligman Pollard mortality model parameter estimation using Bayesian Melding with Incremental Mixture Importance Sampling |

HPO.db | A set of annotation maps describing the Human Phenotype Ontology |

HPOSim | Analysis similarities between HPO terms and phenotypic similarity between genes and between diseases |

HSAUR | A Handbook of Statistical Analyses Using R |

HSAUR2 | A Handbook of Statistical Analyses Using R (2nd Edition) |

hSDM | hierarchical Bayesian species distribution models |

hsicCCA | Canonical Correlation Analysis based on Kernel Independence Measures |

hsmm | Hidden Semi Markov Models |

HSROC | Joint meta-analysis of diagnostic test sensitivity and specificity with or without a gold standard reference test |

HTMLUtils | Facilitates automated HTML report creation |

hts | Hierarchical and grouped time series |

HTSCluster | Clustering high throughput sequencing (HTS) data |

httpRequest | Basic HTTP Request |

httpuv | HTTP and WebSocket server library |

httr | Tools for working with URLs and HTTP |

huge | High-dimensional Undirected Graph Estimation |

hwde | Models and tests for departure from Hardy-Weinberg equilibrium and independence between loci |

HWEBayes | Bayesian investigation of Hardy-Weinberg Equilibrium via estimation and testing |

HWEintrinsic | Objective Bayesian Testing for the Hardy-Weinberg Equilibrium Problem |

HW.pval | Testing Hardy-Weinberg Equilibrium for Multiallelic Genes |

hwriter | HTML Writer – Outputs R objects in HTML format |

hwriterPlus | hwriterPlus: Extending the hwriter Package |

hybridHclust | Hybrid hierarchical clustering |

HybridMC | Implementation of the Hybrid Monte Carlo and Multipoint Hybrid Monte Carlo sampling techniques |

hydroGOF | Goodness-of-fit functions for comparison of simulated and observed hydrological time series |

HydroMe | R codes for estimating water retention and infiltration model parameters using experimental data |

hydroPSO | Particle Swarm Optimisation, with focus on Environmental Models |

hydroTSM | Time series management, analysis and interpolation for hydrological modelling |

HyperbolicDist | The hyperbolic distribution |

hyperdirichlet | A generalization of the Dirichlet distribution |

hypergeo | The hypergeometric function |

hyperSpec | Interface for hyperspectral data, i.e. spectra + meta info (spatial, time, concentration, …) |

HyPhy | Macroevolutionary phylogentic analysis of species trees and gene trees |

hypothesestest | Confidence Intervals and Tests of Statistical Hypotheses |

hypred | Simulation of genomic data in applied genetics |

hzar | Hybrid Zone Analysis using R |

IASD | Model selection for index of asymmetry distribution |

ibd | INCOMPLETE BLOCK DESIGNS |

IBDhaploRtools | Functions for the Analysis of IBD Haplo output |

ibdreg | Regression Methods for IBD Linkage With Covariates |

IBDsim | Simulation of chromosomal regions shared by family members |

IBHM | Approximation using the IBHM method |

Iboot | Iboot: iterated bootstrap tests and confidence sets |

ibr | Iterative Bias Reduction |

IBrokers | R API to Interactive Brokers Trader Workstation |

iBUGS | An Interface to WinBUGS/OpenBUGS/JAGS by gWidgets |

IC2 | Inequality and Concentration Indices and Curves |

ic50 | Standardized high-throughput evaluation of cell-based compound screens |

icaOcularCorrection | Independent Components Analysis (ICA) based artifact correction |

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 |

icensmis | Study Design and Data Analysis in the presence of error-prone diagnostic tests and self-reported outcomes |

ic.infer | Inequality constrained inference in linear normal situations |

iCluster | Integrative clustering of multiple genomic data types |

icomp | ICOMP criterion |

ICS | Tools for Exploring Multivariate Data via ICS/ICA |

ICSNP | Tools for Multivariate Nonparametrics |

idbg | R debugger |

identity | Jacquard Condensed Coefficients of Identity |

IDPmisc | Utilities of Institute of Data Analyses and Process Design (www.idp.zhaw.ch) |

idr | Irreproducible discovery rate |

ieeeround | Functions to set and get the IEEE rounding mode |

ifa | Independent Factor Analysis |

iFad | An integrative factor analysis model for drug-pathway association inference |

ifs | Iterated Function Systems |

ifultools | Insightful Research Tools |

iGasso | Genetic association tests and utilities |

IgorR | Read binary files saved by Igor Pro (including Neuromatic data) |

igraph | Network analysis and visualization |

igraph0 | Network analysis and visualization, old, deprecated package |

igraphdata | A collection of network data sets for the igraph package |

igraphtosonia | Convert iGraph graps to SoNIA .son files |

IM | Orthogonal Moment Analysis |

Imap | Interactive Mapping |

imguR | Share plots using the imgur.com image hosting service |

IMIS | Increamental Mixture Importance Sampling |

ImpactIV | Identifying Causal Effect for Multi-Component Intervention Using Instrumental Variable Method |

imprProbEst | Minimum distance estimation in an imprecise probability model |

imputation | imputation |

imputeMDR | The Multifactor Dimensionality Reduction (MDR) Analysis for Incomplete Data |

imputeYn | Imputing the last largest censored observation/observations under weighted least squares |

inarmix | Mixture models for longitudinal count data |

IndependenceTests | Nonparametric tests of independence between random vectors |

indicspecies | Studying the statistical relationship between species and groups of sites |

ineq | Measuring Inequality, Concentration, and Poverty |

InfDim | Infine-dimensional model (IDM) to analyse phenotypic variation in growth trajectories |

inference | Functions to extract inferential values of a fitted model object |

InferenceSMR | Inference about the standardized mortality ratio when evaluating the effect of a screening program on survival |

inflection | Finds the inflection point of a curve |

influence.ME | Tools for detecting influential data in mixed effects models |

infoDecompuTE | Information Decomposition of Two-phase Experiments |

informR | R Tools for Creating Sequence Statistics |

infotheo | Information-Theoretic Measures |

infutil | Information Utility |

inline | Inline C, C++, Fortran function calls from R |

inlinedocs | Convert inline comments to documentation |

InPosition | Inference Tests for ExPosition |

insideRODE | insideRODE includes buildin functions with deSolve solver and C/FORTRAN interfaces to nlme, together with compiled codes |

insol | Solar Radiation |

installr | Functions for updating and installing a new version of R and other software – from R |

int64 | 64 bit integer types |

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 |

Interact | Tests for marginal interactions in a 2 class response model |

InteractiveIGraph | interactive network analysis and visualization |

interactivity | toggle R interactive mode |

intergraph | Coercion routines for network data objects in R |

Interpol | Interpolation of amino acid sequences |

Interpol.T | Hourly interpolation of multiple temperature daily series |

interval | Weighted Logrank Tests and NPMLE for interval censored data |

intervals | Tools for working with points and intervals |

intpoint | linear programming solver by the interior point method and graphically (two dimensions) |

intReg | Interval Regression |

intRegGOF | Integrated Regression Goodness of Fit |

introgress | methods for analyzing introgression between divergent lineages |

intsvy | International Assessment Data Manager |

ipdmeta | Tools for subgroup analyses with multiple trial data using aggregate statistics |

ipfp | Fast implementation of the iterative proportional fitting procedure in C |

iplots | iPlots – interactive graphics for R |

IPMpack | Builds and analyses Integral Projection Models (IPMs) |

ipred | Improved Predictors |

IPSUR | Introduction to Probability and Statistics Using R |

ipw | Estimate inverse probability weights |

IQCC | Improved Quality Control Charts |

irace | Iterated Racing Procedures |

iRefR | iRefIndex Manager |

iRegression | Regression methods for interval-valued variables |

irlba | Fast partial SVD by implicitly-restarted Lanczos bidiagonalization |

irr | Various Coefficients of Interrater Reliability and Agreement |

irtoys | Simple interface to the estimation and plotting of IRT models |

irtProb | Utilities and Probability Distributions Related to Multidimensional Person Item Response Models (IRT) |

irtrees | Estimation of Tree-Based Item Response Models |

isa2 | The Iterative Signature Algorithm |

ISBF | Iterative Selection of Blocks of Features – ISBF |

isdals | Provides datasets for Introduction to Statistical Data Analysis for the Life Sciences |

ISDA.R | interval symbolic data analysis for R |

ISIPTA | ISIPTA network analysis |

ISLR | Data for An Introduction to Statistical Learning with Applications in R |

ismev | An Introduction to Statistical Modeling of Extreme Values |

Iso | Functions to perform isotonic regression |

isocir | Isotonic Inference for Circular data |

ISOcodes | Selected ISO codes |

IsoGene | Testing for monotonic relationship between gene expression and doses in a microarray experiment |

isopam | Isopam (Clustering) |

isopat | Calculation of isotopic pattern for a given molecular formula |

isotone | Active set and generalized PAVA for isotone optimization |

IsotopeR | Stable isotope analysis |

ISOweek | Week of the year and weekday according to ISO 8601 |

iSubpathwayMiner | The package can implement the graph-based reconstruction and analyses of the KEGG pathways |

isva | Independent Surrogate Variable Analysis |

ISwR | Introductory Statistics with R |

iteRates | Parametric rate comparison |

iterators | Iterator construct for R |

iterLap | Approximate probability densities by iterated Laplace Approximations |

itertools | Iterator Tools |

itree | Tools for classification and regression trees, with an emphasis on interpretability |

its | Irregular Time Series |

itsmr | Time series analysis package for students |

IUPS | Incorporating Uncertainties in Propensity Scores |

ivbma | Bayesian Instrumental Variable Estimation and Model Determination via Conditional Bayes Factors |

ivivc | A data analysis tool for in vitro-in vivo correlation (IVIVC) |

iWebPlots | Interactive web-based plots |

iWeigReg | Improved methods for causal inference and missing data problems |

iwtp | Numerical evaluation willingness to pay based on interval data |

jaatha | A Fast Parameter Estimation Method for Evolutionary Biology |

jackknifeKME | Jackknife estimates of Kaplan-Meier estimators or integrals |

JADE | JADE and other BSS methods as well as some BSS performance criteria |

JASPAR | R modules for JASPAR databases: a collection of transcription factor DNA-binding preferences, modeled as matrices |

JavaGD | Java Graphics Device |

JGL | Performs the Joint Graphical Lasso for sparse inverse covariance estimation on multiple classes |

JGR | JGR – Java GUI for R |

JJcorr | Calculates polychorical correlations for several copula families |

JM | Joint Modeling of Longitudinal and Survival Data |

JMbayes | Joint Modeling of Longitudinal and Time-to-Event Data under a Bayesian Approach |

jmec | Fit joint model for event and censoring with cluster-level frailties |

Jmisc | Julian Miscellaneous Function |

JMLSD | Joint Modeling of Longitudinal and Survival Data – Power Calculation |

Johnson | Johnson Transformation |

JohnsonDistribution | Johnson Distribution |

joineR | Joint modelling of repeated measurements and time-to-event data |

jointDiag | Joint Approximate Diagonalization of a set of square matrices |

JointRegBC | Joint Modelling of Mixed Correlated Binary and Continuous Responses : A Latent Variable Approach |

JOP | Joint Optimization Plot |

JoSAE | Functions for unit-level small area estimators and their variances |

jpeg | Read and write JPEG images |

JPSurv | Methods for population-based cancer survival analysis |

jtrans | Johnson transformation for normality |

JudgeIt | JudgeIt: A Program for Evaluating Electoral Systems and Redistricting Plans |

Julia | Fractal Image Data Generator |

jvmr | Integration of R, Java, and Scala |

KappaGUI | GUI for Cohen’s and Fleiss’ Kappa |

kappalab | Non-additive measure and integral manipulation functions |

kappaSize | Sample Size Estimation Functions for Studies of Interobserver Agreement |

kaps | K Adaptive Partitioning for Survival data |

kdetrees | Nonparametric method for identifying discordant trees |

kelvin | Calculate solutions to Kelvin differential equation using Bessel functions |

Kendall | Kendall rank correlation and Mann-Kendall trend test |

kequate | The kernel method of test equating |

kerdiest | Nonparametric kernel estimation of the distribution function. Bandwidth selection and estimation of related functions |

kernelFactory | Kernel Factory: An ensemble of kernel Machines |

kernlab | Kernel-based Machine Learning Lab |

KernSmooth | Functions for kernel smoothing for Wand & Jones (1995) |

KernSmoothIRT | Nonparametric Item Response Theory |

KFAS | Kalman Filter and Smoother for Exponential Family State Space Models |

kin.cohort | Analysis of kin-cohort studies |

kinfit | Routines for fitting kinetic models to chemical degradation data |

kinship2 | Pedigree functions |

kitagawa | Model the spectral response of a closed water-well to harmonic strains at seismic frequencies |

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 |

Kmisc | Miscellaneous functions intended to improve the R coding experience |

kml | K-means for Longitudinal data |

kml3d | K-means for joint Longitudinal data |

KMsurv | Data sets from Klein and Moeschberger (1997), Survival Analysis |

knitcitations | Citations for knitr markdown files |

knitr | A general-purpose package for dynamic report generation in R |

knitrBootstrap | Knitr Bootstrap framework |

knnGarden | Multi-distance based k-Nearest Neighbors |

knorm | Microarray Data From Multiple Biologically Interrelated Experiments |

kobe | Tools for providing advice for the Tuna Regional Fisheries Management Organisations |

kohonen | Supervised and unsupervised self-organising maps |

kolmim | An improved evaluation of Kolmogorov’s distribution |

KoNLP | Korean NLP Package |

koRpus | An R Package for Text Analysis |

Kpart | Spline Fitting |

kriging | Ordinary Kriging |

KrigInv | Kriging-based Inversion for Deterministic and Noisy Computer Experiments |

KRLS | Kernel-based Regularized Least Squares (KRLS) |

ks | Kernel smoothing |

kSamples | K-Sample Rank Tests and their Combinations |

KsPlot | Check the power of seveal statistical models |

kst | Knowledge Space Theory |

ktspair | k-Top Scoring Pairs for Microarray Classification |

kulife | Datasets 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 |

l2boost | l2boost – Friedman’s boosting algorithm for regularized linear regression |

labdsv | Ordination and Multivariate Analysis for Ecology |

labeledLoop | Labeled Loop |

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 |

LaF | Fast access to large ASCII files |

Lahman | Sean Lahman’s Baseball Database |

Lambda4 | Collection of Internal Consistency Reliability Coefficients |

lambda.r | Functional programming in R |

LambertW | Analyze and Gaussianize skewed, heavy-tailed data |

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” |

LARF | LARF: Local Average Response Functions for Estimating Treatment Effects |

LargeRegression | Large Regressions |

lars | Least Angle Regression, Lasso and Forward Stagewise |

lasso2 | L1 constrained estimation aka ‘lasso’ |

lassoshooting | L1 regularized regression (Lasso) solver using the Cyclic Coordinate Descent algorithm aka Lasso Shooting |

latdiag | Draws diagrams useful for checking latent scales |

latentnet | Latent position and cluster models for statistical networks |

Laterality | Functions to calculate common laterality statistics in primatology |

lattice | Lattice Graphics |

latticeDensity | Density estimation and nonparametric regression on irregular regions |

latticeExtra | Extra Graphical Utilities Based on Lattice |

LatticeKrig | Multiresolution Kriging based on Markov random fields |

latticist | A graphical user interface for exploratory visualisation |

lava | Linear Latent Variable Models |

lavaan | Latent Variable Analysis |

lavaan.survey | Complex survey structural equation modeling (SEM) |

lava.tobit | LVM with censored and binary outcomes |

lawstat | An R package for biostatistics, public policy, and law |

lazyData | A LazyData Facility |

lazyWeave | LaTeX Wrappers for R Users |

lbiassurv | Length-biased correction to survival curve estimation |

LCAextend | Latent Class Analysis (LCA) with familial dependence in extended pedigrees |

lcd | Learn Chain graphs via Decomposition |

lcda | Latent Class Discriminant Analysis |

LCFdata | Data sets for package “LMERConvenienceFunctions” |

lcmm | Estimation of latent class mixed models, joint latent class mixed models and mixed models for curvilinear outcomes |

lcmr | lcmr package |

lda | Collapsed Gibbs sampling methods for topic models |

ldbounds | Lan-DeMets Method for Group Sequential Boundaries |

LDcorSV | Linkage disequilibrium corrected by the structure and the relatedness |

ldDesign | Design of experiments for detection of linkage disequilibrium |

LDExplorer | Efficient Whole-Genome LD Based Haplotpe Block Recognition |

LDheatmap | Graphical display of pairwise linkage disequilibria between SNPs |

ldlasso | LD LASSO Regression for SNP Association Study |

LDOD | Finding Locally D-optimal optimal designs for some nonlinear and generalized linear models |

ldr | Methods for likelihood-based dimension reduction in regression |

LDtests | Exact tests for Linkage Disequilibrium and Hardy-Weinberg Equilibrium |

LeafAngle | Fits, plots, and summarizes leaf angle distributions |

LEAPFrOG | Likelihood Estimation of Admixture in Parents From Offspring Genotypes |

leapp | latent effect adjustment after primary projection |

leaps | regression subset selection |

LearnBayes | Functions for Learning Bayesian Inference |

LearnEDA | Functions for Learning Exploratory Data Analysis |

leiv | Bivariate linear errors-in-variables estimation |

LeLogicielR | Functions and datasets to accompany the book “Le logiciel R: Maitriser le langage, Effectuer des analyses statistiques” (french) |

lemma | Laplace approximated EM Microarray Analysis |

lessR | Less Code, More Results |

lestat | A package for LEarning STATistics |

lfe | Linear Group Fixed Effects |

lfstat | Calculation of Low Flow Statistics for daily stream flow data |

lga | Tools for linear grouping analysis (LGA) |

lgcp | Log-Gaussian Cox Process |

LGS | simulating Linkage Group Selection (LGS) |

lgtdl | A set of methods for longitudinal data objects |

lhs | Latin Hypercube Samples |

libamtrack | Computational routines for proton and ion radiotherapy |

LiblineaR | Linear Predictive Models Based On The Liblinear C/C++ Library |

LICurvature | Sensitivity Analysis for Case Weight in Normal Linear Regression |

lifecontingencies | A package to perform actuarial mathematics for life contingencies insurances |

LifeTables | A package to implement HMD model life table system |

LIHNPSD | Poisson Subordinated Distribution |

likelihood | Methods for maximum likelihood estimation |

LIM | Linear Inverse Model examples and solution methods |

limitplot | Jitter/CI Plot with Ordered Points Below the Limit of Detection |

limSolve | Solving Linear Inverse Models |

LinearizedSVR | Linearized Support Vector Regression |

lineup | Lining up two sets of measurements |

linkcomm | Tools for Generating, Visualizing, and Analysing Link Communities in Networks |

linLIR | linear Likelihood-based Imprecise Regression |

linprog | Linear Programming / Optimization |

lint | Tools to check R code style |

liso | Fitting lasso penalised additive isotone models |

lisp | List-processing à la SRFI-1 |

lisrelToR | Import output from LISREL into R |

list | Statistical Methods for the Item Count Technique and List Experiment |

LIStest | Longest Increasing Subsequence Independence Test |

ljr | Logistic Joinpoint Regression |

llama | Leveraging Learning to Automatically Manage Algorithms |

lle | Locally linear embedding |

lmbc | Linear Model Bias Correction for RNA-Seq Data |

lme4 | Linear mixed-effects models using S4 classes |

lmec | Linear Mixed-Effects Models with Censored Responses |

lmeNB | Fit negative binomial mixed-effect regression model |

lmeNBBayes | Sample from the posterior of the negative binomial mixed-effect regression model. The random effect is modeled with DP mixture of beta distributions |

LMERConvenienceFunctions | A suite of functions to back-fit fixed effects and forward-fit random effects, as well as other miscellaneous functions |

lmeSplines | Add smoothing spline modelling capability to nlme |

LMest | Fit Latent Markov models in basic versions |

lmf | Functions for estimation and inference of selection in age-structured populations |

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 |

lmomco | L-moments, Censored L-moments, Trimmed L-moments, L-comoments, and Many Distributions |

Lmoments | L-moments and quantile mixtures |

lmomRFA | Regional frequency analysis using L-moments |

lmPerm | Permutation tests for linear models |

lmSupport | Support for Linear Models |

lmtest | Testing Linear Regression Models |

localdepth | Local Depth |

localgauss | Estimating local Gaussian parameters |

locfdr | Computes local false discovery rates |

locfit | Local Regression, Likelihood and Density Estimation |

Lock5Data | Datasets for “Statistics: UnLocking the Power of Data” |

locpol | Kernel local polynomial regression |

log4r | A simple logging system for R, based on log4j |

LogConcDEAD | Log-concave Density Estimation in Arbitrary Dimensions |

logconcens | Maximum likelihood estimation of a log-concave density based on censored data |

logcondens | Estimate a Log-Concave Probability Density from iid Observations |

logcondens.mode | Compute MLE of Log-Concave Density on R with Fixed Mode, and Perform Inference for the Mode |

logcondiscr | Estimate a Log-Concave Probability Mass function from Discrete i.i.d. Observations |

logging | R logging package |

LogicReg | Logic Regression |

logistf | Firth’s bias reduced logistic regression |

logistiX | Exact logistic regression including Firth correction |

LogitNet | Infer network based on binary arrays using regularized logistic regression |

logitnorm | Functions for the logitnormal distribution |

loglognorm | Double log normal distribution functions |

logmult | Log-multiplicative models, including association models |

LogrankA | Logrank Test for Aggregated Survival Data |

logregperm | Inference in Logistic Regression |

logspline | Logspline density estimation routines |

lokern | Kernel Regression Smoothing with Local or Global Plug-in Bandwidth |

longCatEDA | Package for Plotting Categorical Longitudinal and Time-Series Data |

longclust | Model-Based Clustering and Classification for Longitudinal Data |

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 |

loop | loop decomposition of weighted directed graphs for life cycle analysis, providing flexbile network plotting methods, and analyzing food chain properties in ecology |

LoopAnalyst | A collection of tools to conduct Levins’ Loop Analysis |

lordif | Logistic Regression Differential Item Functioning using IRT |

lorec | LOw Rand and sparsE Covariance matrix estimation |

lossDev | Robust Loss Development Using MCMC |

LOST | Missing morphometric data simulation and estimation |

LowRankQP | Low Rank Quadratic Programming |

lpc | Lassoed principal components for testing significance of features |

LPCM | Local principal curve methods |

lpint | Local polynomial esitmators of intensity function or its derivatives |

LPmerge | Merging linkage maps by linear programming |

lpridge | Local Polynomial (Ridge) Regression |

lpSolve | Interface to Lp_solve v. 5.5 to solve linear/integer programs |

lpSolveAPI | R Interface for lp_solve version 5.5.2.0 |

lqa | Penalized Likelihood Inference for GLMs |

lqmm | Linear Quantile Mixed Models |

LS2W | Locally stationary two-dimensional wavelet process estimation scheme |

lsa | Latent Semantic Analysis |

LSD | Lots of Superior Depictions |

lsdv | Fixed effect panel data regression |

lshorth | The Length of the Shorth |

lsmeans | Least-squares means |

lspls | LS-PLS Models |

lsr | Companion package to “Learning Statistics with R” |

lss | the accelerated failure time model to right censored data based on least-squares principle |

ltm | Latent Trait Models under IRT |

ltmle | Longitudinal Targeted Maximum Likelihood Estimation |

LTPDvar | LTPD and AOQL plans for acceptance sampling inspection by variables |

LTR | Perform LTR analysis on microarray data |

ltsa | Linear time series analysis |

ltsbase | Ridge and Liu Estimates based on LTS (Least Trimmed Squares) Method |

lubridate | Make dealing with dates a little easier |

luca | Likelihood inference from case-control data Under Covariate Assumptions (LUCA) |

Luminescence | Package for Luminescence Dating data analysis |

LVMMCOR | A Latent Variable Model for Mixed Continuous and Ordinal Responses |

LVQTools | Learning Vector Quantization Tools |

lxb | Fast LXB file reader |

lymphclon | Accurate Estimation of Clonal Coincidences and Abundances from Biological Replicates |

M3 | Reading M3 files |

MAc | Meta-Analysis with Correlations |

MAclinical | Class prediction based on microarray data and clinical parameters |

MAd | Meta-Analysis with Mean Differences |

mada | Meta-Analysis of Diagnostic Accuracy (mada) |

MADAM | This package provides some basic methods for meta-analysis |

madsim | A Flexible Microarray Data Simulation Model |

Maeswrap | Wrapper functions for MAESTRA/MAESPA |

magic | create and investigate magic squares |

magicaxis | Pretty scientific plotting with minor-tick and log minor-tick support |

magma | Matrix Algebra on GPU and Multicore Architectures |

magnets | Simulate micro-magnets dynamics |

Sending Email Notifications from R | |

MAINT.Data | Model and Analize Interval Data |

makeProject | Creates an empty package framework for the LCFD format |

makeR | Package for managing projects with multiple versions derived from a single source repository |

malaria.em | EM Estimation of Malaria Haplotype Probabilities from Multiply Infected Human Blood Samples |

MALDIquant | Quantitative Analysis of Mass Spectrometry Data |

MALDIquantForeign | Import/Export routines for MALDIquant |

MAMA | Meta-Analysis of MicroArray |

MAMS | Designing Multi-Arm Multi-Stage Studies |

MAMSE | Calculation of Minimum Averaged Mean Squared Error (MAMSE) weights |

Mangrove | Risk prediction on trees |

mapdata | Extra Map Databases |

MapGAM | Mapping Smoothed Odds Ratios from Individual-Level Data |

MAPLES | Smoothed age profile estimation |

mapplots | Data visualisation on maps |

mapproj | Map Projections |

maps | Draw Geographical Maps |

maptools | Tools for reading and handling spatial objects |

maptree | Mapping, pruning, and graphing tree models |

mAr | Multivariate AutoRegressive analysis |

1-Mar | Multivariate Autoregressive Modeling for Analysis of Community Time-Series Data |

mar1s | Multiplicative AR(1) with Seasonal Processes |

marelac | Tools for Aquatic Sciences |

margie | Log Marginal Likelihood of Gaussian Mixture |

marginalmodelplots | Marginal Mean Model Plots |

markdown | Markdown rendering for R |

marked | R Code for mark-recapture analysis |

MarkedPointProcess | Analysis of Marks of Marked Point Processes |

maRketSim | Market simulator for R |

marmap | Import, plot and analyze bathymetric and topographic data |

marqLevAlg | An algorithm for least-squares curve fitting |

MARSS | Multivariate Autoregressive State-Space Modeling |

MASS | Support Functions and Datasets for Venables and Ripley’s MASS |

MASSTIMATE | Body Mass Estimation Equations for Vertebrates |

MasterBayes | ML and MCMC Methods for Pedigree Reconstruction and Analysis |

MAT | Multidimensional Adaptive Testing (MAT) |

Matching | Multivariate and Propensity Score Matching with Balance Optimization |

MatchIt | MatchIt: Nonparametric Preprocessing for Parametric Casual Inference |

mathgraph | Directed and undirected graphs |

maticce | Mapping Transitions in Continuous Character Evolution |

matie | Measuring Association and Testing Independence Efficiently |

matlab | MATLAB emulation package |

Matrix | Sparse and Dense Matrix Classes and Methods |

matrixcalc | Collection of functions for matrix calculations |

MatrixEQTL | Matrix eQTL: Ultra fast eQTL analysis via large matrix operations |

MatrixModels | Modelling with Sparse And Dense Matrices |

matrixStats | Methods that apply to rows and columns of a matrix |

MATTOOLS | Modern Calibration Functions for the Modern Analog Technique (MAT) |

MAVTgsa | Ordinary least square test and Multivariate Analysis Of Variance test with n contrasts |

MaXact | Exact max-type Cochran-Armitage trend test(CATT) |

maxent | Low-memory Multinomial Logistic Regression with Support for Text Classification |

maxLik | Maximum Likelihood Estimation |

maxlike | Model species distributions by estimating the probability of occurrence using presence-only data |

maxstat | Maximally Selected Rank Statistics |

MBA | Multilevel B-spline Approximation |

MBCluster.Seq | Model-Based Clustering for RNA-seq Data |

MBESS | MBESS |

MBI | (M)ultiple-site (B)iodiversity (I)ndices Calculator |

MBmca | Nucleic Acid Melting Curve Analysis on Microbead Surfaces with R |

mbmdr | Model Based Multifactor Dimensionality Reduction |

mboost | Model-Based Boosting |

mc2d | Tools for Two-Dimensional Monte-Carlo Simulations |

MCAPS | MCAPS data and results |

mcbiopi | Matrix Computation Based Identification Of Prime Implicants |

mcclust | Process an MCMC Sample of Clusterings |

mcga | Machine coded genetic algorithms for real-valued optimization problems |

mcgibbsit | Warnes and Raftery’s MCGibbsit MCMC diagnostic |

mchof | multicore higher-order functions |

MChtest | Monte Carlo hypothesis tests with Sequential Stopping |

mcIRT | IRT models for multiple choice items (mcIRT) |

mcll | Monte Carlo Local Likelihood Estimation |

mclogit | Mixed Conditional Logit |

mclust | Normal Mixture Modeling for Model-Based Clustering, Classification, and Density Estimation |

mcmc | Markov Chain Monte Carlo |

MCMCglmm | MCMC Generalised Linear Mixed Models |

MCMChybridGP | Hybrid Markov chain Monte Carlo using Gaussian Processes |

MCMCpack | Markov chain Monte Carlo (MCMC) Package |

mcmcplots | Create Plots from MCMC Output |

MCMC.qpcr | Bayesian analysis of qRT-PCR data |

mcmcse | Monte Carlo Standard Errors for MCMC |

mco | Multi criteria optimization algorithms and related functions |

Mcomp | Data from the M-competitions |

MConjoint | Conjoint Analysis through Averaging of Multiple Analyses |

MCPAN | Multiple comparisons using normal approximation |

McParre | Run a Regenerative Markov chain in Parallel on a Cluster |

MCPerm | A Monte Carlo permutation method for multiple test correlation |

MCPMod | Design and Analysis of Dose-Finding Studies (see also DoseFinding package) |

mcprofile | Multiple Contrast Profiles |

mcr | Method Comparison Regression |

mcsm | Functions for Monte Carlo Methods with R |

McSpatial | Nonparametric spatial data analysis |

MCUSUM | Multivariate Cumulative Sum (MCUSUM) Control Chart |

mda | Mixture and flexible discriminant analysis |

mded | Measuring the difference between two empirical distributions |

MDM | Multinomial Diversity Model |

MDPtoolbox | Markov Decision Processes toolbox |

MDR | Detect gene-gene interactions using multifactor dimensionality reduction |

MDSGUI | A GUI for interactive MDS in R |

meboot | Maximum Entropy Bootstrap for Time Series |

mederrRank | Bayesian Methods for Identifying the Most Harmful Medication Errors |

mediation | R Package for Causal Mediation Analysis |

MedOr | Median Ordering Statistical R package |

medSTC | A max-margin supervised Sparse Topical Coding Model |

MEET | MEET: Motif Elements Estimation Toolkit |

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 |

MEMSS | Data sets from Mixed-effects Models in S |

memuse | Estimate the memory usage of dense, in-core, numeric objects |

MergeGUI | A GUI for Merging Datasets in R |

merror | Accuracy and Precision of Measurements |

MESS | Miscellaneous esoteric statistical scripts |

meta | Meta-Analysis with R |

MetABEL | meta-analysis of genome-wide SNP association results |

MetabolAnalyze | Probabilistic latent variable models for metabolomic data |

metabolomics | A collection of functions for analysing metabolomics data |

metacom | Analysis of the ‘elements of metacommunity structure’ |

metacor | Meta-analysis of correlation coefficients |

Metadata | Collates Metadata for Climate Surface Stations |

MetaDE | MetaDE: Microarray meta-analysis for differentially expressed gene detection |

metafor | Meta-Analysis Package for R |

metagen | Generalised Inference in the Random Effects Meta Regression Model |

metaLik | Likelihood inference in meta-analysis and meta-regression models |

metaMA | Meta-analysis for MicroArrays |

metamisc | Diagnostic and prognostic meta analysis (metamisc) |

MetaPath | Perform the Meta-Analysis for Pathway Enrichment analysis (MAPE) |

MetaPCA | MetaPCA: Meta-analysis in the Dimension Reduction of Genomic data |

MetaQC | MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis |

MetaSKAT | Meta analysis for SNP-set (Sequence) Kernel Association Test |

metatest | Fit and test metaregression models |

meteogRam | Tools for plotting meteograms |

Meth27QC | Meth27QC: sample quality analysis, and sample control analysis |

MethComp | Functions for analysis of agreement in method comparison studies |

Metrics | Evaluation metrics for machine learning |

metRology | Support for metrological applications |

metrumrg | Pharmacometric tools for data preparation, modeling, simulation, and reporting |

mets | Analysis of Multivariate Event Times |

MEWMA | Multivariate Exponentially Weighted Moving Average (MEWMA) Control Chart |

MExPosition | Multi-table ExPosition |

MFDA | Model Based Functional Data Analysis |

mFilter | Miscellaneous time series filters |

mfp | Multivariable Fractional Polynomials |

mfr | Minimal Free Resolutions of Graph Edge Ideals |

MFSAS | Creation and Evaluation of Multilevel Fixed and Sequential Sampling Plans |

mgcv | Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation |

mgpd | mgpd: Functions for multivariate generalized Pareto distribution (MGPD of Type II) |

mgraph | Graphing map attributes and non-map variables in R |

MHadaptive | General Markov Chain Monte Carlo for Bayesian Inference using adaptive Metropolis-Hastings sampling |

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 |

mice | Multivariate Imputation by Chained Equations |

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 |

MiClip | A Model-based Approach to Identify Binding Sites in CLIP-Seq Data |

microbenchmark | Sub microsecond accurate timing functions |

micromap | Linked Micromap Plots |

micromapST | Linked Micromap Plots for U. S. States |

MicroStrategyR | MicroStrategyR Package |

MIfuns | Pharmacometric tools for data preparation, modeling, simulation, and reporting |

MigClim | Implementing dispersal into species distribution models |

migest | Useful R code for the Estimation of Migration |

migration.indices | Migration indices |

migui | Graphical User Interface of the mi Package |

MImix | Mixture summary method for multiple imputation |

MindOnStats | Data sets included in Utts and Heckard’s Mind on Statistics |

minerva | minerva: Maximal Information-Based Nonparametric Exploration R package for Variable Analysis |

Miney | Implementation of the Well-Known Game to Clear Bombs from a Given Field (Matrix) |

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, plus support for bounds |

minPtest | Gene region-level testing procedure for SNP data, using the min P test resampling approach |

minqa | Derivative-free optimization algorithms by quadratic approximation |

minxent | Entropy Optimization Distributions |

miP | Multiple Imputation Plots |

MIPHENO | Mutant Identification through Probabilistic High throughput Enabled NOrmalization |

miRada | MicroRNA Microarray Data Analysis |

mirt | Multidimensional Item Response Theory |

miRtest | combined miRNA- and mRNA-testing |

misc3d | Miscellaneous 3D Plots |

miscF | Miscellaneous Functions |

miscFuncs | Miscellaneous Useful Functions |

MiscPsycho | Miscellaneous Psychometric Analyses |

miscTools | Miscellaneous Tools and Utilities |

missForest | Nonparametric Missing Value Imputation using Random Forest |

MissingDataGUI | A GUI for Missing Data Exploration |

missMDA | Handling missing values with/in multivariate data analysis (principal component methods) |

MissMech | Testing Homoscedasticity, Multivariate Normality, and Missing Completely at Random |

MiST | Mixed effects Score Test for continuous outcomes |

mistral | Methods in Structural Reliability |

MitISEM | Mixture of Student t Distributions using Importance Sampling and Expectation Maximization |

mitools | Tools for multiple imputation of missing data |

mix | Estimation/multiple Imputation for Mixed Categorical and Continuous Data |

mixAK | Multivariate normal mixture models and mixtures of generalized linear mixed models including model based clustering |

mixcat | Mixed effects cumulative link and logistic regression models |

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 |

MixMAP | Implements the MixMAP algorithm |

mixOmics | Omics Data Integration Project |

mixPHM | Mixtures of proportional hazard models |

mixRasch | Mixture Rasch Models with JMLE |

mixreg | Functions to fit mixtures of regressions |

mixsep | Forensic Genetics DNA Mixture Separation |

MixSim | Simulating Data to Study Performance of Clustering Algorithms |

mixsmsn | Fitting finite mixture of scale mixture of skew-normal distributions |

mixstock | functions for mixed stock analysis |

mixtools | Tools for analyzing finite mixture models |

mixture | Mixture Models for Clustering and Classification |

MixtureInf | Inference for Finite Mixture Models |

mkin | Routines for fitting kinetic models with one or more state variables to chemical degradation data |

MKLE | Maximum kernel likelihood estimation |

MKmisc | Miscellaneous Functions from M. Kohl |

mkssd | Efficient multi-level k-circulant supersaturated designs |

mlbench | Machine Learning Benchmark Problems |

MLCM | Maximum Likelihood Conjoint Measurement |

MLDA | Methylation Linear Discriminant Analysis (MLDA) |

mlDNA | Machine Learning-based Differential Network Analysis of Transcriptome Data |

MLDS | Maximum Likelihood Difference Scaling |

mlearning | Machine learning algorithms with unified interface and confusion matrices |

MLEcens | Computation of the MLE for bivariate (interval) censored data |

mlegp | Maximum Likelihood Estimates of Gaussian Processes |

MLEP | Maximum likelihood estimate of penetrance parameters |

mleur | Maximum likelihood unit root test |

mlgt | Multi-Locus Geno-Typing |

mlica2 | Independent Component Analysis using Maximum Likelihood |

mlmmm | ML estimation under multivariate linear mixed models with missing values |

mlmRev | Examples from Multilevel Modelling Software Review |

mlogit | multinomial logit model |

mlogitBMA | Bayesian Model Averaging for Multinomial Logit Models |

MLPAstats | MLPA analysis to detect gains and loses in genes |

mlPhaser | Multi-Locus Haplotype Phasing |

MM | The multiplicative multinomial distribution |

mmand | Mathematical Morphology in Any Number of Dimensions |

mmap | Map Pages of Memory |

mmcm | Modified Maximum Contrast Method |

mmds | Mixture Model Distance Sampling (mmds) |

mmeln | MMELN : Estimation of multinormal mixture distribution |

mmeta | Multivariate Meta-Analysis Using Sarmanov Beta Prior Distributions |

MMIX | Model selection uncertainty and model mixing |

mmm | an R package for analyzing multivariate longitudinal data with multivariate marginal models |

mmm2 | Multivariate marginal models with shared regression parameters |

mmod | Modern measures of population differentiation |

MMST | DATASETS FROM MMST |

MNM | Multivariate Nonparametric Methods. An Approach Based on Spatial Signs and Ranks |

mnormt | The multivariate normal and t distributions |

MNP | R Package for Fitting the Multinomial Probit Model |

mobForest | Model based Random Forest analysis |

Mobilize | Mobilize plots and functions |

MOCCA | Multi-objective optimization for collecting cluster alternatives |

Modalclust | Hierarchical Modal Clustering |

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 |

ModelGood | Validation of risk prediction models |

ModelMap | Creates Random Forest and Stochastic Gradient Boosting Models, and applies them to GIS .img files to build detailed prediction maps |

modeltools | Tools and Classes for Statistical Models |

modiscloud | R tools for processing Level 2 Cloud Mask products from MODIS |

MODISTools | MODIS Subsetting Tools |

modTempEff | Modelling temperature effects using time series data |

moduleColor | Basic module functions |

MOJOV | Mojo Variants: Rare Variants analysis |

mokken | Mokken Scale Analysis in R |

mombf | Moment and Inverse Moment Bayes factors |

moments | Moments, cumulants, skewness, kurtosis and related tests |

Momocs | Shape Analysis of Outlines |

mondate | Keep track of dates in terms of months |

MonetDB.R | Connect MonetDB to R |

monmlp | Monotone multi-layer perceptron neural network |

monomvn | Estimation for multivariate normal and Student-t data with monotone missingness |

MonoPoly | Functions to fit monotone polynomials |

monreg | Nonparametric monotone regression |

moonsun | Basic astronomical calculations with R |

mopsocd | MOPSOCD: Multi-objective Particle Swarm Optimization with Crowding Distance |

Morpho | Calculations and visualisations related to Geometric Morphometrics |

MorseGen | Simple raw data generator based on user-specified summary statistics |

MortalitySmooth | Smoothing and forecasting Poisson counts with P-splines |

mosaic | Project MOSAIC (mosaic-web.org) statistics and mathematics teaching utilities |

moult | Models for Analysing Moult in Birds |

move | Visualizing and analyzing animal track data |

movMF | Mixtures of von Mises-Fisher Distributions |

mpa | CoWords Method |

MPCI | Multivariate Process Capability Indices (MPCI) |

MPDiR | Data sets and scripts for Modeling Psychophysical Data in R |

MPINet | The package can implement the network-based metabolite pathway identification of pathways |

MplusAutomation | Automating Mplus Model Estimation and Interpretation |

mpm | Multivariate Projection Methods |

mpMap | Multi-parent RIL genetic analysis |

mpmcorrelogram | Multivariate Partial Mantel Correlogram |

mpoly | Symbolic computation and more with multivariate polynomials |

mpt | Multinomial Processing Tree (MPT) Models |

MPTinR | Analyze Multinomial Processing Tree Models |

MPV | Data Sets from Montgomery, Peck and Vining’s Book |

mra | Analysis of Mark-Recapture data |

mratios | Inferences for ratios of coefficients in the general linear model |

MRCE | Multivariate regression with covariance estimation |

MRCV | Methods for Analyzing Multiple Response Categorical Variables (MRCVs) |

mrdrc | Model-robust concentration-response analysis |

mrds | Mark-Recapture Distance Sampling (mrds) |

mritc | MRI tissue classification |

mRm | An R package for conditional maximum likelihood estimation in mixed Rasch models |

mRMRe | R package for parallelized mRMR ensemble feature selection |

msap | Statistical analysis for Methylation-sensitive Amplification Polymorphism data |

msarc | Draws diagrams (mis)representing the results of mass spec experiments |

MsatAllele | Visualizes the scoring and binning of microsatellite fragment sizes |

MSBVAR | Markov-Switching, Bayesian, Vector Autoregression Models |

mseapca | Metabolite set enrichment analysis for factor loading in principal component analysis |

MSeasy | Preprocessing of Gas Chromatography-Mass Spectrometry (GC-MS) data |

MSeasyTkGUI | MSeasy Tcl/Tk Graphical User Interface |

mseq | Modeling non-uniformity in short-read rates in RNA-Seq data |

MSG | Data and functions for the book Modern Statistical Graphics |

msgl | High dimensional multiclass classification using sparse group lasso |

msgpackR | A library to serialize or unserialize data in MessagePack format |

msgps | Degrees of freedom of elastic net, adaptive lasso and generalized elastic net |

msir | Model-based Sliced Inverse Regression |

msm | Multi-state Markov and hidden Markov models in continuous time |

msme | Functions and Datasets for “Methods of Statistical Model Estimation” |

MSQC | Multivariate Statistical Quality Control |

msr | Morse-Smale approximation, regression and visualization |

msSurv | Nonparametric Estimation for Multistate Models |

mstate | Data preparation, estimation and prediction in multi-state models |

MSwM | Fitting Markov Switching Models |

mtcreator | Creating MAGE-TAB files using mtcreator |

mtsdi | Multivariate time series data imputation |

MTSKNN | Multivariate two-sample tests based on K-nearest-neighbors |

MTurkR | Access to Amazon Mechanical Turk Requester API via R |

MUCflights | Munich Franz-Josef-Strauss Airport Pattern Analysis |

MuFiCokriging | Multi-Fidelity Cokriging models |

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 |

MultEq | Multiple Equivalence Tests and Simultaneous Confidence Intervals |

multgee | GEE Solver for Correlated Nominal or Ordinal Multinomial Responses |

multibiplotGUI | Multibiplot Analysis in R |

multic | Quantitative linkage analysis tools using the variance components approach |

MultiChIPmixHMM | MultiChIPmixHMM, an R package for ChIP-chip data analysis modeling spatial dependencies and multiple replicates |

Multiclasstesting | Performance of N-ary classification testing |

multicool | Permutations of multisets in cool-lex order |

multicore | Parallel processing of R code on machines with multiple cores or CPUs |

MultiLCIRT | Multidimensional latent class Item Response Theory models |

multilevel | Multilevel Functions |

multilevelPSA | Multilevel Propensity Score Analysis |

MultinomialCI | Simultaneous confidence intervals for multinomial proportions according to the method by Sison and Glaz |

multinomRob | Robust Estimation of Overdispersed Multinomial Regression Models |

MultiOrd | Generation of multivariate ordinal variates |

MultiPhen | MultiPhen, a package for the genetic association testing of multiple phenotypes |

multiPIM | Variable Importance Analysis with Population Intervention Models |

multipol | multivariate polynomials |

multisensi | Multivariate Sensitivity Analysis |

multitable | Simultaneous manipulation of multiple arrays of data, with data.list objects |

multitaper | Multitaper spectral analysis tools |

multivator | A multivariate emulator |

multmod | Testing of multiple outcomes |

multxpert | Common Multiple Testing Procedures and Gatekeeping Procedures |

muma | Metabolomics Univariate and Multivariate Analysis |

MuMIn | Multi-model inference |

munfold | Metric Unfolding |

munsell | Munsell colour system |

muRL | Mailmerge using R, LaTeX, and the Web |

muscle | Multiple Sequence Alignment |

muStat | Prentice Rank Sum Test and McNemar Test |

mutatr | Mutable objects for R |

mutoss | Unified multiple testing procedures |

mutossGUI | A graphical user interface for the MuToss Project |

MVA | An Introduction to Applied Multivariate Analysis with R |

mvabund | statistical methods for analysing multivariate abundance data |

MVB | Mutivariate Bernoulli log-linear model |

mvbutils | Workspace organization, code and documentation editing, package prep and editing, etc |

mvc | Multi-View Clustering |

mvinfluence | Influence Measures and Diagnostic Plots for Multivariate Linear Models |

mvmeta | Multivariate meta-analysis and meta-regression |

MVN | Multivariate Normality Tests |

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 |

MVPARTwrap | MVPARTwrap: Additional functionnalities for package mvpart |

MVpower | Give power for a given effect size using multivariate classification methods |

mvProbit | Multivariate Probit Models |

MVR | Mean-Variance Regularization |

mvsf | Shapiro-Francia Multivariate Normality Test |

mvShapiroTest | Generalized Shapiro-Wilk test for multivariate normality |

mvtBinaryEP | Generates Correlated Binary Data |

mvtmeta | Multivariate meta-analysis |

mvtnorm | Multivariate Normal and t Distributions |

mvtsplot | Multivariate Time Series Plot |

mxkssd | Efficient mixed-level k-circulant supersaturated designs |

myepisodes | MyEpisodes RSS/API functions |

Myrrix | Interface to Myrrix. Myrrix is a complete, real-time, scalable clustering and recommender system, evolved from Apache Mahout |

Myrrixjars | External jars required for package Myrrix |

nacopula | Nested Archimedean Copulas |

NADA | Nondetects And Data Analysis for environmental data |

nadiv | Functions to construct (non)additive genetic relatedness matrices and facilitate animal model analyses |

namespace | Provide namespace managment functions not (yet) present in base R |

nanop | tools for nanoparticle simulation and PDF calculation |

NanoStringNorm | Normalize NanoString miRNA and mRNA data |

naturalsort | Natural Ordering |

NBDdirichlet | NBD-Dirichlet model of consumer buying behavior for marketing research |

nbpMatching | functions for non-bipartite optimal matching |

NBPSeq | Negative Binomial Models for RNA-Sequencing Data |

nCal | Nonlinear Calibration |

NCBI2R | NCBI2R-An R package to navigate and annotate genes and SNPs |

ncbit | retrieve and build NBCI taxonomic data |

ncdf | Interface to Unidata netCDF data files |

ncdf4 | Interface to Unidata netCDF (version 4 or earlier) format data files |

nCDunnett | Noncentral Dunnett’s test distribution |

ncf | spatial nonparametric covariance functions |

ncg | Computes the noncentral gamma function |

NCmisc | Miscellaneous general purpose functions |

ncvreg | Regularization paths for SCAD- and MCP-penalized regression models |

ndl | Naive Discriminative Learning |

ndtv | Network Dynamic Temporal Visualizations |

ndvits | NDVI Time series extraction and analysis |

neariso | Near-Isotonic Regression |

NeatMap | Non-clustered heatmap alternatives |

needy | needy |

negenes | Estimating the number of essential genes in a genome |

neldermead | R port of the Scilab neldermead module |

nephro | Biostatistics utilities for nephrology |

NestedCohort | Survival Analysis for Cohorts with Missing Covariate Information |

netClass | netClass: An R Package for Network-Based Biomarker Discovery |

NetCluster | Clustering for networks |

NetComp | Network Generation and Comparison |

NetData | Network Data for McFarland’s SNA R labs |

NetIndices | Estimating network indices, including trophic structure of foodwebs in R |

netmeta | Network meta-analysis with R |

NetPreProc | NetPreProc: Network Pre-Processing and normalization |

nets | Network Estimation for Time Series |

netweavers | NetWeAvers: Weighted Averages for Networks |

network | Classes for Relational Data |

NetworkAnalysis | Statistical inference on populations of weighted or unweighted networks |

networkDynamic | Dynamic Extensions for Network Objects |

networksis | Simulate bipartite graphs with fixed marginals through sequential importance sampling |

networkTomography | Tools for network tomography |

neuralnet | Training of neural networks |

neuroblastoma | Neuroblastoma copy number profiles |

neuRosim | Functions to generate fMRI data including activated data, noise data and resting state data |

nFactors | Parallel Analysis and Non Graphical Solutions to the Cattell Scree Test |

nga | NGA Earthquake Ground Motion Prediction Equations |

ngramr | Retrieve and plot Google n-gram data |

ngspatial | Classes for Spatial Data |

NHEMOtree | Non-hierarchical evolutionary multi-objective tree learner to perform cost-sensitive classification |

nhlscrapr | Compiling the NHL Real Time Scoring System Database for easy use in R |

NHPoisson | Modelling and validation of non homogeneous Poisson processes |

nice | Get or Set UNIX Niceness |

NightDay | Night and Day Boundary Plot Funtion |

Nippon | Japanese utility functions and data |

NISTnls | Nonlinear least squares examples from NIST |

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 |

nlmeU | Datasets and utility functions enhancing functionality of nlme package |

nlmrt | Functions for nonlinear least squares solutions |

nloptr | R interface to NLopt |

nloptwrap | Wrapper for Package nloptr |

NLRoot | searching for the root of equation |

nlrwr | Nonlinear regression with R |

nls2 | Non-linear regression with brute force |

nlsmsn | Fitting nonlinear models with scale mixture of skew-normal distributions |

nlstools | Tools for nonlinear regression diagnostics |

NlsyLinks | Utilities and kinship information for Behavior Genetics and Developmental research using the NLSY |

nlt | A nondecimated lifting transform for signal denoising |

nlts | (non)linear time series analysis |

NMF | Algorithms and framework for Nonnegative Matrix Factorization (NMF) |

NMFN | Non-negative Matrix Factorization |

NMOF | Numerical Methods and Optimization in Finance |

NMRS | NMR Spectroscopy |

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 |

nonparaeff | Nonparametric Methods for Measuring Efficiency and Productivity |

NonpModelCheck | Model Checking and Variable Selection in Nonparametric Regression |

nontarget | Detecting, combining and filtering isotope, adduct and homologue series relations in high-resolution mass spectrometry (HRMS) data |

nopp | Nash Optimal Party Positions |

nor1mix | Normal (1-d) Mixture Models (S3 Classes and Methods) |

nordklimdata1 | Dataset for climate analysis with data from the Nordic region |

norm | Analysis of multivariate normal datasets with missing values |

NormalGamma | Normal-gamma convolution model |

normalp | Package for exponential power distributions (EPD) |

NORMT3 | Evaluates complex erf, erfc, Faddeeva, and density of sum of Gaussian and Student’s t |

normwhn.test | Normality and White Noise Testing |

nortest | Tests for Normality |

nose | nose Package for R |

notifyR | Send push notifications to your smartphone via pushover.net (ACCOUNT REQUIRED!) |

noweb | Noweb system for R |

Nozzle.R1 | Nozzle Reports |

np | Nonparametric kernel smoothing methods for mixed data types |

nparcomp | Perform multiple comparisons and compute simultaneous confidence intervals for the nonparametric relative contrast effects |

nparLD | Nonparametric Analysis of Longitudinal Data in Factorial Experiments |

NPCD | Nonparametric Methods for Cognitive Diagnosis |

NPCirc | Nonparametric Circular Methods |

npde | Normalised prediction distribution errors for nonlinear mixed-effect models |

NPHMC | Sample Size Calculation for the Proportional Hazards Mixture Cure Model |

nplplot | Plotting non-parametric linkage results |

npmlreg | Nonparametric maximum likelihood estimation for random effect models |

NPMPM | tertiary probabilistic model in predictive microbiology for use in food manufacture |

npmv | Nonparametric Comparison of Multivariate Samples |

NPMVCP | Nonparametric Multivariate Change Point Model |

nppbib | Nonparametric Partially-Balanced Incomplete Block Design Analysis |

npRmpi | Parallel nonparametric kernel smoothing methods for mixed data types |

NPsimex | Nonparametric Smoothing for contaminated data using Simulation-Extrapolation |

NRAIA | Data sets from “Nonlinear Regression Analysis and Its Applications” |

nricens | NRI for risk prediction models with time to event and binary response data |

NSA | Post-normalization of total copy numbers |

NScluster | Simulation and Estimation of the Neyman-Scott Type Spatial Cluster Models |

nsga2R | Elitist Non-dominated Sorting Genetic Algorithm based on R |

nsprcomp | Non-Negative Sparse PCA |

nsRFA | Non-supervised Regional Frequency Analysis |

nullabor | Tools for graphical inference |

numbers | Number-theoretic Functions |

numConversion | Test of accuracy of formatting numbers |

numDeriv | Accurate Numerical Derivatives |

nutshell | Data for “R in a Nutshell” |

nutshell.audioscrobbler | Audioscrobbler data for “R in a Nutshell” |

nutshell.bbdb | Baseball Database for “R in a Nutshell” |

nws | R functions for NetWorkSpaces and Sleigh |

OAIHarvester | Harvest Metadata Using OAI-PMH v2.0 |

Oarray | Arrays with arbitrary offsets |

objectProperties | A factory of self-describing properties |

objectSignals | objectSignals |

obliclus | Cluster-based factor rotation |

obliqueRF | Oblique Random Forests from Recursive Linear Model Splits |

oblique.tree | Oblique Trees for Classification Data |

obsSens | Sensitivity analysis for Observational studies |

oc | OC Roll Call Analysis Software |

occ | Estimates PET neuroreceptor occupancies |

oce | Analysis of Oceanographic data |

ODB | Open Document Databases (.odb) management |

odfWeave | Sweave processing of Open Document Format (ODF) files |

odfWeave.survey | Support for odfWeave on the survey package |

ODMconverter | tools to convert ODM files |

odprism | Optimal design and performance of random intercept and slope models |

oem | Orthogonalizing Expectation maximization |

Ohmage | R Client for Mobilize/Andwellness server |

OIdata | Data sets and supplements (OpenIntro) |

OIsurv | Survival analysis supplement to OpenIntro guide |

OjaNP | Multivariate Methods Based on the Oja Median and Related Concepts |

okmesonet | Retrieve Oklahoma Mesonet climatological data |

OligoSpecificitySystem | Oligo Specificity System |

OLScurve | OLS growth curve trajectories |

omd | filter the molecular descriptors for QSAR |

OmicKriging | OmicKriging for Phenotypic Prediction |

oncomodel | Maximum likelihood tree models for oncogenesis |

Oncotree | Estimating oncogenetic trees |

OneHandClapping | Prediction of condition-specific transcription factor interactions |

onemap | Software for constructing genetic maps in experimental crosses: full-sib, RILs, F2 and backcrosses |

OneTwoSamples | Deal with one and two (normal) samples |

onion | octonions and quaternions |

OOmisc | Ozgur-Ozlem Miscellaneous |

OpasnetUtils | Utility functions for dealing with data in Opasnet (www.opasnet.org) environment |

OPDOE | OPtimal Design Of Experiments |

OPE | Outer-product emulator |

opefimor | Option Pricing and Estimation of Financial Models in R |

openair | Tools for the analysis of air pollution data |

OpenCL | Interface allowing R to use OpenCL |

opencpu.demo | OpenCPU Demo apps |

opencpu.encode | opencpu object encoder/decoder |

openintro | OpenIntro data sets and supplemental functions |

OpenMPController | Control number of OpenMP threads dynamically |

openNLP | openNLP Interface |

openNLPmodels.en | openNLP Models for English |

openNLPmodels.es | openNLP Models for Spanish |

OpenRepGrid | Tools to analyse repertory grid data |

OpenStreetMap | Access to open street map raster images |

operators | Additional binary operators for the R language |

operator.tools | Utilities for working with R’s operators |

OPI | Open Perimetry Interface |

opm | Tools for analysing OmniLog(R) Phenotype Microarray data |

opmdata | Example data for analyzing OmniLog(R) Phenotype Microarray data |

oposSOM | Package for analysis and visualization of metagenes |

ops | Optimal Power Space Transformation |

optAUC | Optimal Combinations of Diagnostic Tests Based on AUC |

optBiomarker | Estimation of optimal number of biomarkers for two-group microarray based classifications at a given error tolerance level for various classification rules |

OptimalCutpoints | Computing optimal cutpoints in diagnostic tests |

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 |

OptInterim | Optimal Two and Three Stage Designs for Single-Arm and Two-Arm Randomized Controlled Trials with a Long-Term Binary Endpoint |

optmatch | Functions for optimal matching |

optparse | Command line option parser |

ora | Convenient Tools for Working with Oracle Databases |

orclus | ORCLUS subspace clustering |

ORCME | Order Restricted Clustering for Microarray Experiments |

orcutt | Estimate procedure in case of first order autocorrelation |

orddom | Ordinal Dominance Statistics |

ORDER2PARENT | Estimate parent distributions with data of several order statistics |

orderbook | Orderbook visualization/Charting software |

OrdFacReg | Least squares, logistic, and Cox-regression with ordered predictors |

ordinal | Regression Models for Ordinal Data |

OrdMonReg | Compute least squares estimates of one bounded or two ordered isotonic regression curves |

ordPens | Selection and/or Smoothing of Ordinal Predictors |

OrgMassSpecR | Organic Mass Spectrometry |

ORIClust | Order-restricted Information Criterion-based Clustering Algorithm |

orientlib | Support for orientation data |

orloca | The package deals with Operations Research LOCational Analysis models |

orloca.es | Spanish version of orloca package |

ORMDR | ORMDR |

oro.dicom | Rigorous – DICOM Input / Output |

oro.nifti | Rigorous – NIfTI+ANALYZE+AFNI Input / Output |

oro.pet | Rigorous – Positron Emission Tomography |

orQA | Order Restricted Assessment Of Microarray Titration Experiments |

orsk | Converting Odds Ratio to Relative Risk in Cohort Studies 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 | OpenStreetMap and R |

ouch | Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses |

outbreaker | Bayesian inference of outbreak dynamics based on epidemiological and genetic information |

OutlierDC | Outlier Detection using Quantile Regression for Censored Data |

outliers | Tests for outliers |

OUwie | Analysis of evolutionary rates in an OU framework |

overlap | Estimates of coefficient of overlapping for animal activity patterns |

oz | Plot the Australian coastline and states |

p2distance | Welfare’s Synthetic Indicator |

p3state.msm | Analyzing survival data |

pa | Performance Attribution for Equity Portfolios |

pacbpred | PAC-Bayesian Estimation and Prediction in Sparse Additive Models |

pack | Convert values to/from raw vectors |

packClassic | Toy example of Pack Classic |

packdep | Mapping dependencies among R packages |

packHV | A few useful functions for statisticians |

packS4 | Toy example of S4 package |

pacose | iPACOSE, PACOSE and other methods for covariance selection |

PAGI | The package can identify the dysregulated KEGG pathways based on global influence from the internal effect of pathways and crosstalk between pathways |

pairedCI | Confidence intervals for the ratio of locations and for the ratio of scales of two paired samples |

PairedData | Paired Data Analysis |

pairheatmap | A tool for comparing heatmaps |

PairViz | Visualization using Eulerian tours and Hamiltonian decompositions |

pairwise | Rasch Model Parameters by Pairwise Algorithm |

pairwiseCI | Confidence intervals for two sample comparisons |

palaeoSig | Significance tests for palaeoenvironmental reconstructions |

paleoMAS | Paleoecological Analysis |

paleotree | Paleontological and Phylogenetic Analyses of Evolution |

paleoTS | Analyze paleontological time-series |

PamGeneMixed | Preprocessing and Modeling Kinase Activity Profiles in PamChip Data |

pamm | Power analysis for random effects in mixed models |

pamr | Pam: prediction analysis for microarrays |

pan | Multiple imputation for multivariate panel or clustered data |

pander | An R pandoc writer |

papeR | A toolbox for writing Sweave or other LaTeX-based papers and reports |

parallelize.dynamic | Automate parallelization of function calls by means of dynamic code analysis |

ParamHelpers | Helpers for parameters in black-optimization, tuning and maching learning |

paramlink | Parametric linkage analysis in R |

paran | Horn’s Test of Principal Components/Factors |

parcor | Regularized estimation of partial correlation matrices |

ParDNAcopy | parallel implementation of the “segment” function of package “DNAcopy” |

parfm | Parametric Frailty Models |

parfossil | Parallelized functions for palaeoecological and palaeogeographical analysis |

parma | Portfolio Allocation and Risk Management Applications |

parmigene | Parallel Mutual Information estimation for Gene Network reconstruction |

parspatstat | Parallel spatial statistics |

partDSA | Partitioning using deletion, substitution, and addition moves |

partialOR | Partial Odds Ratio |

partitionMap | Partition Maps |

partitionMetric | Compute a distance metric between two partitions of a set |

partitions | Additive partitions of integers |

partsm | Periodic Autoregressive Time Series Models |

party | A Laboratory for Recursive Partytioning |

partykit | A Toolkit for Recursive Partytioning |

parviol | Parviol |

PAS | Polygenic Analysis System (PAS) |

pass | Prediction and Stability Selection of Tuning Parameters |

pastecs | Package for Analysis of Space-Time Ecological Series |

pastis | Phylogenetic Assembly with Soft Taxonomic Inferences |

PASWR | PROBABILITY and STATISTICS WITH R |

patchDVI | Package to patch .dvi files |

patchPlot | Scatterplots of image patches |

pathClass | Classification using biological pathways as prior knowledge |

pathdiagram | Basic functions for drawing path diagrams |

pathmox | Segmentation Trees in Partial Least Squares Path Modeling |

PatternClass | Class-focused pattern metric comparisons using simulation |

pavo | Perceptual analysis, visualization and organization of spectral color data in R |

PAWL | Implementation of the PAWL algorithm |

pbapply | Adding Progress Bar to ‘*apply’ Functions |

pbatR | P2BAT |

pbdBASE | Programming with Big Data – Base Wrappers for Distributed Matrices |

pbdDEMO | Programming with Big Data – Demonstrations of pbd Packages |

pbdDMAT | Programming with Big Data – Distributed Matrix Methods |

pbdMPI | Programming with Big Data – Interface to MPI |

pbdNCDF4 | Programming with Big Data – Interface to Parallel Unidata NetCDF4 Format Data Files |

pbdPROF | Programming with Big Data — MPI Profiling Tools |

pbdSLAP | Programming with Big Data – Scalable Linear Algebra Packages |

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” |

pbivnorm | Vectorized Bivariate Normal CDF |

pbkrtest | Parametric bootstrap and Kenward Roger based methods for mixed model comparison |

pbs | Periodic B Splines |

PBSadmb | ADMB for R Using Scripts or GUI |

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 |

pca3d | Three dimensional PCA plots |

pcaL1 | Three L1-Norm PCA Methods |

pcalg | Estimation of CPDAG/PAG and causal inference using the IDA algorithm |

pcaPP | Robust PCA by Projection Pursuit |

pcenum | Permutations and Combinations Enumeration |

PCICt | Implementation of POSIXct work-alike for 365 and 360 day calendars |

PCIT | PCIT algorithm – Partial Correlation Coefficient with Information Theory |

PCovR | Principal Covariates Regression |

pcrcoal | A package implementing the coalescent approach to PCR simulation developed by Weiss and von Haeseler (NAR, 1997) |

pcrsim | Simulation of the forensic DNA process |

PCS | Calculate the probability of correct selection (PCS) |

pcse | Panel-Corrected Standard Error Estimation in R |

pcurve | Principal curve analysis |

pdc | Permutation Distribution Clustering |

pdfCluster | Cluster analysis via nonparametric density estimation |

pdist | Partitioned Distance Function |

PDSCE | Positive definite sparse covariance estimators |

Peak2Trough | Estimation of the peak-to-trough ratio of a seasonal variation component |

Peaks | Peaks |

pear | Package for Periodic Autoregression Analysis |

pearson7 | Maximum Likelihood Inference for the Pearson VII Distribution with Shape Parameter 3/2 |

PearsonDS | Pearson Distribution System |

PearsonICA | Independent component analysis using score functions from the Pearson system |

pec | Prediction Error Curves for Survival Models |

pedantics | Functions to facilitate power and sensitivity analyses for genetic studies of natural populations |

pedigree | Pedigree functions |

pedigreemm | Pedigree-based mixed-effects models |

pegas | Population and Evolutionary Genetics Analysis System |

PEIP | Functions for Aster Book on Inverse Theory |

penalized | L1 (lasso and fused 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 |

penDvine | Flexible Pair-Copula Estimation in D-vines using Bivariate Penalized Splines |

PenLNM | Group l1 penalized logistic normal multinomial (LNM) regression model |

pensim | Simulation of high-dimensional data and parallelized repeated penalized regression |

peperr | Parallelised Estimation of Prediction Error |

peplib | Peptide Library Analysis Methods |

pequod | Moderated regression package |

perARMA | Package for Periodic Time Series Analysis |

PerfMeas | PerfMeas: Performance Measures for ranking and classification tasks |

PerformanceAnalytics | Econometric tools for performance and risk analysis |

perm | Exact or Asymptotic permutation tests |

PermAlgo | Permutational algorithm to simulate survival data |

permGPU | permPGU: Using GPUs in Statistical Genomics |

permtest | Permutation test to compare variability within and distance between two groups |

permute | Functions for generating restricted permutations of data |

PERregress | Regression Functions and Datasets |

perry | Resampling-based prediction error estimation for regression models |

persiandictionary | English to Persian dictionary |

perturb | Tools for evaluating collinearity |

pesticides | Analysis of single serving and composite pesticide residue measurements |

PET | Simulation and Reconstruction of PET Images |

PF | Functions related to prevented fraction |

pfa | Estimates False Discovery Proportion Under Arbitrary Covariance Dependence |

pgam | Poisson-Gamma Additive Models |

pgirmess | Data analysis in ecology |

pglm | panel generalized linear model |

pGLS | Generalized Least Square in comparative Phylogenetics |

pgmm | Parsimonious Gaussian mixture models |

pgnorm | The p-generalized normal distribution |

pgs | Precision of Geometric Sampling |

phangorn | Phylogenetic analysis in R |

PhaseType | Inference for Phase-type Distributions |

phcfM | Modelling anthropogenic deforestation |

pheatmap | Pretty Heatmaps |

phenex | Auxiliary functions for phenological data analysis |

pheno | Auxiliary functions for phenological data analysis |

pheno2geno | Pheno2Geno – Generating genetic markers and maps from molecular phenotypes |

phenology | Tools to manage a parametric function that describes phenology |

phia | Post-Hoc Interaction Analysis |

phmm | Proportional Hazards Mixed-effects Model (PHMM) |

phom | Persistent Homology in R |

phonR | R tools for phoneticians and phonologists |

phonTools | Functions for phonetics in R |

phtt | Panel Data Analysis with Heterogeneous Time Trends |

PhViD | PhViD: an R package for PharmacoVigilance signal Detection |

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 Modeling |

phylolm | Phylogenetic Linear Regression |

phylosim | R package for simulating biological sequence evolution |

phylotools | Phylogenetic tools for Eco-phylogenetics |

phyloTop | Phylogenetic Tree Topological Properties Evaluator |

PhysicalActivity | Process Physical Activity Accelerometer Data |

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 |

PIN | Estimates the parameters of a trading-tree model for the computation of the probability of informed trading |

PIPS | Predicted Interval Plots |

pitchRx | Tools for Collecting and Visualizing Major League Baseball PITCHfx Data |

PivotalR | R front-end to PostgreSQL and Pivotal (Greenplum) database, wrapper for MADlib |

pixmap | Bitmap Images (“Pixel Maps”) |

PK | Basic Non-Compartmental Pharmacokinetics |

PKfit | A Data Analysis Tool for Pharmacokinetics |

pkgmaker | Package development utilities |

PKgraph | Model diagnostics for population pharmacokinetic models |

pkgutils | pkgutils – Utilities for creating R packages |

PKI | Public Key Infrastucture for R based on the X.509 standard |

PKmodelFinder | Software for Pharmacokinetic model |

PKPDmodels | Pharmacokinetic/pharmacodynamic models |

PKreport | A reporting pipeline for checking population pharmacokinetic model assumption |

pks | Probabilistic Knowledge Structures |

PKtools | unified computational interfaces for pop PK |

plan | Tools for project planning |

planar | Multilayer optics |

planor | Generation of regular factorial designs |

PlayerRatings | Dynamic Updating Methods For Player Ratings Estimation |

playitbyr | Representing and exploring data through sound |

playwith | A GUI for interactive plots using GTK+ |

plfm | Probabilistic latent feature analysis of two-way two-mode frequency data |

plgp | Particle Learning of Gaussian Processes |

plink | IRT Separate Calibration Linking Methods |

PLIS | Multiplicity control using Pooled LIS statistic |

plm | Linear Models for Panel Data |

plmDE | Additive partially linear models for differential gene expression analysis |

plmm | Partially Linear Mixed Effects Model |

pln | Polytomous logit-normit (graded logistic) model estimation |

plotGoogleMaps | Plot SP or SPT(STDIF,STFDF) data as HTML map mashup over Google Maps |

plotKML | Visualization of spatial and spatio-temporal objects in Google Earth |

plotmo | Plot a model’s response while varying the values of the predictors |

plotpc | Plot principal component histograms around a scatter plot |

PlotRegionHighlighter | Creates an envelope that surrounds a set of points plotted in a two dimensional space |

plotrix | Various plotting functions |

plotSEMM | Graphing nonlinear latent variable interactions in SEMM |

PL.popN | Population Size Estimation |

plRasch | Log Linear by Linear Asscociation models |

PLRModels | Statistical inference in partial linear regression models |

pls | Partial Least Squares and Principal Component regression |

plsdepot | Partial Least Squares (PLS) Data Analysis Methods |

plsdof | Degrees of Freedom and Statistical Inference for Partial Least Squares Regression |

plsgenomics | PLS analyses for genomics |

plspm | Tools for Partial Least Squares Path Modeling |

plsRbeta | Partial least squares Regression for beta regression models |

plsRcox | Partial least squares Regression for Cox models and related techniques |

plsRglm | Partial least squares Regression for generalized linear models |

plugdensity | Plug-in Kernel Density Estimation |

plumbr | Mutable and dynamic data models |

plus | Penalized Linear Unbiased Selection |

plyr | Tools for splitting, applying and combining data |

PMA | Penalized Multivariate Analysis |

pmclust | Parallel Model-Based Clustering |

pmg | Poor Man’s GUI |

pmlr | Penalized Multinomial Logistic Regression |

pmml | Generate PMML for various models |

pmmlTransformations | Transforms input data from a PMML perspective |

pmr | Probability Models for Ranking Data |

png | Read and write PNG images |

pnmtrem | Probit-Normal Marginalized Transition Random Effects Models |

pnn | Probabilistic neural networks |

pocrm | Dose-finding in drug combination Phase I trials using the partial order continual reassessment method (PO-CRM) |

POET | Principal Orthogonal ComplEment Thresholding (POET) method |

poibin | The Poisson Binomial Distribution |

PoiClaClu | Classification and clustering of sequencing data based on a Poisson model |

poilog | Poisson lognormal and bivariate Poisson lognormal distribution |

poisson.glm.mix | Fit high dimensional mixtures of Poisson GLMs |

PoissonSeq | Significance analysis of sequencing data based on a Poisson log linear model |

poistweedie | Poisson-Tweedie exponential family models |

poLCA | Polytomous variable Latent Class Analysis |

polspline | Polynomial spline routines |

polyapost | Simulating from the Polya posterior |

polycor | Polychoric and Polyserial Correlations |

polyCub | Cubature over Polygonal Domains |

polynom | A collection of functions to implement a class for univariate polynomial manipulations |

PolynomF | Polynomials in R |

polysat | Tools for Polyploid Microsatellite Analysis |

polySegratio | Simulate and test marker dosage for dominant markers in autopolyploids |

polySegratioMM | Bayesian mixture models for marker dosage in autopolyploids |

polytomous | Polytomous logistic regression for fixed and mixed effects |

polywog | Bootstrapped Basis Regression with Oracle Model Selection |

pom | POM – Patch Occupancy Models |

Pomic | Pattern Oriented Modelling Information Criterion |

PoMoS | Polynomial (ordinary differential equation) Model Search |

pomp | Statistical inference for partially observed Markov processes |

pooh | Partial Orders and Relations |

popbio | Construction and analysis of matrix population models |

popdemo | Provides Tools For Demographic Modelling Using Projection Matrices |

popgen | Statistical and Population Genetics |

PopGenKit | Useful functions for (batch) file conversion and data resampling in microsatellite datasets |

PopGenome | A swiss army knife for population genetic & genomic analysis |

PopGenReport | PopGen: A simple way to analyse and visualize population genetic data |

popgraph | This is an R package that constructs and manipulates population graphs |

popPK | Summary of Population Pharmacokinetic Analysis |

poppr | an R package for genetic analysis of populations with mixed reproduction |

popReconstruct | Reconstruct population counts, fertility, mortality and migration rates of human populations of the recent past |

portes | Portmanteau Tests for Univariate and Multivariate Time Series Models |

portfolio | Analysing equity portfolios |

portfolioSim | Framework for simulating equity portfolio strategies |

postCP | A package to estimate posterior probabilities and perform model selection in change-point models using constrained HMM |

postgwas | GWAS Post-Processing Utilities |

POT | Generalized Pareto Distribution and Peaks Over Threshold |

potts | Markov Chain Monte Carlo for Potts Models |

PottsUtils | Utility Functions of the Potts Models |

powell | Powell’s UObyQA algorithm |

powerGWASinteraction | Power Calculations for Interactions for GWAS |

poweRlaw | Fitting heavy tailed distributions: the poweRlaw package |

powerMediation | Power/Sample size calculation for mediation analysis |

powerpkg | Power analyses for the affected sib pair and the TDT design |

powerSurvEpi | Power and sample size calculation for survival analysis of epidemiological studies |

PowerTOST | Power and Sample size based on two one-sided t-tests (TOST) for (bio)equivalence studies |

PP | Person Parameter estimation |

ppcor | Partial and Semi-partial (Part) correlation |

ppiPre | Predict protein-protein interactions based on functional and topological similarities |

ppls | Penalized Partial Least Squares |

ppMeasures | Point pattern distances and prototypes |

pps | Functions for PPS sampling |

ppstat | Point Process Statistics |

PPtree | Projection pursuit classification tree |

prabclus | Functions for clustering of presence-absence, abundance and multilocus genetic data |

pracma | Practical Numerical Math Functions |

PracTools | Tools for Designing and Weighting Survey Samples |

pragma | Provides a pragma / directive / keyword syntax for R |

PredictABEL | Assessment of risk prediction models |

PredictiveRegression | Prediction Intervals for Three Basic Statistical Models |

predmixcor | Classification rule based on Bayesian mixture models with feature selection bias corrected |

prefmod | Utilities to fit paired comparison models for preferences |

PReMiuM | Dirichlet Process Bayesian Clustering, Profile Regression |

PresenceAbsence | Presence-Absence Model Evaluation |

PResiduals | Probability scale residuals and residual correlations |

prettyGraphs | publication-quality graphics |

prettyR | Pretty descriptive stats |

prevalence | The prevalence package |

prevR | Estimating regional trends of a prevalence from a DHS |

prim | Patient Rule Induction Method (PRIM) |

primer | Functions and data for A Primer of Ecology with R |

princurve | Fits a Principal Curve in Arbitrary Dimension |

PRISMA | Protocol Inspection and State Machine Analysis |

PrivateLR | Differentially private regularized logistic regression |

prLogistic | Estimation of Prevalence Ratios using Logistic Models |

prob | Elementary Probability on Finite Sample Spaces |

probemapper | Connects to QBRC’s ProbeMapper platform |

ProbForecastGOP | Probabilistic weather forecast using the GOP method |

probsvm | probsvm: Class probability estimation for Support Vector Machines |

pROC | display and analyze ROC curves |

processdata | Process Data |

ProDenICA | Product Density Estimation for ICA using tilted Gaussian density estimates |

prodlim | Product Limit Estimation for event history and survival analysis |

profanal | Implements profile analysis described in Davison & Davenport (2002) |

PROFANCY | The package can prioritize candidate disease metabolites based on global functional relationships between metabolites in the context of metabolic pathways |

profdpm | Profile Dirichlet Process Mixtures |

ProfessR | Grades Setting and Exam Maker |

ProfileLikelihood | Profile Likelihood for a Parameter in Commonly Used Statistical Models |

profileModel | Tools for profiling inference functions for various model classes |

profr | An alternative display for profiling information |

proftools | Profile Output Processing Tools for R |

ProgGUIinR | support package for “Programming Graphical User Interfaces in R” |

proj4 | A simple interface to the PROJ.4 cartographic projections library |

ProjectTemplate | Automates the creation of new statistical analysis projects |

PropCIs | Various confidence interval methods for proportions |

PropClust | Propensity Clustering and Decomposition |

PropScrRand | Propensity score methods for assigning treatment in randomized trials |

proteomicdesign | Optimization of a multi-stage proteomic study |

protiq | Protein (identification and) quantification based on peptide evidence |

proto | Prototype object-based programming |

protoclass | Interpretable classification with prototypes |

protoclust | Hierarchical clustering with prototypes |

PROTOLIDAR | PRocess TOol LIdar DAta in R |

protr | Protein Sequence Feature Extraction with R |

protViz | Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics |

proxy | Distance and Similarity Measures |

PSAgraphics | Propensity Score Analysis Graphics |

psbcGroup | Penalized semi-parametric Bayesian Cox (PSBC) models with shrinkage and grouping priors |

PSCBS | Analysis of Parent-Specific DNA Copy Numbers |

pscl | Political Science Computational Laboratory, Stanford University |

psd | Adaptive, sine-multitaper power spectral density estimation |

pseudo | Pseudo – observations |

psgp | Projected Spatial Gaussian Process (psgp) methods |

psidR | Build panel data sets from PSID raw data |

PSM | Non-Linear Mixed-Effects modelling using Stochastic Differential Equations |

pso | Particle Swarm Optimization |

pspearman | Spearman’s rank correlation test |

pspline | Penalized Smoothing Splines |

PST | Probabilistic Suffix Trees |

psy | Various procedures used in psychometry |

psych | Procedures for Psychological, Psychometric, and Personality Research |

psychometric | Applied Psychometric Theory |

psychomix | Psychometric Mixture Models |

psychotools | Infrastructure for Psychometric Modeling |

psychotree | Recursive Partitioning Based on Psychometric Models |

psyphy | Functions for analyzing psychophysical data in R |

psytabs | Produce well-formatted tables for psychological research |

PTAk | Principal Tensor Analysis on k modes |

ptinpoly | Point-In-Polyhedron Test (2D and 3D) |

PtProcess | Time Dependent Point Process Modelling |

ptw | Parametric Time Warping |

pumilioR | Pumilio in R |

PurBayes | Bayesian Estimation of Tumor Purity and Clonality |

PVAClone | Population Viability Analysis with Data Cloning |

pvar | p-variation |

pvclass | P-values for Classification |

pvclust | Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling |

PVR | Computes phylogenetic eigenvectors regression (PVR) and phylogenetic signal-representation curve (PSR) (with null and Brownian expectations) |

pvsR | An R package to interact with the Project Vote Smart API for scientific research |

pwr | Basic functions for power analysis |

PwrGSD | Power in a Group Sequential Design |

pwt | Penn World Table (Versions 5.6, 6.x, 7.x) |

pwt8 | Penn World Table (Version 8.0) |

pxR | PC-Axis with R |

pycno | Pycnophylactic Interpolation |

pyramid | Functions to draw population pyramid |

qat | Quality Assurance Toolkit |

QCA | Qualitative Comparative Analysis |

QCA3 | Yet another package for Qualitative Comparative Analysis |

QCAGUI | QCA Graphical User Interface |

qcc | Quality Control Charts |

qdap | Bridging the gap between qualitative data and quantitative analysis |

qfa | Tools for modelling the growth dynamics of arrays of large numbers of colonies and performing quantitative fitness analysis (QFA) |

qgraph | Network representations of relationships in data |

qLearn | Estimation and inference for Q-learning |

qlspack | Quasi Least Square Package |

QLSpline | QLSpline |

qmap | Statistical transformations for post-processing climate model output |

qmrparser | Parser combinator in R |

qp | q-order partial correlation graph search algorithm |

qpcR | Modelling and analysis of real-time PCR data |

qPCR.CT | qPCR data analysis and plot package |

qrfactor | Simultaneous simulation of Q and R mode factor analyses with Spatial data |

QRM | Provides R-language code to examine Quantitative Risk Management concepts |

qrnn | Quantile regression neural network |

QSARdata | Quantitative Structure Activity Relationship (QSAR) Data Sets |

QT | QT Knowledge Management System |

qtbase | Interface between R and Qt |

qtl | Tools for analyzing QTL experiments |

qtlbim | QTL Bayesian Interval Mapping |

qtlbook | Datasets for the R/qtl book |

qtlDesign | Design of QTL experiments |

qtlhot | Inference for QTL Hotspots |

qtlmt | Tools for mapping multiple complex traits |

qtlnet | Causal Inference of QTL Networks |

QTLRel | Tools for mapping of quantitative traits of genetically related individuals and calculating identity coefficients from a pedigree |

qtpaint | Qt-based painting infrastructure |

qtutils | Miscellaneous Qt-based utilities |

QuACN | QuACN: Quantitative Analysis of Complex Networks |

quadprog | Functions to solve Quadratic Programming Problems |

quadrupen | Sparsity by Worst-Case Quadratic Penalties |

qualityTools | Statistical Methods for Quality Science |

qualV | Qualitative Validation Methods |

Quandl | Quandl Data Connection |

quantchem | Quantitative chemical analysis: calibration and evaluation of results |

quantmod | Quantitative Financial Modelling Framework |

QuantPsyc | Quantitative Psychology Tools |

quantreg | Quantile Regression |

quantregForest | Quantile Regression Forests |

quantregGrowth | Growth charts via regression quantiles |

quantspec | Quantile-based Spectral Analysis of Time Series |

QuasiSeq | QuasiSeq |

questionr | Functions to make surveys processing easier |

queueing | Analysis of Queueing Networks and Models |

QUIC | Regularized sparse inverse covariance matrix estimation |

qvcalc | Quasi variances for factor effects in statistical models |

QZ | Generalized Eigenvalues and QZ Decomposition |

R0 | Estimation of R0 and real-time reproduction number from epidemics |

R1magic | Compressive Sampling: Sparse signal recovery utilities |

R2admb | ADMB to R interface functions |

R2BayesX | Estimate Structured Additive Regression Models with BayesX |

R2Cuba | Multidimensional Numerical Integration |

r2dRue | 2d Rain Use Efficience model |

R2G2 | Converting R CRAN outputs into Google Earth |

R2HTML | HTML exportation for R objects |

R2jags | A Package for Running jags from R |

r2lh | R to LaTeX and HTML |

R2MLwiN | Running MLwiN from within R |

R2OpenBUGS | Running OpenBUGS from R |

R2PPT | Simple R Interface to Microsoft PowerPoint using rcom or RDCOMClient |

R2STATS | A GTK GUI for fitting and comparing GLM and GLMM in R |

r2stl | r2stl, R package for visualizing data using a 3D printer |

R2SWF | Convert R Graphics to Flash Animations |

R2wd | Write MS-Word documents from R |

R2WinBUGS | Running WinBUGS and OpenBUGS from R / S-PLUS |

R330 | An R package for Stats 330 |

r4ss | R code for Stock Synthesis |

race | Racing methods for the selection of the best |

RAD | Fit RAD models to biological data |

RadialPlotter | Package for statistical age models analysis in optically stimulated luminescence dating |

RadioSonde | Tools for plotting skew-T diagrams and wind profiles |

RadOnc | Analytical Tools for Radiation Oncology |

RAFM | Admixture F-model |

rainbow | Rainbow plots, bagplots and boxplots for functional data |

rAltmetric | Retrieves altmerics data for any published paper from altmetrics.com |

Rambo | The Random Subgraph Model |

RAMpath | Structural Equation Modeling using RAM Notation |

ramps | Bayesian Geostatistical Modeling with RAMPS |

randaes | Random number generator based on AES cipher |

random | True random numbers using random.org |

RandomFields | Simulation and Analysis of Random Fields |

randomForest | Breiman and Cutler’s random forests for classification and regression |

randomForestSRC | Random Forests for Survival, Regression and Classification (RF-SRC) |

randomGLM | Random General Linear Model Prediction |

randomizeBE | Function to create a random list for crossover studies |

randomLCA | Random Effects Latent Class Analysis |

randomNames | Random name generating function and data set |

random.polychor.pa | A Parallel Analysis With Polychoric Correlation Matrices |

randomSurvivalForest | Random Survival Forests |

randtoolbox | toolbox for pseudo and quasi random number generation and RNG tests |

RandVar | Implementation of random variables |

rangeMapper | A platform for the study of macroecology of life history traits |

RankAggreg | Weighted rank aggregation |

rankhazard | Rank-hazard plots |

RANN | Fast Nearest Neighbour Search (wraps Arya and Mount’s ANN library) |

RAP | Reversal Association Pattern |

RAppArmor | RAppArmor |

rapport | A report templating system |

RArcInfo | Functions to import data from Arc/Info V7.x binary coverages |

Rarity | Calculation of rarity indices for species and assemblages of species |

RaschSampler | Rasch Sampler |

rasclass | Supervised Raster Image Classification |

raster | raster: Geographic data analysis and modeling |

rasterVis | Visualization methods for the raster package |

rateratio.test | Exact rate ratio test |

rationalfun | Manipulation of Rational Functions |

RAtmosphere | Standard Atmosperic profiles |

rattle | Graphical user interface for data mining in R |

rAverage | Parameter estimation for the averaging model of Information Integration Theory |

rawFasta | Memory efficient handling of FASTA sequence files, a pure R implementation |

rbamtools | Reading, manipulation and writing BAM (Binary alignment) files |

rbefdata | BEFdata R package |

rbenchmark | Benchmarking routine for R |

RBerkeley | R API to Oracle Berkeley DB |

rBeta2009 | The Beta Random Number and Dirichlet Random Vector Generating Functions |

RbioRXN | RbioRXN – process Rhea and MetaCyc (BioCyc, EcoCyc) biochemical reaction data |

rbmn | Handling Linear Gaussian Bayesian Networks |

rbounds | Perform Rosenbaum bounds sensitivity tests for matched and unmatched data |

rbugs | Fusing R and OpenBugs and Beyond |

rbundler | Rbundler manages an application’s dependencies systematically and repeatedly |

RC | Reproducible Computing |

R.cache | Fast and light-weight caching (memoization) of objects and results to speed up computations |

RCALI | Calculation of the Integrated Flow of Particles between Polygons |

Rcapture | Loglinear Models for Capture-Recapture Experiments |

rCarto | This package builds maps with a full cartographic layout |

RCassandra | R/Cassandra interface |

rcdd | rcdd (Computational Geometry) |

rcdk | rcdk – Interface to the CDK Libraries |

rcdklibs | rcdklib – CDK libraries packaged for R |

Rcell | Microscopy Based Cytometry Data Analysis Package |

Rcgmin | Conjugate gradient minimization of nonlinear functions with box constraints |

rChoiceDialogs | rChoiceDialogs collection |

RCircos | Circos 2D Track Plot |

RClimMAWGEN | RClimMAWGEN (R Climate Index Multi-site Auto-regressive Weather GENeretor): a package to generate time series of climate indices from RMAWGEN generations |

rCMA | CMA-ES R-to-Java interface |

Rcmdr | R Commander |

RcmdrPlugin.BCA | Rcmdr Plug-In for Business and Customer Analytics |

RcmdrPlugin.coin | Rcmdr Coin Plug-In |

RcmdrPlugin.depthTools | R commander Depth Tools Plug-In |

RcmdrPlugin.doBy | Rcmdr doBy Plug-In |

RcmdrPlugin.DoE | R Commander Plugin for (industrial) Design of Experiments |

RcmdrPlugin.doex | Rcmdr plugin for Stat 4309 course |

RcmdrPlugin.EACSPIR | Plugin de R-Commander para el manual EACSPIR |

RcmdrPlugin.EBM | Rcmdr Evidence Based Medicine Plug-In package |

RcmdrPlugin.epack | Rcmdr plugin for time series |

RcmdrPlugin.EZR | R Commander Plug-in for the EZR (Easy R) Package |

RcmdrPlugin.HH | Rcmdr support for the HH package |

RcmdrPlugin.IPSUR | An IPSUR Plugin for the R Commander |

RcmdrPlugin.KMggplot2 | An Rcmdr Plug-In for Kaplan-Meier Plots and Other Plots by Using the ggplot2 Package |

RcmdrPlugin.lfstat | Rcmdr Plug-In for low flow analysis |

RcmdrPlugin.MA | Graphical User Interface for Conducting Meta-Analyses in R |

RcmdrPlugin.mosaic | Adds menu items to produce mosaic plots and assoc plots to Rcmdr |

RcmdrPlugin.MPAStats | R Commander Plug-in for MPA Statistics |

RcmdrPlugin.orloca | orloca Rcmdr Plug-in |

RcmdrPlugin.plotByGroup | Rcmdr plots by group using lattice |

RcmdrPlugin.qcc | Rcmdr qcc Plug-In |

RcmdrPlugin.qual | Rcmdr plugin for quality control course |

RcmdrPlugin.sampling | Tools for sampling in Official Statistical Surveys |

RcmdrPlugin.SCDA | Rcmdr plugin for designing and analyzing single-case experiments |

RcmdrPlugin.seeg | Rcmdr Plugin for seeg |

RcmdrPlugin.SLC | SLC Rcmdr Plug-in |

RcmdrPlugin.SM | Rcmdr Sport Management Plug-In |

RcmdrPlugin.StatisticalURV | Statistical URV Rcmdr Plug-In |

RcmdrPlugin.survival | R Commander Plug-in for the survival Package |

RcmdrPlugin.TeachingDemos | Rcmdr Teaching Demos Plug-In |

RcmdrPlugin.temis | Graphical Integrated Text Mining Solution |

RcmdrPlugin.UCA | UCA Rcmdr Plug-in |

Rcolombos | Interface to Colombos Compendia using the exposed REST API |

RColorBrewer | ColorBrewer palettes |

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 |

rcppbugs | R binding for cppbugs |

RcppClassic | Deprecated ‘classic’ Rcpp API |

RcppClassicExamples | Examples using RcppClassic to interface R and C++ |

RcppCNPy | Rcpp bindings for NumPy files |

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 |

RcppOctave | Seamless Interface to Octave – and Matlab |

RcppProgress | An interruptible progress bar with OpenMP support for c++ in R packages |

RcppRoll | Fast rolling functions through Rcpp and RcppArmadillo |

RcppSMC | Rcpp bindings for Sequential Monte Carlo |

RcppXts | Interface the xts API via Rcpp |

rcqp | Interface to the Corpus Query Protocol |

Rcsdp | R interface to the CSDP semidefinite programming library |

rCUR | CUR decomposition package |

RCurl | General network (HTTP/FTP/…) client interface for R |

Rd2roxygen | Convert Rd to roxygen documentation and utilities to improve documentation |

rda | Shrunken Centroids Regularized Discriminant Analysis |

rdatamarket | Data access API for DataMarket.com |

rdd | Regression Discontinuity Estimation |

rdetools | Relevant Dimension Estimation (RDE) in Feature Spaces |

R.devices | Unified handling of graphics devices |

RDIDQ | It perform Quality check on data |

RDieHarder | R interface to the dieharder RNG test suite |

Rdistance | Distance sampling analyses |

rDNA | R Bindings for the Discourse Network Analyzer |

Rdpack | Update and manipulate Rd documentation objects |

Rdrools | A rules engine for R based on Drools |

Rdroolsjars | Rdrools jars |

rdryad | Dryad API interface |

RDS | R Functions for Respondent-Driven Sampling |

Rdsm | Threads Environment for R |

RDSTK | An R wrapper for the Data Science Toolkit API |

rdyncall | Improved Foreign Function Interface (FFI) and Dynamic Bindings to C Libraries (e.g. OpenGL) |

ReacTran | Reactive transport modelling in 1D, 2D and 3D |

readbitmap | Read bitmap images (BMP,JPEG,PNG) without external dependencies |

readBrukerFlexData | Reads mass spectrometry data in Bruker *flex format |

Read.isi | Automated access to old World Fertility Survey data saved in fixed-width format based on ISI-formatted codebooks |

readMETEO | Weather Data Download from WWW.METEOGALICIA.COM |

readMLData | Reading machine learning benchmark data sets from different sources in their original format |

readMzXmlData | Reads mass spectrometry data in mzXML format |

reams | Resampling-Based Adaptive Model Selection |

Rearrangement | Monotonize point and interval functional estimates by rearrangement |

REBayes | Empirical Bayes Estimation and Inference in R |

rebird | Interface to eBird |

rebmix | The Rebmix Package |

reccsim | Simulation of Rare Events Case-Control Studies |

ReCiPa | Redundancy Control in Pathways databases |

recluster | Ordination methods for the analysis of beta-diversity indices |

recommenderlab | Lab for Developing and Testing Recommender Algorithms |

recommenderlabBX | Book-Crossing Dataset (BX) for recommenderlab |

recommenderlabJester | Jester Dataset for recommenderlab |

RecordLinkage | Record Linkage in R |

Records | Record Values and Record Times |

REEMtree | Regression Trees with Random Effects for Longitudinal (Panel) Data |

ref | References for R |

refGenome | Managing data from Ensembl and UCSC genome browsers |

refund | refund: Regression with Functional Data |

REGENT | REGENT: Risk Estimation for Genetic and Environmental Traits |

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 |

rehh | Searching for footprints of selection using Haplotype Homozygosity based tests |

rela | Item Analysis Package with Standard Errors |

relaimpo | Relative importance of regressors in linear models |

relations | Data Structures and Algorithms for Relations |

RelativeRisk | Relative Risk |

relax | relax – R Editor for Literate Analysis and lateX |

relaxnet | Relaxation of glmnet models (as in relaxed lasso, Meinshausen 2007) |

relaxo | Relaxed Lasso |

reldist | Relative Distribution Methods |

relevent | Relational Event Models |

Reliability | Functions for estimating parameters in software reliability models |

ReliabilityTheory | Tools for structural reliability analysis |

reliaR | Package for some probability distributions |

relimp | Relative Contribution of Effects in a Regression Model |

relSim | Relative Simulator |

relsurv | Relative survival |

remix | Remix your data |

rEMM | Extensible Markov Model (EMM) for Data Stream Clustering in R |

remMap | Regularized Multivariate Regression for Identifying Master Predictors |

Renext | Renewal method for extreme values extrapolation |

RenextGUI | GUI for Renext |

rentrez | Entrez in R |

Reol | R interface to the Encyclopedia of Life |

RepeatedHighDim | Detection of global group effect in microarrays data |

repmis | A collection of miscellaneous tools for reproducible research with R |

repolr | Repeated measures proportional odds logistic regression |

reportr | A general message and error reporting system |

reports | An R package to assist in the workflow of writing academic articles and other reports |

reporttools | Generate LaTeX tables of descriptive statistics |

REPPlab | R interface to EPP-lab, a Java program for exploratory projection pursuit |

represent | Determine the representativity of two multidimensional data sets |

REQS | R/EQS Interface |

reshape | Flexibly reshape data |

reshape2 | Flexibly reshape data: a reboot of the reshape package |

reshapeGUI | A GUI for the reshape2 and plyr packages |

ResistorArray | electrical properties of resistor networks |

ResourceSelection | Resource Selection (Probability) Functions for Use-Availability Data |

restlos | Robust estimation of location and scatter |

restorepoint | Debugging with restore points |

retimes | Reaction Time Analysis |

review | Manage Review Logs |

reweight | Adjustment of Survey Respondent Weights |

rexpokit | R wrappers for EXPOKIT; other matrix functions |

rFerns | Random ferns classifier |

RFGLS | a family GWAS data-analysis tool that uses a generalized least squares method to perform single-marker association analysis |

rfigshare | an R interface to figshare.com |

R.filesets | Easy handling of and access to files organized in structured directories |

rfishbase | R Interface to FishBASE |

rfisheries | R interface for fisheries data |

Rfit | Rank Estimation for Linear Models |

RFLPtools | Tools to analyse RFLP data |

RfmriVC | Varying stimulus coefficient fMRI models in R |

RFOC | Graphics for Spherical Distributions and Earthquake Focal Mechanisms |

RForcecom | RForcecom provides the connection to Force.com and Salesforce.com from R |

rforensicbatwing | BATWING for calculating forensic trace-suspect match probabilities |

rfPermute | Estimate permutation p-values for Random Forest importance metrics |

rgam | Robust Generalized Additive Model |

rGammaGamma | Gamma convolutions for methylation array background correction |

rgbif | Interface to the Global Biodiversity Information Facility API methods |

Rgbp | Bayesian Hierarchical Modeling and Frequentist Method Check |

RGCCA | RGCCA and Sparse GCCA for multi-block data analysis |

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) |

rgexf | An R package to build GEXF graph files |

rggobi | Interface between R and GGobi |

RghcnV3 | Global Historical Climate Network Version 3 |

RGIFT | Create quizzes in GIFT Format |

rgl | 3D visualization device system (OpenGL) |

Rglpk | R/GNU Linear Programming Kit Interface |

Rgnuplot | Rgnuplot, R interface for gnuplot |

RgoogleMaps | Overlays on Google map tiles in R |

rgp | R genetic programming framework |

rgr | The GSC Applied Geochemistry EDA Package |

RGraphics | Data and Functions from the book R Graphics, Second Edition |

rgrs | Functions to make R usage in social sciences easier (in french) |

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 |

rHadoopClient | hadoop client interface for R |

Rhh | Calculating multilocus heterozygosity and heterozygosity-heterozygosity correlation |

RHmm | Hidden Markov Models simulations and estimations |

rhosp | Side effect risks in hospital : simulation and estimation |

rHpcc | Interface between HPCC and R |

RHRV | Heart rate variability analysis of ECG data |

RHT | Regularized Hotelling’s T-square Test for Pathway (Gene Set) Analysis |

R.huge | Methods for accessing huge amounts of data [DEPRECATED] |

ri | ri: R package for performing randomization-based inference for experiments |

rich | Computes and compares species richnesses |

ridge | Ridge Regression with automatic selection of the penalty parameter |

Ridit | Ridit Analysis (An extension of the Kruskal-Wallis Test.) |

RiDMC | R interface to the idmclib library |

RIFS | Random Iterated Function System (RIFS) |

rImpactStory | Retrieves altmetrics from ImpactStory. See http://impactstory.org for more about the metrics |

rindex | Indexing for R |

ringbuffer | Ring buffer (circular buffer) data structure |

ringscale | Ringscale |

RInside | C++ classes to embed R in C++ applications |

RInSp | R Individual Specialization (RInSp) package |

rioja | Analysis of Quaternary Science Data |

risaac | A fast cryptographic random number generator using ISAAC by Robert Jenkins |

riskRegression | Risk regression for survival analysis |

risksetROC | Riskset ROC curve estimation from censored survival data |

RISmed | Download content from NCBI databases |

Ritc | Isothermal Titration Calorimetry (ITC) Data Analysis |

rite | The Right Editor to Write R |

RItools | Randomization inference tools |

riv | Robust instrumental variables estimator |

Rivivc | In vitro in vivo correlation linear level A |

RJaCGH | Reversible Jump MCMC for the analysis of CGH arrays |

rjags | Bayesian graphical models using MCMC |

rJava | Low-level R to Java interface |

rJavax | rJava extensions |

RJDBC | Provides access to databases through the JDBC interface |

rje | Miscellaneous useful functions |

Rjms | R messaging using ActiveMQ and jms |

Rjmsjars | Rjms jars |

rJPSGCS | R-interface to gene drop Java Programs for Statistical Genetics and Computational Statistics (JPSGCS) |

rjson | JSON for R |

RJSONIO | Serialize R objects to JSON, JavaScript Object Notation |

rJython | R interface to Python via Jython |

RKEA | R/KEA interface |

Rknots | Rknots |

rkt | Mann-Kendall test, Seasonal and Regional Kendall Tests |

Rlab | Functions and Datasets Required for ST370 class |

Rlabkey | Data exchange between R and LabKey Server |

rlandscape | Generates random landscapes with specifiable spatial characteristics |

RLastFM | R interface to last.fm API |

rlecuyer | R interface to RNG with multiple streams |

rlme | Rank-based Estimation and Prediction in Random Effects Nested Models |

RLRsim | Exact (Restricted) Likelihood Ratio tests for mixed and additive models |

RM2 | Revenue Management and Pricing Package |

rmac | calculate RMAC or FMAC agreement coefficients |

RMallow | Fit Multi-Modal Mallows’ Models to ranking data |

Rmalschains | Continuous Optimization using Memetic Algorithms with Local Search Chains (MA-LS-Chains) in R |

RMark | R Code for MARK Analysis |

R.matlab | Read and write of MAT files together with R-to-MATLAB connectivity |

RMAWGEN | RMAWGEN (R Multi-site Auto-regressive Weather GENerator), a package to generate daily time series of precipitation and temperature from monthly mean values |

RMC | Functions for fitting Markov models |

RMendeley | Interface to Mendeley API methods |

RMessenger | IM Client for R |

rmeta | Meta-analysis |

R.methodsS3 | Utility function for defining S3 methods |

rmgarch | Multivariate GARCH models |

rminer | Simpler use of data mining methods (e.g. NN and SVM) in classification and regression |

Rmisc | Rmisc: Ryan Miscellaneous |

Rmixmod | An interface of MIXMOD |

rmmseg4j | R interface to the Java Chinese word segmentation system of mmseg4j |

RMongo | MongoDB Client for R |

rmongodb | R-MongoDB driver |

Rmosek | The R-to-MOSEK Optimization Interface |

rmp | Rounded Mixture Package. Performs probability mass function estimation with Dirichlet process mixtures of rounded kernels |

Rmpfr | R MPFR – Multiple Precision Floating-Point Reliable |

Rmpi | Interface (Wrapper) to MPI (Message-Passing Interface) |

rms | Regression Modeling Strategies |

rms.gof | Root-mean-square goodness-of-fit test for simple null hypothesis |

RMTstat | Distributions, Statistics and Tests derived from Random Matrix Theory |

RMySQL | R interface to the MySQL database |

RnavGraph | Using graphs as a navigational infrastructure |

RnavGraphImageData | Some image data used in the RnavGraph package demos |

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 |

RND | Risk Neutral Density |

rneos | rneos: XML-RPC Interface to NEOS |

RNetCDF | R Interface to NetCDF Datasets |

RNetLogo | Provides an interface to the agent-based modelling platform NetLogo |

rngSetSeed | Initialization of the R base random number generator Mersenne-Twister with a vector of an arbitrary length |

rngtools | Utility functions for working with Random Number Generators |

rngWELL | toolbox for WELL random number generators |

rngwell19937 | WELL19937a random number generator implemented with 53 bit output |

Rniftilib | Rniftilib – R Interface to NIFTICLIB (V2.0.0: 2010-07-20) |

RNiftyReg | Medical image registration using the NiftyReg library |

ROAuth | R interface for OAuth |

RobAStBase | Robust Asymptotic Statistics |

robCompositions | Robust Estimation for Compositional Data |

robeth | R functions for robust statistics |

robfilter | Robust Time Series Filters |

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 |

robust | Robust Library |

RobustAFT | Truncated Maximum Likelihood fit and Robust Accelerated Failure Time regression for Gaussian and log-Weibull case |

robustbase | Basic Robust Statistics |

robustfa | An Object Oriented Framework for Robust Factor Analysis |

robustgam | Robust Estimation for Generalized Additive Models |

robustHD | Robust methods for high-dimensional data |

robustlmm | Robust Linear Mixed Effects Models |

robustloggamma | Robust estimation of the generalized log gamma model |

RobustRankAggreg | Methods for robust rank aggregation |

robustreg | Robust Regression Functions |

robustX | eXperimental Functionality for Robust Statistics |

rocc | ROC based classification |

rockchalk | Regression Estimation and Presentation |

rococo | RObust rank COrrelation COefficient and test |

rocplus | ROC, Precision-Recall, Convex Hull and other plots |

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 |

ROI | R Optimization Infrastructure |

ROI.plugin.glpk | ROI-plugin GLPK |

ROI.plugin.quadprog | ROI-plugin quadprog |

ROI.plugin.symphony | ROI-plugin symphony |

rolasized | Solarized colours in R |

R.oo | R object-oriented programming with or without references |

Rook | Rook – a web server interface for R |

rootSolve | Nonlinear root finding, equilibrium and steady-state analysis of ordinary differential equations |

ropensnp | Interface to OpenSNP API methods |

ROptEst | Optimally robust estimation |

ROptEstOld | Optimally robust estimation – old version |

ROptRegTS | Optimally robust estimation for regression-type models |

ror | Robust Ordinal Regression MCDA library |

ROracle | OCI based Oracle database interface for R |

ROSE | ROSE: Random Over-Sampling Examples |

roxygen | Literate Programming in R |

roxygen2 | In-source documentation for R |

roxyPackage | Utilities to automate package builds |

royston | Royston’s H Test: Multivariate Normality Test |

rpanel | Simple interactive controls for R using the tcltk library |

rpart | Recursive Partitioning |

rpart.plot | Plot rpart models. An enhanced version of plot.rpart |

rpartScore | Classification trees for ordinal responses |

RPCLR | RPCLR (Random-Penalized Conditional Logistic Regression) |

rpf | Response Probability Functions |

rphast | R interface to PHAST software for comparative genomics |

rPlant | R interface to the iPlant Discovery Environment |

rplos | Interface to PLoS Journals search and altmetrics API’s |

rplotengine | R as a plotting engine |

RPMG | Graphical User Interface (GUI) for interactive R analysis sessions |

RPMM | Recursively Partitioned Mixture Model |

Rpoppler | PDF tools based on Poppler |

rportfolios | Random portfolio generation |

RPostgreSQL | R interface to the PostgreSQL database system |

RPPanalyzer | Reads, annotates, and normalizes reverse phase protein array data |

RProtoBuf | R Interface to the Protocol Buffers API |

rpsychi | Statistics for psychiatric research |

rpubchem | rpubchem – Interface to the PubChem Collection |

rpud | R functions for computation on GPU |

RPyGeo | ArcGIS Geoprocessing in R via Python |

rPython | Package allowing R to call Python |

RQDA | R-based Qualitative Data Analysis |

Rquake | Seismic Hypocenter Determination |

RQuantLib | R interface to the QuantLib library |

Rramas | Matrix population models |

rrBLUP | Ridge regression and other kernels for genomic selection |

rrBlupMethod6 | Re-parametrization of RR-BLUP to allow for a fixed residual variance |

rrcov | Scalable Robust Estimators with High Breakdown Point |

rrcovHD | Robust multivariate Methods for High Dimensional Data |

rrcovNA | Scalable Robust Estimators with High Breakdown Point for Incomplete Data |

rrdf | rrdf – support for the Resource Description Framework |

rrdflibs | rrdflibs – package with Jena and Apache HTTP libraries for use with rrdf |

rredis | Redis client for R |

RRF | Regularized Random Forest |

rriskBayes | Predefined Bayes models fitted with Markov chain Monte Carlo (MCMC) (related to the ‘rrisk’ project) |

rriskDistributions | Fitting distributions to given data or known quantiles |

rrlda | Robust Regularized Linear Discriminant Analysis |

R.rsp | Dynamic generation of scientific reports |

rrules | Generic rule engine for R |

RSA | Response surface analysis |

RSADBE | Data related to the book “R Statistical Application Development by Example” |

rsae | Robust Small Area Estimation |

RSAGA | SAGA Geoprocessing and Terrain Analysis in R |

RSAP | SAP Netweaver RFC connector for R |

RSclient | Client for Rserve |

rscproxy | statconn: provides portable C-style interface to R (StatConnector) |

RSDA | RSDA – R to Symbolic Data Analysis |

RSearchYJ | RSearchYJ |

RSeed | borenstein analysis |

rseedcalc | Estimating the proportion of genetically modified stacked seeds in seedlots via multinomial group testing |

RSEIS | Seismic Time Series Analysis Tools |

rsem | Robust Structural Equation Modeling with Missing Data and Auxiliary Variables |

Rserve | Binary R server |

rSFA | Slow Feature Analysis in R |

rsgcc | Gini methodology-based correlation and clustering analysis of microarray and RNA-Seq gene expression data |

RSGHB | Functions for Hierarchical Bayesian Estimation: A Flexible Approach |

RSiena | Siena – Simulation Investigation for Empirical Network Analysis |

RSiteCatalyst | Adobe (Omniture) Reporting API |

RSKC | Robust sparse K-means |

rsm | Response-surface analysis |

RSNNS | Neural Networks in R using the Stuttgart Neural Network Simulator (SNNS) |

RSofia | Port of sofia-ml (http://code.google.com/p/sofia-ml/) to R |

Rsolnp | General Non-linear Optimization |

rspa | Adapt numerical records to fit (in)equality restrictions with the Successive Projection Algorithm |

rspear | Calculate SPEARpesticide in R (http://www.systemecology.eu/SPEAR/index.php) |

rsprng | R interface to SPRNG (Scalable Parallel Random Number Generators) |

RSQLite | SQLite interface for R |

RSQLite.extfuns | Math and String Extension Functions for RSQLite |

Rssa | A collection of methods for singular spectrum analysis |

rstiefel | Random orthonormal matrix generation on the Stiefel manifold |

rstream | Streams of random numbers |

Rsundials | Suite of Nonlinear Differential Algebraic Equations Solvers in R |

RSurvey | Analysis of Spatially Distributed Data |

RSvgDevice | An R SVG graphics device |

RSVGTipsDevice | An R SVG graphics device with dynamic tips and hyperlinks |

Rsymphony | Symphony in R |

rSymPy | R interface to SymPy computer algebra system |

rtape | Manage and manipulate large collections of R objects stored as tape-like files |

RTConnect | Tools for analyzing sales report files of iTunes Connect |

RTDAmeritrade | RTDAmeritrade |

RTextTools | Automatic Text Classification via Supervised Learning |

rtf | Rich Text Format (RTF) Output |

rtfbs | R Transcription Factor Binding Site identification tool |

rtiff | A tiff reader for R |

RTisean | R interface to Tisean algorithms |

RTOMO | Visualization for seismic tomography |

rtop | Interpolation of data with variable spatial support |

RTriangle | Triangle – A 2D Quality Mesh Generator and Delaunay Triangulator |

rts | Raster time series analysis |

Rttf2pt1 | Package for ttf2pt1 program |

rugarch | Univariate GARCH models |

RUnit | R Unit test framework |

Runiversal | Runiversal – Package for converting R objects to Java variables and XML |

runjags | Interface utilities for MCMC models in Just Another Gibbs Sampler (JAGS) using parallel and distributed computing methods |

Runuran | R interface to the UNU.RAN random variate generators |

RunuranGUI | A GUI for the UNU.RAN random variate generators |

R.utils | Various programming utilities |

rv | Simulation-based random variable objects |

RVAideMemoire | Diverse basic statistical and graphical functions |

Rvelslant | Downhole Seismic Analysis in R |

rvertnet | Search VertNet database from R |

rvgtest | Tools for Analyzing Non-Uniform Pseudo-Random Variate Generators |

rvHPDT | Calling haplotype-based and variant-based pedigree disequilibrium test for rare variants in pedigrees |

RVideoPoker | Play Video Poker with R |

Rvmmin | Variable metric nonlinear function minimization with bounds constraints |

RVowpalWabbit | R interface to the Vowpal Wabbit |

RVtests | Rare Variant Tests |

Rwave | Time-Frequency analysis of 1-D signals |

RWeather | R wrapper around the Yahoo! Weather, Google Weather and NOAA APIs |

RWebMA | RWebMA |

RWeka | R/Weka interface |

RWekajars | R/Weka interface jars |

RWiener | Wiener process distribution functions |

RWinEdt | R Interface to WinEdt |

Rwinsteps | Running Winsteps in R |

rwm | R Workspace Management |

rworldmap | Mapping global data, vector and raster |

rworldxtra | Country boundaries at high resolution |

rwt | Rice Wavelet Toolbox wrapper |

RxCEcolInf | R x C Ecological Inference With Optional Incorporation of Survey Information |

RXKCD | Get XKCD comic from R |

RXMCDA | An XMCDA parser for R |

RXshrink | Maximum Likelihood Shrinkage via Generalized Ridge or Least Angle Regression |

Ryacas | R interface to the yacas computer algebra system |

rysgran | Grain size analysis, textural classifications and distribution of unconsolidated sediments |

Rz | GUI Tool for Data Management like SPSS or Stata |

rzmq | R binding for zmq (http://www.zeromq.org/) |

s20x | Stats 20x |

s4vd | Biclustering via sparse singular value decomposition incorporating stability selection |

sac | Semiparametric Analysis of Changepoint |

sae | Small Area Estimation |

saemix | Stochastic Approximation Expectation Maximization (SAEM) algorithm |

SAFD | Statistical Analysis of Fuzzy Data |

safeBinaryRegression | Safe Binary Regression |

SAM | Sparse Additive Modelling |

SamplerCompare | A framework for comparing the performance of MCMC samplers |

sampleSelection | Sample Selection Models |

samplesize | Sample size calculation for various t-Tests and Wilcoxon-Test |

SampleSizeMeans | Sample size calculations for normal means |

SampleSizeProportions | Calculating sample size requirements when estimating the difference between two binomial proportions |

sampling | Survey Sampling |

samplingbook | Survey Sampling Procedures |

samplingEstimates | Sampling Estimates |

SamplingStrata | Optimal stratification of sampling frames for multipurpose sampling surveys |

samplingVarEst | Sampling Variance Estimation |

sampSurf | Sampling Surface Simulation for Areal Sampling Methods |

samr | SAM: Significance Analysis of Microarrays |

SAMURAI | Sensitivity Analysis of a Meta-analysis with Unpublished but Registered Analytical Investigations |

sandwich | Robust Covariance Matrix Estimators |

sanon | Stratified Analysis with Nonparametric covariable adjustment |

sapa | Spectral Analysis for Physical Applications |

SAPP | Statistical Analysis of Point Processes |

sas7bdat | SAS Database Reader (experimental) |

SAScii | Import ASCII files directly into R using only a SAS input script |

SASmixed | Data sets from “SAS System for Mixed Models” |

SASPECT | Significant AnalysiS of PEptide CounTs |

SASxport | Read and Write SAS XPORT Files |

SAVE | Bayesian emulation, calibration and validation of computer models |

saves | Fast load variables |

saws | Small-Sample Adjustments for Wald tests Using Sandwich Estimators |

sBF | Smooth Backfitting |

sbgcop | Semiparametric Bayesian Gaussian copula estimation and imputation |

SBSA | Simplified Bayesian Sensitivity Analysis |

sca | Simple Component Analysis |

scagnostics | Compute scagnostics – scatterplot diagnostics |

scaleboot | Approximately Unbiased P-values via Multiscale Bootstrap |

scales | Scale functions for graphics |

scam | Shape constrained additive models |

scape | Statistical Catch-at-Age Plotting Environment |

scapeMCMC | MCMC Diagnostic Plots |

scar | Shape-Constrained Additive Regression: a Maximum Likelihood Approach |

scaRabee | Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models |

scatterplot3d | 3D Scatter Plot |

SCEPtER | Stellar CharactEristics Pisa Estimation gRid |

SCEPtERextras | Additional grids for SCEPtER |

SCGLR | Supervised Component Generalized Linear Regression (SCGLR) |

schoolmath | Functions and datasets for math used in school |

schoRsch | Tools for analyzing factorial experiments |

schwartz97 | A package on the Schwartz two-factor commodity model |

scidb | An R interface to SciDB |

SciencePo | A Tool for Analyzing Political Behaviour |

scio | Sparse Column-wise Inverse Operator |

sciplot | Scientific Graphing Functions for Factorial Designs |

SciViews | SciViews GUI API – Main package |

SCMA | Single-Case Meta-Analysis |

scoring | Proper scoring rules |

ScottKnott | The ScottKnott Clustering Algorithm |

scout | Implements the Scout method for Covariance-Regularized Regression |

SCperf | Supply Chain Perform |

scrapeR | Tools for Scraping Data from HTML and XML Documents |

ScreenClean | Screen and clean variable selection procedures |

scrime | Analysis of High-Dimensional Categorical Data such as SNP Data |

scriptests | Transcript-based unit tests that are easy to create and maintain |

SCRT | Single-Case Randomization Tests |

scuba | Scuba diving calculations and decompression models |

SCVA | Single-Case Visual Analysis |

sda | Shrinkage Discriminant Analysis and CAT Score Variable Selection |

SDaA | Sampling: Design and Analysis |

SDBP | Calculate the third-order accurate Unbiased P-values via Speedy double bootstrap method |

sdcMicro | Statistical Disclosure Control methods for the production of public- and scientific-use files |

sdcMicroGUI | Graphical user interface for package sdcMicro |

sdcTable | Methods for SDC (statistical disclosure control) in tabular data |

SDD | Serial Dependence Diagrams |

SDDA | Stepwise Diagonal Discriminant Analysis |

sddpack | Semidiscrete Decomposition |

sde | Simulation and Inference for Stochastic Differential Equations |

sdef | Synthesizing List of Differentially Expressed Features |

SDisc | Integrated methodology for the identification of homogeneous subtypes in data |

SDMTools | Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises |

sdnet | Soft Discretization-based Bayesian Network Inference |

sdprisk | Measures of Risk for the Compound Poisson Risk Process with Diffusion |

sdtoolkit | Scenario Discovery Tools to Support Robust Decision Making |

seacarb | seawater carbonate chemistry with R |

SearchTrees | Spatial Search Trees |

seas | Seasonal analysis and graphics, especially for climatology |

season | Seasonal analysis of health data |

SECP | Statistical Estimation of Cluster Parameters (SECP) |

secr | Spatially explicit capture-recapture |

seeg | Statistics for Environmental Sciences, Engineering, and Geography |

seem | Simulation of Ecological and Environmental Models |

SEER2R | reading and writing SEER*STAT data files |

SEERaBomb | SEER Setup and Use with A-Bomb Data |

seewave | Sound analysis and synthesis |

seg | A set of tools for residential segregation research |

segmented | Segmented relationships in regression models with breakpoints/changepoints estimation |

Segmentor3IsBack | A Fast Segmentation Algorithm |

SE.IGE | Standard errors of estimated genetic parametes |

Sejong | KoNLP static dictionaries and Sejong project resources |

SEL | Semiparametric elicitation |

selectiongain | Expected gain from multi-stage selection and its optimization |

selectMeta | Estimation of weight functions in meta analysis |

selectr | Translate CSS Selectors to XPath Expressions |

SeleMix | Selective Editing via Mixture models |

sem | Structural Equation Models |

semdiag | Structural equation modeling diagnostics |

semGOF | Goodness-of-fit indexes for structural equation models |

SEMID | Identifiability of linear structural equation models |

SemiMarkov | Multi-States Semi-Markov Models |

SemiPar | Semiparametic Regression |

SemiParBIVProbit | Semiparametric Bivariate Probit Modelling |

SemiParSampleSel | Semiparametric Sample Selection Modelling with Continuous Response |

semisupKernelPCA | Kernel PCA projection, and semi-supervised variant |

SEMModComp | Model Comparisons for SEM |

semPlot | Path diagrams and visual analysis of various SEM packages’ output |

semPLS | Structural Equation Modeling Using Partial Least Squares |

semTools | Useful tools for structural equation modeling |

sendmailR | send email using R |

sendplot | Tool for sending interactive plots with tool-tip content |

sensitivity | Sensitivity Analysis |

SensitivityCaseControl | Sensitivity Analysis for Case-Control Studies |

sensitivityPStrat | Principal Stratification Sensitivity Analysis Functions |

SensoMineR | Sensory data analysis with R |

sensR | Thurstonian models for sensory discrimination |

SenSrivastava | Datasets from Sen & Srivastava |

separationplot | Separation Plots |

seq2R | Simple method to detect compositional changes in genomic sequences |

seqCBS | CN Profiling using Sequencing and CBS |

SeqGrapheR | Simple GUI for graph based visualization of cluster of DNA sequence reads |

seqinr | Biological Sequences Retrieval and Analysis |

seqMeta | Efficient meta analysis for the SKAT test |

seqminer | Efficiently Read Sequencing Data (VCF format, METAL format) into R |

seqmon | Sequential Monitoring of Clinical Trials |

seqPERM | Generates a permutation matrix based upon a sequence |

seqRFLP | Simulation and visualization of restriction enzyme cutting pattern from DNA sequences |

sequences | Generic and biological sequences |

Sequential | Exact Sequential Analysis for Poisson Data |

seriation | Infrastructure for seriation |

SesIndexCreatoR | Computation and visualization of socioeconomic indices and categories distributions |

session | Functions for interacting with, saving and restoring R sessions |

sessionTools | Tools for saving, restoring and teleporting R sessions |

SetMethods | SetMethods: A Package Companion to “Set-Theoretic Methods for the Social Sciences” |

setRNG | Set (Normal) Random Number Generator and Seed |

sets | Sets, Generalized Sets, Customizable Sets and Intervals |

setwidth | Set the value of options(“width”) on terminal emulators |

severity | Mayo’s Post-data Severity Evaluation |

sExtinct | Calculates the historic date of extinction given a series of sighting events |

sfa | Stochastic Frontier Analysis |

sfsmisc | Utilities from Seminar fuer Statistik ETH Zurich |

sft | Functions for Systems Factorial Technology Analysis of Data |

SGCS | Spatial Graph based Clustering Summaries for spatial point patterns |

sgeostat | An Object-oriented Framework for Geostatistical Modeling in S+ |

SGL | Fit a GLM (or cox model) with a combination of lasso and group lasso regularization |

sgof | Multiple hypotheses testing |

SGP | An R Package for the Calculation and Visualization of Student Growth Percentiles & Percentile Growth Trajectories |

sGPCA | Sparse Generalized Principal Component Analysis |

SGPdata | Exemplar data sets for SGP analyses |

sgr | Sample Generation by Replacement |

shape | Functions for plotting graphical shapes, colors |

shapefiles | Read and Write ESRI Shapefiles |

shapes | Statistical shape analysis |

SharpeR | Statistical significance of Sharpe ratio |

sharx | Models and Data Sets for the Study of Species-Area Relationships |

shiny | Web Application Framework for R |

SHIP | SHrinkage covariance Incorporating Prior knowledge |

shotGroups | Analyze shot group data |

shrink | Global, Parameterwise, and Joint Shrinkage of Regression Coefficients |

siar | Stable Isotope Analysis in R |

sideChannelAttack | Side Channel Attack |

sidier | SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships |

sifds | Swedish inflation forecast data set |

sig | Print function signatures |

sigclust | Statistical Significance of Clustering |

SightabilityModel | Wildlife Sightability Modeling |

signal | Signal processing |

signalextraction | Real-Time Signal Extraction (Direct Filter Approach) |

sigora | SIGNATURE OVERREPRESENTATION ANALYSIS |

SigWinR | SigWin-detector implementation in R |

SII | Calculate ANSI S3.5-1997 Speech Intelligibility Index |

simba | A Collection of functions for similarity analysis of vegetation data |

simboot | Simultaneous inference for diversity indices |

SimComp | Simultaneous Comparisons for Multiple Endpoints |

SimCorMultRes | Simulates Correlated Multinomial Responses |

simctest | Safe implementation of Monte Carlo tests |

simecol | Simulation of ecological (and other) dynamic systems |

simex | SIMEX- and MCSIMEX-Algorithm for measurement error models |

simexaft | simexaft |

simFrame | Simulation framework |

SimHap | A comprehensive modeling framework for epidemiological outcomes and a simulation-based approach to haplotypic analysis of population-based data |

Simile | Interact with Simile models |

SIMMS | Subnetwork Integration for Multi-Modal Signatures |

simMSM | Simulation of event histories based on nonlinear hazard rate functions and potentially nonlinear covariate effects |

simPH | Tools for simulating and plotting quantities of interest estimated from Cox Proportional Hazards models |

simpleboot | Simple Bootstrap Routines |

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 |

simPopulation | Simulation of synthetic populations for surveys based on sample data |

Simpsons | Detecting Simpson’s Paradox |

simsem | SIMulated Structural Equation Modeling |

simSummary | Simulation summary |

SimultAnR | Correspondence and Simultaneous Analysis |

SIN | A SINful Approach to Selection of Gaussian Graphical Markov Models |

sinartra | A simple web app framework for R, based on sinatra |

sirad | Functions for calculating daily solar radiation and evapotranspiration |

sirt | Supplementary Item Response Theory Models |

SIS | Sure Independence Screening |

sisus | SISUS: Stable Isotope Sourcing using Sampling |

sitools | Format a number to a string with SI prefix |

SixSigma | Six Sigma Tools for Quality and Process Improvement |

SiZer | SiZer: Significant Zero Crossings |

sjdbc | JDBC Driver Interface |

SKAT | SNP-set (Sequence) Kernel Association Test |

skatMeta | Efficient meta analysis for the SKAT test |

SkewHyperbolic | The Skew Hyperbolic Student t-Distribution |

skewt | The Skewed Student-t Distribution |

skewtools | Information Tools for analyze Skew-Elliptical distributions and related models |

Skillings.Mack | The Skillings-Mack test Statistic for block designs with missing observations |

skmeans | Spherical k-Means Clustering |

slam | Sparse Lightweight Arrays and Matrices |

SLC | Slope and level change |

Sleuth2 | Data sets from Ramsey and Schafer’s “Statistical Sleuth (2nd ed)” |

Sleuth3 | Data sets from Ramsey and Schafer’s “Statistical Sleuth (3rd ed)” |

SLHD | Maximin-Distance (Sliced) Latin Hypercube Designs |

SlimPLS | SlimPLS multivariate feature selection |

sltl | Time Series Decomposition using Loess and Harmonic Regression |

sm | Smoothing methods for nonparametric regression and density estimation |

smaa | Stochastic Multi-criteria Acceptability Analysis |

smacof | SMACOF for Multidimensional Scaling |

smart | Sparse Multivariate Analysis via Rank Transformation |

SmarterPoland | A set of tools developed by the Foundation SmarterPoland.pl |

smatr | (Standardised) Major Axis Estimation and Testing Routines |

SMC | Sequential Monte Carlo (SMC) Algorithm |

smco | A simple Monte Carlo optimizer using adaptive coordinate sampling |

SMCP | Smoothed minimax concave penalization (SMCP) method for genome-wide association studies |

SMCRM | Data Sets for Statistical Methods in Customer Relationship Management by Kumar and Petersen (2012) |

smcure | Fit Semiparametric Mixture Cure Models |

smcUtils | Utility functions for sequential Monte Carlo |

smdata | Data to accompany Smithson & Merkle, 2014 |

smdc | Document Similarity |

sme | Smoothing-splines Mixed-effects Models |

SMFI5 | R functions and data from Chapter 5 of ‘Statistical Methods for Financial Engineering’ |

smfsb | SMfSB 2e: Stochastic Modelling for Systems Biology, second edition |

SMIR | Companion to Statistical Modelling in R |

smirnov | Provides two taxonomic coefficients from E. S. Smirnov “Taxonomic analysis” (1969) book |

SmithWilsonYieldCurve | Smith-Wilson Yield Curve Construction |

SMNCensReg | Fitting univariate censored regression model under the scale mixture of normal distributions |

SmoothHazard | Fitting illness-death model for interval-censored data |

smoothHR | Smooth Hazard Ratio Curves taking a Reference Value |

smoothie | Two-dimensional Field Smoothing |

smoothmest | Smoothed M-estimators for 1-dimensional location |

smoothSurv | Survival Regression with Smoothed Error Distribution |

smoothtail | Smooth Estimation of GPD Shape Parameter |

SMPracticals | Practicals for use with Davison (2003) Statistical Models |

SMR | Studentized Midrange Distribution |

sms | Spatial Microsimulation |

SMVar | Structural Model for variances |

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 |

Snowball | Snowball Stemmers |

SnowballC | Snowball stemmers based on the C libstemmer UTF-8 library |

snowfall | Easier cluster computing (based on snow) |

snowFT | Fault Tolerant Simple Network of Workstations |

snpEnrichment | SNPs enrichment analysis |

SNPmaxsel | Maximally selected statistics for SNP data |

SNPMClust | A bivariate Gaussian genotype clustering and calling algorithm for Illumina microarrays |

snp.plotter | snp.plotter |

SNPRelate | Parallel Computing Toolset for Genome-Wide Association Studies (GWAS) |

snpStatsWriter | Flexible writing of snpStats objects to flat files |

SNPtools | Accessing, subsetting and plotting mouse SNPs |

SNSequate | Standard and Nonstandard Statistical Models and Methods for Test Equating |

SOAR | Memory management in R by delayed assignments |

SoDA | Functions and Examples for “Software for Data Analysis” |

SODC | Optimal Discriminant Clustering(ODC) and Sparse Optimal Discriminant Clustering(SODC) |

softclassval | Soft classification performance measures |

softImpute | matrix completion via iterative soft-thresholded svd |

soilDB | Soil Database Interface |

SoilR | Models of Soil Organic Matter Decomposition |

soil.spec | Soil spectral file conversion, data exploration and regression functions |

soiltexture | Functions for soil texture plot, classification and transformation |

soilwater | soilwater: Implements parametric formulas for soil water retention or conductivity curve |

solaR | Solar Photovoltaic Systems |

SOLOMON | Parentage analysis |

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 |

soobench | Single Objective Optimization Benchmark Functions |

SortableHTMLTables | Turns a data frame into an HTML file containing a sortable table |

sos | Search contributed R packages, sort by package |

sos4R | An R client for the OGC Sensor Observation Service |

source.gist | Read R code from a GitHub Gist |

sp | classes and methods for spatial data |

spa | Implements The Sequential Predictions Algorithm |

SPA3G | SPA3G: R package for the method of Li and Cui (2012) |

spaa | SPecies Association Analysis |

space | Sparse PArtial Correlation Estimation |

SPACECAP | A Program to Estimate Animal Abundance and Density using Bayesian Spatially-Explicit Capture-Recapture Models |

spaceExt | Extension of SPACE |

spacejam | Sparse conditional graph estimation with joint additive models |

spacetime | classes and methods for spatio-temporal data |

spacodiR | Spatial and Phylogenetic Analysis of Community Diversity |

spacom | Spatially weighted context data for multilevel modelling |

spam | SPArse Matrix |

sparcl | Perform sparse hierarchical clustering and sparse k-means clustering |

sparkTable | Sparklines and graphical tables for tex and html |

sparktex | Generate LaTeX sparklines in R |

SPARQL | SPARQL client |

sparr | The sparr package: SPAtial Relative Risk |

sparsediscrim | Sparse Discriminant Analysis |

SparseGrid | Sparse grid integration in R |

sparseHessianFD | Interface to ACM TOMS Algorithm 636, for computing sparse Hessians |

sparseLDA | Sparse Discriminant Analysis |

sparseLTSEigen | RcppEigen back end for sparse least trimmed squares regression |

SparseM | Sparse Linear Algebra |

sparsenet | Fit sparse linear regression models via nonconvex optimization |

SparseTSCGM | Sparse time series chain graphical models |

spartan | Spartan (Simulation Parameter Analysis R Toolkit ApplicatioN) |

spatcounts | Spatial count regression |

spate | Spatio-temporal modeling of large data using a spectral SPDE approach |

spatgraphs | Graphs for spatial point patterns |

spatial | Functions for Kriging and Point Pattern Analysis |

spatialCovariance | Computation of spatial covariance matrices for data on rectangles |

SpatialEpi | Performs various spatial epidemiological analyses |

SpatialExtremes | Modelling Spatial Extremes |

spatialkernel | Nonparameteric estimation of spatial segregation in a multivariate point process |

SpatialNP | Multivariate nonparametric methods based on spatial signs and ranks |

SpatialPack | Package for analysis of spatial data |

spatialprobit | Spatial Probit Models |

spatialsegregation | Segregation measures for multitype spatial point patterns |

spatial.tools | R functions for working with spatial data |

SpatialTools | Tools for spatial data analysis |

SpatialVx | Spatial Forecast Verification |

SpatioTemporal | Spatio-Temporal Model Estimation |

spatstat | Spatial Point Pattern analysis, model-fitting, simulation, tests |

spBayes | Univariate and Multivariate Spatial-temporal Modeling |

spc | Statistical Process Control – Collection of Some Useful Functions |

spcadjust | Functions for calibrating control charts |

spclust | Selective phenotyping for experimental crosses |

spcosa | Spatial Coverage Sampling and Random Sampling from Compact Geographical Strata |

spcov | Sparse Estimation of a Covariance Matrix |

spd | Semi Parametric Distribution |

spdep | Spatial dependence: weighting schemes, statistics and models |

spe | Stochastic Proximity Embedding |

SPECIES | Statistical package for species richness estimation |

specificity | Specificity of personality trait-outcome associations |

spectralGP | Approximate Gaussian processes using the Fourier basis |

speedglm | Fitting Linear and Generalized Linear Models to large data sets |

speedRlibs | Package containing the required libraries (jars) for speedR |

speedRlibTF | speedR’s table filter library |

speff2trial | Semiparametric efficient estimation for a two-sample treatment effect |

SPEI | Calculation of the Standardised Precipitation-Evapotranspiration Index |

sperich | Auxiliary functions to estimate centers of biodiversity |

sperrorest | Spatial Error Estimation and Variable Importance |

spGoogle | Interacting R with Google maps: Spatial visualization tool |

spgrass6 | Interface between GRASS 6+ geographical information system and R |

spgwr | Geographically weighted regression |

sphereplot | Spherical plotting |

SphericalCubature | Numerical integration over spheres and balls in n-dimensions; multivariate polar coordinates |

SpherWave | Spherical Wavelets and SW-based Spatially Adaptive Methods |

sphet | Estimation of spatial autoregressive models with and without heteroskedastic innovations |

spi | Compute SPI index |

SPIAssay | A genetic-based assay for the identification of cell lines |

spider | Species Identity and Evolution in R |

spikeslab | Prediction and variable selection using spike and slab regression |

spikeSlabGAM | Bayesian variable selection and model choice for generalized additive mixed models |

SPIn | Simulation-efficient Shortest Probability Intervals |

splancs | Spatial and Space-Time Point Pattern Analysis |

splm | Econometric Models for Spatial Panel Data |

spls | Sparse Partial Least Squares (SPLS) Regression and Classification |

splus2R | Supplemental S-PLUS functionality in R |

splusTimeDate | Times and Dates from S-PLUS |

splusTimeSeries | Time Series from S-PLUS |

spMC | Continuous Lag Spatial Markov Chains |

SPMS | Sub-Pathway Mining Software |

sporm | Semiparametric proportional odds rate model |

SportsAnalytics | Infrastructure for Sports Analytics |

SPOT | Sequential Parameter Optimization |

sprint | Simple Parallel R INTerface |

sprsmdl | Sparse modeling toolkit |

SPSL | Site Percolation on Square Lattice (SPSL) |

spsmooth | spsmooth: An Extension Package for ‘mgcv’ |

spsurvey | Spatial Survey Design and Analysis |

spt | Sierpinski Pedal Triangle |

spTimer | Spatio-Temporal Bayesian Modelling Using R |

spuRs | Functions and Datasets for “Introduction to Scientific Programming and Simulation Using R” |

sqldf | Perform SQL Selects on R Data Frames |

sqlshare | API for access to SQLShare database |

sqlutils | Utilities for working with SQL files |

SQN | subset quantile normalization |

SQUAREM | Squared extrapolation methods for accelerating fixed-point iterations |

squash | Color-based plots for multivariate visualization |

sra | Selection Response Analysis |

SRMA | SRMA Analysis of Array-based Sequencing Data |

sROC | Nonparametric Smooth ROC Curves for Continuous Data |

SRPM | Shared Reproducibility Package Management |

SRRS | The Stepwise Response Refinement Screener (SRRS) |

ssanv | Sample Size Adjusted for Nonadherence or Variability of input parameters |

SSDforR | SSD for R to analyze single system data |

ssfit | Fitting of parametric models using summary statistics |

ssize.fdr | Sample Size Calculations for Microarray Experiments |

ssmrob | Robust estimation and inference in sample selection models |

SSN | Spatial Modeling on Stream Networks |

sspir | State Space Models in R |

sss | Tools for importing files in the triple-s .(Standard Survey Structure) format |

SSsimple | State space models |

st | Shrinkage t Statistic and CAT Score |

stab | data analysis of drug stability for shelf life estimation |

stabledist | Stable Distribution Functions |

Stack | Stylized concatenation of data.frames or ffdfs |

stacomirtools | stacomi ODBC connection class |

stam | Spatio-Temporal Analysis and Modelling |

StAMPP | Statistical Analysis of Mixed Ploidy Populations |

StandardizeText | Standardize Text |

standGL | Standardized Group Lasso |

STAR</ |