| ade4 | Title:Analysis of Environmental Data : Exploratory and Euclidean methods in Environmental sciences Description:Multivariate data analysis and graphical display |
| adlift | Title:An adaptive lifting scheme algorithm Description:Adaptive Wavelet transforms for signal denoising |
| affy | Title:Methods for Affymetrix Oligonucleotide Arrays Description:The package contains functions for exploratory oligonucleotide array analysis. The dependance to tkWidgets only concerns few convenience functions. 'affy' is fully functional without it |
| agce | Title:analysis of growth curve experiments Description:This package contains some simple functions for the analysis of growth curve experiments |
| alr3 | Title:Methods and data to accompany Applied Linear Regression 3rd edition Description:This library is a companion to the textbook S. Weisberg (2005), "Applied Linear Regression," 3rd edition, Wiley. It includes all the data sets discussed in the book (except one), and several few functions that are tailored to the methods discussed in the book. Ver. 1.0.3 corrects bugs in (1) weights for POD models; (2) use of 'subset' arguments with boot.case. Ver. 1.0.4 corrects a few bugs with overparameterized models. Ver. 1.0.5 changes one default argument. Ver 1.0.6 replaces the pure.error.anova function so it prints nicer and works with interactions |
| annotate | Title:Annotation for microarrays Description:Using R enviroments for annotation |
| apTreeshape | Title:Analyses of Phylogenetic Treeshape Description:apTreeshape is mainly dedicated to simulation and analysis of phylogenetic tree topologies using statistical indices. It is a companion library of the 'ape' package. It provides additional functions for reading, plotting, manipulating phylogenetic trees. It also offers convenient web-access to public databases, and enables testing null models of macroevolution using corrected test statistics. Trees of class "phylo" (from 'ape' package) can be converted easily |
| base | Title:The R Base Package Description:Base R functions |
| car | Title:Companion to Applied Regression Description:This package accompanies J. Fox, An R and S-PLUS Companion to Applied Regression, Sage, 2002. The package contains mostly functions for applied regression, linear models, and generalized linear models, with an emphasis on regression diagnostics, particularly graphical diagnostic methods. There are also some utility functions. With some exceptions, I have tried not to duplicate capabilities in the basic distribution of R, nor in widely used packages. Where relevant, the functions in car are consistent with na.action = na.omit or na.exclude |
| cba | Title:Clustering for Business Analytics Description:Implements clustering techniques such as Proximus and Rock, utility functions for efficient computation of cross distances and data manipulation |
| chplot | Title:Augmented Convex Hull Plots Description:Informative and nice plots for grouped bivariate data |
| class | Title:Functions for Classification Description:Various functions for classification |
| cluster | Title:Cluster Analysis Extended Rousseeuw et al. Description:Cluster Analysis, extended original from Peter Rousseeuw, Anja Struyf and Mia Hubert |
| coda | Title:Output analysis and diagnostics for MCMC Description:Output analysis and diagnostics for Markov Chain Monte Carlo simulations |
| colorspace | Title:Colorspace Manipulation Description:Carries out mapping between assorted color spaces |
| DAAG | Title:Data Analysis And Graphics Description:various data sets used in examples and exercises in the book Maindonald, J.H. and Braun, W.J. (2003) "Data Analysis and Graphics Using R" |
| datasets | Title:The R Datasets Package Description:Base R datasets |
| denpro | Title:Visualization of multivariate, functions, sets, and data Description:The package provides tools to (1) visualize multivariate density functions and density estimates with level set trees, (2) visualize level sets with shape trees, (3) visualize multivariate data with tail trees, (4) visualize scales of multivariate density estimates with mode graphs and branching maps, and (5) visualize anisotropic spread with 2D volume functions and 2D probability conetent functions. With level set trees one visualizes mode structure, with shape trees one visualizes shapes of level sets of unimodal densities, and with tail trees one visualizes connected data sets. The kernel estimator is implemented but the package may be applied for visualizing other density estimates, which have to be setwise constant |
| Design | Title:Design Package Description:Regression modeling, testing, estimation, validation, graphics, prediction, and typesetting by storing enhanced model design attributes in the fit. Design is a collection of about 180 functions that assist and streamline modeling, especially for biostatistical and epidemiologic applications. It also contains new functions for binary and ordinal logistic regression models and the Buckley-James multiple regression model for right-censored responses, and implements penalized maximum likelihood estimation for logistic and ordinary linear models. Design works with almost any regression model, but it was especially written to work with logistic regression, Cox regression, accelerated failure time models, ordinary linear models, the Buckley-James model, and generalized least squares for serially or spatially correlated observations |
| dichromat | Title:Color schemes for dichromats Description:Collapse red-green distinctions to simulate the effects of colour-blindness |
| DICOM | Title:Import medical imaging data using the DICOM Standard Description:This package provides functions to import and manipulate medical imaging data via the Digital Imaging and Communications in Medicine (DICOM) Standard |
| dprep | Title:Data preprocessing and visualization functions for classification Description:Functions for normalization, treatment of missing values, discretization, outlier detection, feature selection, and visualization |
| drc | Title:Analysis of dose-response curves Description:Non-linear regression analysis for multiple curves with focus on concentration-response, dose-response and time-response curves used, for example, in environmental sciences, pharmacology, toxicology and weed science |
| edd | Title:expression density diagnostics Description:tools for evaluating cohort distributions of gene expression levels |
| effects | Title:Effect Displays for Linear and Generalized Linear Models Description:Graphical and tabular effect displays, e.g., of interactions, for linear and generalised linear models |
| ElemStatLearn | Title: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. Description:Useful when reading the book above mentioned, in the documentation referred to as `the book' |
| ellipse | Title:Functions for drawing ellipses and ellipse-like confidence regions Description:This package contains various routines for drawing ellipses and ellipse-like confidence regions, implementing the plots described in Murdoch and Chow (1996), A graphical display of large correlation matrices, The American Statistician 50, 178-180. There are also routines implementing the profile plots described in Bates and Watts (1988), Nonlinear Regression Analysis and its Applications |
| flexclust | Title:Flexible Cluster Algorithms Description:The main function kcca implements a general framework for k-centroids cluster analysis supporting arbitrary distance/similarity measures and centroid computation. Further cluster methods include hard competitive learning, neural gas and QT clustering |
| flexmix | Title:Flexible Mixture Modeling Description:FlexMix implements a general framework for finite mixtures of regression models using the EM algorithm. FlexMix provides the E-step and all data handling, while the M-step can be supplied by the user to easily define new models. Existing drivers implement mixtures of standard linear models, generalized linear models and model-based clustering |
| gclus | Title:Clustering Graphics Description:Orders panels in scatterplot matrices and parallel coordinate displays by some merit index. Package contains various indices of merit, ordering functions, and enhanced versions of pairs and parcoord which color panels according to their merit level |
| gdata | Title:Various R programming tools for data manipulation Description:Various R programming tools for data manipulation |
| geneplotter | Title:Grapics related functions for Bioconductor Description:Some basic functions for plotting genetic data |
| GenKern | Title:Functions for generating and manipulating kernel density estimates Description:Computes generalised KDEs |
| geoR | Title:Analysis of geostatistical data Description:Geostatistical analysis including traditional, likelihood-based and Bayesian methods |
| ggm | Title:Graphical Gaussian Models Description:Functions for fitting Gaussian Markov models |
| globaltest | Title:Testing Association of a Group of Genes with a Clinical Variable Description:Testing whether a group of genes (e.g. a pathway) is significantly associated with a clinical variable of interest |
| gplots | Title:Various R programming tools for plotting data Description:Various R programming tools for plotting data |
| graphics | Title:The R Graphics Package Description:R functions for base graphics |
| grDevices | Title:The R Graphics Devices and Support for Colours and Fonts Description:Graphics devices and support for base and grid graphics |
| grid | Title:The Grid Graphics Package Description:A rewrite of the graphics layout capabilities, plus some support for interaction |
| gstat | Title:geostatistical modelling, prediction and simulation Description:variogram modelling; simple, ordinary and universal point or block (co)kriging, sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions |
| Hmisc | Title:Harrell Miscellaneous Description:The Hmisc library contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of S objects to LaTeX code, and recoding variables |
| hopach | Title:Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) Description:The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering) |
| HSAUR | Title:A Handbook of Statistical Analyses Using R Description:Functions, data sets, analyses and examples from the book `A Handbook of Statistical Analyses Using R' (Brian S. Everitt and Torsten Hothorn, Chapman & Hall/CRC, 2006). The first chapter of the book, which is entitled `An Introduction to R', is completely included in this package, for all other chapters, a vignette containing all data analyses is available |
| ISwR | Title:Introductory Statistics with R Description:Data sets and scripts for text examples and exercises in P. Dalgaard (2002), `Introductory Statistics with R', Springer Verlag |
| KernSmooth | Title:Functions for kernel smoothing for Wand & Jones (1995) Description:functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing" |
| klaR | Title:Classification and visualization Description:Miscellaneous functions for classification and visualization developed at the Department of Statistics, University of Dortmund |
| lattice | Title:Lattice Graphics Description:Implementation of Trellis Graphics. See ?Lattice for a brief introduction |
| LDheatmap | Title:Graphical display of pairwise linkage disequilibria between SNPs Description:Produces a graphical display, as a heat map, of measures of pairwise linkage disequilibria between SNPs. Users may optionally include the physical locations or genetic map distances of each SNP on the plot |
| lme4 | Title:Linear mixed-effects models using S4 classes Description:Fit linear and generalized linear mixed-effects models |
| lmtest | Title:Testing Linear Regression Models Description:A collection of tests, data sets and examples for diagnostic checking in linear regression models |
| lodplot | Title:Plot a genome scan Description:Assorted plots of location score versus genetic map position |
| mapproj | Title:Map Projections Description:Converts latitude/longitude into projected coordinates |
| maps | Title:Draw Geographical Maps Description:Display of maps. Projection code and larger maps are in separate packages (mapproj and mapdata) |
| marray | Title:Exploratory analysis for two-color spotted microarray data Description:Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking |
| MASS | Title:Main Package of Venables and Ripley's MASS Description:The main library and the datasets |
| mathgraph | Title:Directed and undirected graphs Description:Simple tools for constructing and manipulating objects of class mathgraph from the book "S Poetry", available at http://www.burns-stat.com/pages/spoetry.html |
| MCMCpack | Title:Markov chain Monte Carlo (MCMC) Package Description:This package contains functions to perform Bayesian inference using posterior simulation for a number of statistical models. All simulation is done in compiled C++ written in the Scythe Statistical Library Version 1.0. All models return coda mcmc objects that can then be summarized using the coda package. MCMCpack also contains some useful utility functions, including some additional density functions and pseudo-random number generators for statistical distributions, a general purpose Metropolis sampling algorithm, and tools for visualization |
| mgcv | Title:GAMs with GCV smoothness estimation and GAMMs by REML/PQL Description:Routines for GAMs and other generalized ridge regression with multiple smoothing parameter selection by GCV or UBRE. Also GAMMs by REML or PQL. Includes a gam() function |
| misc3d | Title:Miscellaneous 3D Plots Description:A collection of miscellaneous 3d plots, including rgl-based isosurfaces |
| multtest | Title:Resampling-based multiple hypothesis testing Description:Non-parametric bootstrap and permutation resampling-based multiple testing procedures for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Single-step and step-wise methods are implemented. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models) are included. Results are reported in terms of adjusted p-values, confindence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments |
| nlme | Title:Linear and nonlinear mixed effects models Description:Fit and compare Gaussian linear and nonlinear mixed-effects models |
| nnet | Title:Feed-forward Neural Networks and Multinomial Log-Linear Models Description:Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models |
| pixmap | Title:Bitmap Images (``Pixel Maps'') Description:Functions for import, export, plotting and other manipulations of bitmapped images |
| RadioSonde | Title:Tools for plotting skew-T diagrams and wind profiles Description:RadioSonde is a collection of programs for reading and plotting SKEW-T,log p diagrams and wind profiles for data collected by radiosondes (the typical weather balloon-borne instrument), which we will call "flights", "sondes", or "profiles" throughout the associated documentation. The raw data files are in a common format that has a header followed by specific variables. Use "help(ExampleSonde)" for the full explanation of the data files |
| rpart | Title:Recursive Partitioning Description:Recursive partitioning and regression trees |
| sandwich | Title:Robust Covariance Matrix Estimators Description:Model-robust standard error estimators for cross-sectional, time series and longitudinal data |
| seas | Title:Seasonal statistics, analysis and graphics, especially for climatology Description:Capable of deriving seasonal statistics, such as "normals", and analysis of seasonal data, such as departures. This package also has graphics capabilities for representing seasonal data, including boxplots for seasonal parameters, and bars for summed normals. There are many specific functions related to climatology, including precipitation normals, temperature normals, degree days and precipitation interarrivals. However, this package is designed to represent any time-varying parameter with a discernible seasonal signal, such as found in hydrology and ecology |
| seewave | Title:Time wave analysis and graphical representation Description:seewave provides functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, cross correlation and autocorrelation, zero-crossing, dominant frequency, 2D and 3D spectrograms, 2D and 3D Wigner-Ville distributions |
| sfsmisc | Title:Utilities from Seminar fuer Statistik ETH Zurich Description:Useful utilities [`goodies'] from Seminar fuer Statistik ETH Zurich, many ported from S-plus times |
| siggenes | Title:SAM and Efron's empirical Bayes approaches Description:Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM) |
| sm | Title:Smoothing methods for nonparametric regression and density estimation Description:This is software linked to the book `Applied Smoothing Techniques for Data Analysis: The Kernel Approach with S-Plus Illustrations' Oxford University Press |
| sma | Title:Statistical Microarray Analysis Description:The package contains some simple functions for exploratory microarray analysis |
| som | Title:Self-Organizing Map Description:Self-Organizing Map (with application in gene clustering) |
| sp | Title:classes and methods for spatial data Description:A package that provides classes and methods for spatial data. The classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc |
| spatial | Title:Functions for Kriging and Point Pattern Analysis Description:Functions for kriging and point pattern analysis |
| splines | Title:Regression Spline Functions and Classes Description:Regression spline functions and classes |
| stats | Title:The R Stats Package Description:R statistical functions |
| stats4 | Title:Statistical Functions using S4 Classes Description:Statistical Functions using S4 classes |
| strucchange | Title:Testing for Structural Change Description:Testing, dating and monitoring of structural change in linear regression relationships. strucchange features tests/methods from the generalized fluctuation test framework as well as from the F test (Chow test) framework. This includes methods to fit, plot and test fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F statistics, respectively. It is possible to monitor incoming data online using fluctuation processes. Finally, the breakpoints in regression models with structural changes can be estimated together with confidence intervals. Emphasis is always given to methods for visualizing the data |
| survival | Title:Survival analysis, including penalised likelihood. Description:survival analysis: descriptive statistics, two-sample tests, parametric accelerated failure models, Cox model. Delayed entry (truncation) allowed for all models; interval censoring for parametric models |
| tseries | Title:Time series analysis and computational finance Description:Package for time series analysis and computational finance |
| utils | Title:The R Utils Package Description:R utility functions |
| vcd | Title:Visualizing Categorical Data Description:Visualization techniques, data sets, summary and inference procedures aimed particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was inspired by the book "Visualizing Categorical Data" by Michael Friendly |
| vioplot | Title:Violin plot Description:A violin plot is a combination of a box plot and a kernel density plot |
| vsn | Title:Variance stabilization and calibration for microarray data Description:The package implements a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references. The model incorporates data calibration (aka normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription |
| zoo | Title:Z's ordered observations Description:An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with with ts and base R by providing methods to extend standard generics |
