The R Project SVN – R – Diff – /branches/R-gcontext/FAQ

 * R FAQ: (R-FAQ).               The R statistical system FAQ.
 END-INFO-DIR-ENTRY
    R FAQ
 Frequently Asked Questions on R
-Version 1.8-10, 2003-10-24
+Version 1.8-12, 2003-10-31
 ISBN 3-900051-01-1
 Kurt Hornik
 Table of Contents
      Resonance Imaging (fMRI) datasets stored in the ANALYZE format.
 *Bhat*
      Functions for general likelihood exploration (MLE, MCMC, CIs).
+*CDNmoney*
+     Components of Canadian monetary aggregates.
 *CGIwithR*
      Facilities for the use of R to write CGI scripts.
 *CircStats*
      Circular Statistics, from "Topics in Circular Statistics" by S. Rao
 *GenKern*
      Functions for generating and manipulating generalised binned kernel
      density estimates.
+*HI*
+     Simulation from distributions supported by nested hyperplanes.
 *Hmisc*
      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
 *mapdata*
      Supplement to package *maps*, providing the larger and/or
      higher-resolution databases.
+*mapproj*
+     Map Projections: converts latitude/longitude into projected
+     coordinates.
 *maps*
      Draw geographical maps.  Projection code and larger maps are in
      separate packages.
 *maptools*
      Generalization of the Shapiro-Wilk test for multivariate variables.
 *mvtnorm*
      Multivariate normal and t distributions.
+*ncdf*
+     Interface to Unidata netCDF data files.
 *ncomplete*
      Functions to perform the regression depth method (RDM) to binary
      regression to approximate the minimum number of observations that can
      be removed such that the reduced data set has complete separation.
 *DynDoc*
      Functionality to create and interact with dynamic documents, vignettes,
      and other navigable documents.
+*MAGEML*
+     Functionality to handle MAGEML documents.
 *RBGL*
      An interface between the graph package and the Boost graph libraries,
      allowing for fast manipulation of graph objects in R.
 *ROC*
      Receiver Operating Characteristic (ROC) approach for identifying genes
      that are differentially expressed in two types of samples.
+*RdbiPgSQL*
+     Methods for accessing data stored in PostgreSQL tables.
 *Rgraphviz*
      An interface with Graphviz for plotting graph objects in R.
 *Ruuid*
      Creates Universally Unique ID values (UUIDs) in R.
 *SAGElyzer*
      Locates genes based on SAGE tags.
+*SNPtools*
+     Rudimentary structures for SNP data.
 *affy*
      Methods for Affymetrix Oligonucleotide Arrays.
+*affyPLM*
+     For fitting Probe Level Models.
 *affycomp*
      Graphics toolbox for assessment of Affymetrix expression measures.
 *affydata*
      Affymetrix data for demonstration purposes.
+*annaffy*
+     Functions for handling data from Bioconductor Affymetrix annotation
+     data packages.
 *annotate*
      Associate experimental data in real time to biological metadata from
      web databases such as GenBank, LocusLink and PubMed.  Process and store
      query results.  Generate HTML reports of analyses.
+*ctc*
+     Tools to export and import Tree and Cluster to other programs.
+*daMA*
+     Functions for the efficient design of factorial two-color microarray
+     experiments and for the statistical analysis of factorial microarray
+     data.
 *edd*
      Expression density diagnostics: graphical methods and pattern
      recognition algorithms for distribution shape classification.
+*externalVector*
+     Basic class definitions and generics for external pointer based vector
+     objects for R.
+*factDesign*
+     A set of tools for analyzing data from factorial designed micraorray
+     experiments.  The functions can be used to evaluate appropriate tests
+     of contrast and perform single outlier detection.
+*gcrma*
+     Background adjustment using sequence information.
 *genefilter*
      Tools for sequentially filtering genes using a wide variety of
      filtering functions.  Example of filters include: number of missing
      value, coefficient of variation of expression measures, ANOVA p-value,
      Cox model p-values.  Sequential application of filtering functions to
 *geneplotter*
      Graphical tools for genomic data, for example for plotting expression
      data along a chromosome or producing color images of expression data
      matrices.
+*globaltest*
+     Testing globally whether a group of genes is significantly related to
+     some clinical variable of interest.
+*gpls*
+     Classification using generalized partial least squares for two-group
+     and multi-group classification.
 *graph*
      Classes and tools for creating and manipulating graphs within R.
 *hexbin*
      Binning functions, in particular hexagonal bins for graphing.
 *limma*
      Linear models for microarray data.
+*makecdfenv*
+     Two functions.  One reads a Affymetrix chip description file (CDF) and
+     creates a hash table environment containing the location/probe set
+     membership mapping.  The other creates a package that automatically
+     loads that environment.
 *marrayClasses*
      Class definitions for pre-normalized and normalized cDNA microarray
      data.  Basic methods for accessing/replacing, printing, and subsetting.
 *marrayInput*
 *marrayTools*
      Miscellaneous functions used in the functional genomics core facility
      in UCB and UCSF.
+*matchprobes*
+     ools for sequence matching of probes on arrays.
 *multtest*
      Multiple testing procedures for controlling the family-wise error rate
      (FWER) and the false discovery rate (FDR).  Tests can be based on t-
      or F-statistics for one- and two-factor designs, and permutation
      procedures are available to estimate adjusted p-values.
+*ontoTools*
+     Graphs and sparse matrices for working with ontologies.
+*pamr*
+     Pam: prediction analysis for microarrays.
 *reposTools*
      Tools for dealing with file repositories and allow users to easily
      install, update, and distribute packages, vignettes, and other files.
 *rhdf5*
      Storage and retrieval of large datasets using the HDF5 library and file
      format.
+*siggenes*
+     Identifying differentially expressed genes and estimating the False
+     Discovery Rate (FDR) with both the Significance Analysis of Microarrays
+     (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).
+*splicegear*
+     A set of tools to work with alternative splicing.
 *tkWidgets*
      Widgets in Tcl/Tk that provide functionality for Bioconductor packages.
 *vsn*
      Calibration and variance stabilizing transformations for both
 *widgetTools*
      Tools for creating Tcl/Tk widgets, i.e., small-scale graphical user
      interfaces.
-   These packages will eventually also be made available via CRAN as well.
 .1.5 Other add-on packages
 ---------------------------
 Jim Lindsey <jlindsey@luc.ac.be> has written a collection of R packages for
 nonlinear regression and repeated measurements, consisting of *event*

The R Project SVN R

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