What documentation exists for R?
What documentation exists for R?
What documentation exists for R?
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Chapter 5: R Add-On Packages 73<br />
tkWidgets Widgets in Tcl/Tk that provide functionality <strong>for</strong> Bioconductor packages.<br />
twilight Estimation of local false discovery rate.<br />
vsn Calibration and variance stabilizing trans<strong>for</strong>mations <strong>for</strong> both Affymetrix and<br />
cDNA array data.<br />
webbioc Integrated web interface <strong>for</strong> doing microarray analysis using several of the Bioconductor<br />
packages.<br />
widgetInvoke<br />
Evaluation widgets <strong>for</strong> functions.<br />
widgetTools<br />
Tools <strong>for</strong> creating Tcl/Tk widgets, i.e., small-scale graphical user interfaces.<br />
xcms LC/MS and GC/MS data analysis: framework <strong>for</strong> processing and visualization<br />
of chromatographically separated mass spectral data.<br />
y2hStat Analysis of Yeast 2-Hybrid data sets.<br />
5.1.5 Other add-on packages<br />
Jim Lindsey has written a collection of R packages <strong>for</strong> nonlinear regression and repeated<br />
measurements, consisting of event (event history procedures and models), gnlm (generalized<br />
nonlinear regression models), growth (multivariate normal and elliptically-contoured<br />
repeated measurements models), repeated (non-normal repeated measurements models),<br />
rmutil (utilities <strong>for</strong> nonlinear regression and repeated measurements), and stable (probability<br />
functions and generalized regression models <strong>for</strong> stable distributions). All analyses<br />
in the new edition of his book “Models <strong>for</strong> Repeated Measurements” (1999, Ox<strong>for</strong>d University<br />
Press) were carried out using these packages. Jim has also started dna, a package<br />
with procedures <strong>for</strong> the analysis of DNA sequences. Jim’s packages can be obtained from<br />
http://popgen.unimaas.nl/~jlindsey/rcode.html.<br />
More code has been posted to the R-help mailing list, and can be obtained from the<br />
mailing list archive.<br />
5.2 How can add-on packages be installed?<br />
(Unix only.) The add-on packages on CRAN come as gzipped tar files named<br />
pkg_version.tar.gz, which may in fact be “bundles” containing more than one package.<br />
Provided that tar and gzip are available on your system, type<br />
$ R CMD INSTALL /path/to/pkg_version.tar.gz<br />
at the shell prompt to install to the library tree rooted at the first directory given in<br />
R_LIBS (see below) if this is set and non-null, and to the default library (the ‘library’<br />
subdirectory of ‘R_HOME’) otherwise. (Versions of R prior to 1.3.0 installed to the default<br />
library by default.)<br />
To install to another tree (e.g., your private one), use<br />
$ R CMD INSTALL -l lib /path/to/pkg_version.tar.gz<br />
where lib gives the path to the library tree to install to.
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