R

=Overview=

R is a software environment for statistical computing and graphics. Amongst other things it include


 * an effective data handling and storage facility
 * a suite of operators for calculations on arrays, in particular matrices
 * a large, coherent, integrated collection of intermediate tools for data analysis
 * graphical facilities for data analysis and display either on-screen or on hardcopy, and
 * a well-developed, simple and effective programming language.

=Installing R=


 * R is freely available as either pre-compiled binaries or source code from [|http://www.r-project.org]

=Installing packages in R=

This example shows how to quickly install a package (in this case a genetic algorithm) that is downloaded from the CRAN repository on the R website. R installs all packages to a local installation directory, which is specified by the user the first time that a package is installed.


 * Download the package containing the genetic algorithm:
 * Open http://www.r-project.org/
 * Click on "CRAN"
 * Choose the closest mirror-site (e.g. Germany/Berlin)
 * Click on "Contributed extension packages"
 * Click on selected package (try "genalg")
 * Click on the link next to package source ("[|genalg_0.1.1.tar.gz]") and save on your computer.
 * Install the package (at the shell prompt):
 * R CMD INSTALL genalg_0.1.1.tar.gz
 * Use the package in R:
 * library(genalg) # this command loads the genalg package.
 * help(rbga) # get help on a specific command in the "genalg" package.
 * Run a demo
 * Copy and paste the first example given in "help(rbga)"

The "genalg" package is a bit unusual in that there is no help file for "genalg" (e.g. help(genalg) doesn't work). For this reason, you may also want to download the manual from the R website (on the same page as [|genalg_0.1.1.tar.gz])

A very useful R package that is not available on the R website is [|Bio3D]. The package was written by [|Barry Grant], who is a postdoc in [|Andrew McCammon's group]. It allows reading and writing of PDB files and molecular dynamics trajectories amongst other useful features.

Packages can also be installed from within R. At the R prompt, try "help(install.packages)" for more information (read the "See Also" section).

Some other useful packages:
 * xtable # write latex and html tables from R

=Example R scripts=

Please see:
 * /net/v215-2/data4/fedorov-group/R/