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1. Introduction

GNU R offers a wide variety of packages for its users. There are all kinds of packages for R, which allow to display graphics or perform statistical tests. Some packages are designed for applications specific to a given industry. Many packages are already a part of the basic R installation, however, some of them need to be additionally installed into GNU R. This article will describe how to install and use packages under R.

2. What is a Package

A package is a set of functions, help files and data files that have been linked together. In order to use a package in R you need to first make sure that it is installed in the local library. In general, the one system-level library is used for storing the default R packages. You can, however, add additional libraries. You also need to remember about loading packages into your current R session. This is very important when using R. It is recommended that you do not load too many packages at the time. Loading a large number of packages may result in errors due to clashes of function names coming from two different packages. 

3. Listing Packages in Local Libraries

In order to check for default packages installed with R it is possible to use the getOption() function as follows:

> getOption("defaultPackages")
[1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "methods" 

In the list above the base package was omitted. This package is always loaded when you start R and it contains the elementary R functions.

You can also list the currently loaded packages by

> (.packages())
[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods" 
[7] "base"

In order to see all available packages we add the all.available option to the above R expression

> (.packages(all.available=TRUE))
 [1] "base"       "boot"       "class"      "cluster"    "codetools"
 [6] "compiler"   "datasets"   "foreign"    "graphics"   "grDevices"
[11] "grid"       "KernSmooth" "lattice"    "MASS"       "Matrix"   
[16] "methods"    "mgcv"       "nlme"       "nnet"       "parallel" 
[21] "rpart"      "spatial"    "splines"    "stats"      "stats4"   
[26] "survival"   "tcltk"      "tools"      "utils" 

Moreover, you can execute the library() function without arguments. This will output all available packages with a short description as shown below.

Packages in library ‘/usr/lib/R/library’:

base                    The R Base Package
boot                    Bootstrap Functions (originally by Angelo Canty
                        for S)
class                   Functions for Classification
cluster                 Cluster Analysis Extended Rousseeuw et al.
codetools               Code Analysis Tools for R
compiler                The R Compiler Package
datasets                The R Datasets Package
foreign                 Read Data Stored by Minitab, S, SAS, SPSS,
                        Stata, Systat, dBase, ...
graphics                The R Graphics Package
grDevices               The R Graphics Devices and Support for Colours
                        and Fonts
grid                    The Grid Graphics Package
KernSmooth              Functions for kernel smoothing for Wand & Jones
                        (1995)
lattice                 Lattice Graphics
MASS                    Support Functions and Datasets for Venables and
                        Ripley's MASS
Matrix                  Sparse and Dense Matrix Classes and Methods
methods                 Formal Methods and Classes
:

4. Loading Packages

Let us now load a package lattice. This can be achieved with the library() function as indicated below.

> library(lattice)

In order to display the documentation related to the loaded package we execute the following command:

> library(help=lattice)

This will list the relevant information to the lattice package with the functions that can be used under such package.
Additional information can be obtained by typing in

>?Lattice

5. Finding and Installing R Packages

One of the biggest sources of R packages is Comprehensive R Archive Network (CRAN). It is hosted by R Foundation, which also oversees the development of R. CRAN is hosted on several mirror sites around the world so pick the one closest to you to minimize the download times.  For example, you can access a list of available R packages in CRAN. There is also relevant documentation available for every package listed in CRAN.

5.1. Installation of R packages from Linux CLI

First, we describe how to install an R package from the Linux command line. Let's say we would like to install the "likelihood" R package. We can download it by:

$ wget -q http://cran.csiro.au/src/contrib/likelihood_1.5.tar.gz

Next we use the R CMD INSTALL command to install it. Please note that depending on the installation destination you may need to have a superuser privileges:

$ sudo R CMD INSTALL likelihood_1.5.tar.gz 
[sudo] password for lubos:
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘likelihood’ ...
** package ‘likelihood’ successfully unpacked and MD5 sums checked
** R
** data
** demo
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (likelihood)

NOTE: Be aware that some packages will require prerequisites. In that case use the above command to install prerequisites prior to your desired package.

5.2.  Installation of R packages from R console

There exists an R function for installing packages from the R console. This function will prompt you to select the mirror closest to your location and will install the desired package. Note the path where the package is being installed. You will need this path when you would like to remove the corresponding package. 

 > install.packages("likelihood")
Installing package(s) into ‘/home/renata/R/x86_64-pc-linux-gnu-library/2.15’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://cran.csiro.au/src/contrib/likelihood_1.5.tar.gz'
Content type 'application/x-gzip' length 36789 bytes (35 Kb)
opened URL
==================================================
downloaded 35 Kb

* installing *source* package ‘likelihood’ ...
** package ‘likelihood’ successfully unpacked and MD5 sums checked
** R
** data
** demo
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (likelihood)

The downloaded source packages are in
    ‘/tmp/RtmpWRwfqI/downloaded_packages’

Let us now remove the package likelihood from the corresponding location. This can be done as follows:

> remove.packages("likelihood", "/home/renata/R/x86_64-pc-linux-gnu-library/2.15")

Of course you need to specify your own path to your package.

6. Conclusion

This article has taken as closer to using custom packages under GNU R. As you have seen the number of R packages is enormous resulting in the extremely wide applications of the GNU R software.


GNU R tutorial series:

Part I: GNU R Introductory Tutorials:

  1. Introduction to GNU R on Linux Operating System
  2. Running GNU R on Linux Operating System
  3. A quick GNU R tutorial to basic operations, functions and data structures
  4. A quick GNU R tutorial to statistical models and graphics
  5. How to install and use packages in GNU R
  6. Building basic packages in GNU R

Part II: GNU R Language:

  1. An overview of GNU R programming language

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