Many of the algorithms needed for machine learning with R are not included as part of the base installation. Instead, the algorithms needed for machine learning are available via a large community of experts who have shared their work freely. These must be installed on top of base R manually. Thanks to R's status as free open source software, there is no additional charge for this functionality.
A collection of R functions that can be shared among users is called a package. Free packages exist for each of the machine learning algorithms covered in this book. In fact, this book only covers a small portion of all of R's machine learning packages.
If you are interested in the breadth of R packages, you can view a list at Comprehensive R Archive Network (CRAN), a collection of web and FTP sites located around the world to provide the most up-to-date versions of R software and packages. If you obtained the R software via download, it was most likely from CRAN at http://cran.r-project.org/index.html.
Tip
If you do not already have R, the CRAN website also provides installation instructions and information on where to find help if you have trouble.
The Packages link on the left side of the page will take you to a page where you can browse packages in an alphabetical order or sorted by the publication date. At the time of writing this, a total 6,779 packages were available—a jump of over 60% in the time since the first edition was written, and this trend shows no sign of slowing!
The Task Views link on the left side of the CRAN page provides a curated list of packages as per the subject area. The task view for machine learning, which lists the packages covered in this book (and many more), is available at http://cran.r-project.org/web/views/MachineLearning.html.
Despite the vast set of available R add-ons, the package format makes installation and use a virtually effortless process. To demonstrate the use of packages, we will install and load the RWeka package, which was developed by Kurt Hornik, Christian Buchta, and Achim Zeileis (see Open-Source Machine Learning: R Meets Weka in Computational Statistics 24: 225-232 for more information). The RWeka package provides a collection of functions that give R access to the machine learning algorithms in the Java-based Weka software package by Ian H. Witten and Eibe Frank. More information on Weka is available at http://www.cs.waikato.ac.nz/~ml/weka/.
Tip
To use the RWeka package, you will need to have Java installed (many computers come with Java preinstalled). Java is a set of programming tools available for free, which allow for the use of cross-platform applications such as Weka. For more information, and to download Java on your system, you can visit http://java.com.
The most direct way to install a package is via the install.packages() function. To install the RWeka package, at the R command prompt, simply type:
> install.packages("RWeka")
R will then connect to CRAN and download the package in the correct format for your OS. Some packages such as RWeka require additional packages to be installed before they can be used (these are called dependencies). By default, the installer will automatically download and install any dependencies.
Tip
The first time you install a package, R may ask you to choose a CRAN mirror. If this happens, choose the mirror residing at a location close to you. This will generally provide the fastest download speed.
The default installation options are appropriate for most systems. However, in some cases, you may want to install a package to another location. For example, if you do not have root or administrator privileges on your system, you may need to specify an alternative installation path. This can be accomplished using the lib option, as follows:
> install.packages("RWeka", lib="/path/to/library")
The installation function also provides additional options for installation from a local file, installation from source, or using experimental versions. You can read about these options in the help file, by using the following command:
> ?install.packages
More generally, the question mark operator can be used to obtain help on any R function. Simply type ? before the name of the function.
In order to conserve memory, R does not load every installed package by default. Instead, packages are loaded by users as they are needed, using the
library() function.
Tip
The name of this function leads some people to incorrectly use the terms library and package interchangeably. However, to be precise, a library refers to the location where packages are installed and never to a package itself.
To load the RWeka package we installed previously, you can type the following:
> library(RWeka)
Aside from RWeka, there are several other R packages that will be used in the later chapters. Installation instructions will be provided as additional packages are used.
To unload an R package, use the detach() function. For example, to unload the RWeka package shown previously use the following command:
> detach("package:RWeka", unload = TRUE)