# R Programming/Packages

An R package includes a set of functions and datasets. Packages are often developed as supplementary material to books. For instance the **MASS** package was developed by Venables and Ripley for their book *Modern Applied Statistics with S* and the **car** package was developed by John Fox for his book *An R and S plus Companion to Applied Regression*.

## Load a package edit

A package is loaded into the current R environment using the `library()`

function. A list of functions and datasets included in a package can be obtained by using the h or help argument of the library function.

```
library("stats4") # loads the package "stats4"
library(h=stats4) # gives help for all functions
data(package="stats4") # gives the list of all available datasets
```

A package can be detached from the current environment by using the `detach()`

function:

```
> detach("package:prettyR")
```

Without any arguments the `library()`

function lists all of the packages currently available to the user.
`env()`

(**gdata**) describe all loaded environments (ie packages). `search()`

gives the list of all loaded packages.

```
> library() # returns the description of all the packages available on the computer
> dir(.libPaths()) # returns the name of all the packages available on the computer (quicker than the previous one)
> search()
> env(unit="MB")
```

`current.packages()`

(**Zelig**) show all the required and suggested packages.

```
> current.packages("sem")
```

Where are my packages stored?

- The
`.libPaths()`

function without arguments prints the library directories - The
`.libPaths()`

function with a directory as argument defines a new directory where to store new libraries.

```
> .libPaths()
[1] "/Users/username/Library/R/library"
[2] "/Library/Frameworks/R.framework/Resources/library"
> .libPaths("W:/AppData/R/library")
```

## Install new packages edit

- Each major distribution of R includes a 'base' set of packages which support many basic statistical functions.
- Many R Users also choose to install additional 'Add-on' packages to provide simplified interfaces to R commands or to add specialist functionality i.e. the ggplot Grammar of Graphics package provides an advanced graphical output capability.
- The exhaustive list of all available packages is on the CRAN website.
- The R community has developed a vast resource of Add-on packages, some with unique functionality, some with overlapping functionality. It is therefore common to find multiple R packages capable of completing the same task i.e. reading and writing Excel spreadsheets. Ultimately which package to use is your choice.
- To install a new package, it is usually necessary to specify the name of the package as an argument of install.packages() function.
- Sometimes you need to specify more options. For instance, this is the case if you are not an administrator of your computer.
- "lib" specifies the directory where you want to store the package.
- "repos" specifies a list of repositories. Note that you can specify a vector of repositories.
- "dep=T" specifies that all the required packages are also downloaded and installed.

```
> install.packages("faraway")
> install.packages("rgrs", lib="W:/AppData/R/library" ,
repos=c("http://r-forge.r-project.org","http://cran.fr.r-project.org/"),
dep=TRUE)
```

- Stay up to date.

If you want to be aware of the latest packages, type new.packages() in R or visit the Revolution Computing Blog which gives each month a list of the new and the updated packages.

```
> new.packages() # displays all the packages available in the repositories
> update.packages() # updates all the packages installed with the newest version available in the repositories
```

We can also install bundles of packages using `install.views()`

or `update.views()`

(**ctv**).

```
> install.packages("ctv")
> library("ctv")
> install.views("Econometrics")
> update.views("Econometrics")
```

We can also remove packages with `remove.packages()`

.

## Package Documentation and Help edit

All R packages install with 'help' documentation, listing their functions and providing syntax and usage examples.

```
> library("tidyr") # load the tidyr package
> help("tidyr") # view the tidyr package's help documentation
```

See the Obtaining Help Documentation section for more details on accessing package 'help' documentation.

## Package Dependencies edit

- Most R packages have dependencies or references to other R packages. You must have all of an R package's 'required' dependencies installed, before you can use the package.
- R package dependencies come in two types, required and suggested.
- Specialist R packages such as the
**ggplot**Grammar of Graphics packages have large package dependency trees. - The
`install.packages()`

function will automatically download and install a package and its dependencies, on a computer with an Internet connection. - The R CMD INSTALL utility will check preinstalled packages for dependencies, but not download missing packages.
- Users must follow separate package download and installation processes when working on a computer with no Internet connection. The
**miniCRAN**package can be used to assist in the offline management of R package dependencies.

## Building R Packages edit

You can write down your own R packages. But, all packages submitted to CRAN (or Bioconductor) must follow specific guidelines, including the folder structure of the package and the other files like DESCRIPTION, NAMESPACE and so on.

- See Friedrich Leisch's introduction (PDF 20 pages)
^{[1]} - See also Duncan Murdoch's tools for building packages using Windows
^{[2]} - See also Hadley Wickham and Jennifer Bryan's online book on current packaging practices (R Packages)
^{[3]}

## References edit

- ↑ Friedrich Leisch
*Creating R Packages : A Tutorial*http://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf - ↑ http://www.r-project.org/conferences/useR-2008/slides/Murdoch.pdf
- ↑ Hadley Wickham and Jennifer Bryan
*R Packages : Organize, Test, Docment and Share your code*https://r-pkgs.org/