R FAQ
How can I manage R packages?

R is a statistical software made up of many user-written packages. The base version of R that is downloaded allows the user to get started in R, but anyone performing data analysis will quickly exhaust the capabilities of base R and need to install additional packages. Here are some basic commands for managing R packages.

Which packages do I already have?

To see what packages are installed, use the installed.packages() command. This will return a matrix with a row for each package that has been installed. Below, we look at the first 5 rows of this matrix.

installed.packages()[1:5,]

        Package   LibPath                           Version  Priority     
base    "base"    "C:/PROGRA~1/r/R-211~1.1/library" "2.11.1" "base"       
boot    "boot"    "C:/PROGRA~1/r/R-211~1.1/library" "1.2-42" "recommended"
car     "car"     "C:/PROGRA~1/r/R-211~1.1/library" "2.0-2"  NA           
class   "class"   "C:/PROGRA~1/r/R-211~1.1/library" "7.3-2"  "recommended"
cluster "cluster" "C:/PROGRA~1/r/R-211~1.1/library" "1.12.3" "recommended"
        Depends                                               Imports LinkingTo
base    NA                                                    NA      NA       
boot    "R (>= 2.9.0), graphics, stats"                       NA      NA       
car     "R (>= 2.1.1), stats, graphics, MASS, nnet, survival" NA      NA       
class   "R (>= 2.5.0), stats, utils"                          "MASS"  NA       
cluster "R (>= 2.9.0), stats, graphics, utils"                NA      NA       
        Suggests                                   Enhances OS_type License            Built   
base    NA                                         NA       NA      "Part of R 2.11.1" "2.11.1"
boot    "survival"                                 NA       NA      "Unlimited"        "2.11.1"
car     "alr3, leaps, lmtest, sandwich, mgcv, rgl" NA       NA      "GPL (>= 2)"       "2.11.1"
class   NA                                         NA       NA      "GPL-2 | GPL-3"    "2.11.1"
cluster NA                                         NA       NA      "GPL (>= 2)"       "2.11.1"

From this output, we will first focus on the Package and Priority columns. The Package column gives the name of the package and the Priority column indicates what is needed to use functions from the package.

• If Priority is "base", then the package is already installed and loaded, so all of its functions are available upon opening R.
• If Priority is "recommended", then the package was installed with base R, but not loaded. Before using the commands from this package, the user will have to load it with the library command, e.g. library(boot).
• If Priority is NA, then the package was installed by the user, but not loaded. Before using the commands from this package, the user will have to load it with the library command, i.e., library(car).

Have I installed a specific package?

Sometimes, you might want to know if you have already installed a specific package. Let's say we want to check if we have installed the package "boot". Instead of checking the entire list of installed packages, we can do the following.

a<-installed.packages()
packages<-a[,1] 
is.element("boot", packages)

[1] TRUE

How can I add or delete packages?

Any package that does not appear in the installed packages matrix must be installed and loaded before its functions can be used. A package can be installed using install.packages("<package name>"). A package can be removed using remove.packages("<package name>").

What packages are available?

The list of available R packages is constantly growing. The actual list can be obtained using available.packages(). This returns a matrix with a row for each package.

p <- available.packages()

dim(p)
[1] 2553   12

p[1:5,]
           Package      Version Priority Depends                                                                                                  Imports
ACCLMA     "ACCLMA"     "1.0"   NA       NA                                                                                                       NA     
ADGofTest  "ADGofTest"  "0.1"   NA       NA                                                                                                       NA     
AER        "AER"        "1.1-7" NA       "R (>= 2.5.0), stats, car (>= 2.0-1), Formula (>= 0.2-0),\nlmtest, sandwich, strucchange, survival, zoo" "stats"
AGSDest    "AGSDest"    "1.0"   NA       "ldbounds"                                                                                               NA     
AICcmodavg "AICcmodavg" "1.11"  NA       NA                                                                                                       NA     
           LinkingTo
ACCLMA     NA       
ADGofTest  NA       
AER        NA       
AGSDest    NA       
AICcmodavg NA       
           Suggests                                                                                                                                                                                       
ACCLMA     NA                                                                                                                                                                                             
ADGofTest  NA                                                                                                                                                                                             
AER        "boot, dynlm, effects, foreign, ineq, KernSmooth, lattice,\nMASS, mlogit, nlme, nnet, np, plm, pscl, quantreg, ROCR,\nsampleSelection, scatterplot3d, systemfit, rgl, truncreg,\ntseries, urca"
AGSDest    NA                                                                                                                                                                                             
AICcmodavg "lme4, MASS, nlme, nnet"                                                                                                                                                                       
           Enhances OS_type License       File Repository                                          
ACCLMA     NA       NA      "GPL-2"       NA   "http://cran.stat.ucla.edu/bin/windows/contrib/2.11"
ADGofTest  NA       NA      "GPL"         NA   "http://cran.stat.ucla.edu/bin/windows/contrib/2.11"
AER        NA       NA      "GPL-2"       NA   "http://cran.stat.ucla.edu/bin/windows/contrib/2.11"
AGSDest    NA       NA      "GPL (>= 2)"  NA   "http://cran.stat.ucla.edu/bin/windows/contrib/2.11"
AICcmodavg NA       NA      "GPL (>= 2 )" NA   "http://cran.stat.ucla.edu/bin/windows/contrib/2.11"

These first five (of 2,553) available packages illustrate that the package names are often acronyms and rarely reveal what the package functions do. A list of the packages available through CRAN including a short package description can be found at CRAN's Contributed Packages page.

What functions and datasets are in a package?

It is easy to access some quick documentation for a package from R with the help command. This opens an R window with package information followed by a list of functions and datasets.

help(package="MASS")

Once a package is loaded, the help command can also be used with all functions and datasets listed here, e.g. help(Null).