How To Instal A Package In R

Installing R Packages

Jeffrey Leek
Johns Hopkins Bloomberg Schoolhouse of Public Wellness

R Packages

When you download R from the Comprehensive R Archive Network (CRAN), you get that ``base" R system
The base R system comes with basic functionality; implements the R language
I reason R is so useful is the big drove of packages that extend the basic functionality of R
R packages are developed and published past the larger R community

Obtaining R Packages

The primary location for obtaining R packages is CRAN
For biological applications, many packages are bachelor from the Bioconductor Projection
Yous can obtain information near the available packages on CRAN with the available.packages() function

              a <- available.packages() head(rownames(a), 3)  ## Show the names of the first few packages

              ## [1] "A3"       "abc"      "abcdeFBA"

There are approximately 5200 packages on CRAN covering a wide range of topics
A listing of some topics is available through the Task Views link, which groups together many R packages related to a given topic

Installing an R Parcel

Packages can be installed with the install.packages() part in R
To install a single package, laissez passer the proper name of the lecture to the install.packages() office every bit the first argument
The following the code installs the slidify package from CRAN

              install.packages("slidify")

This command downloads the slidify bundle from CRAN and installs it on your computer
Whatsoever packages on which this package depends volition also exist downloaded and installed

Installing an R Package

You can install multiple R packages at once with a single phone call to install.packages()
Place the names of the R packages in a grapheme vector

              install.packages(c("slidify", "ggplot2", "devtools"))

Installing an R Bundle in RStudio

Installing an R Package in RStudio

Installing an R Package from Bioconductor

To go the basic installer and basic ready of R packages (alert, will install multiple packages)

              source("http://bioconductor.org/biocLite.R") biocLite()

Identify the names of the R packages in a character vector

              biocLite(c("GenomicFeatures", "AnnotationDbi"))

http://www.bioconductor.org/install/

Loading R Packages

Installing a package does not brand it immediately bachelor to you in R; you must load the bundle
The library() function is used to load packages into R
The following code is used to load the ggplot2 packet into R

              library(ggplot2)

Whatever packages that demand to exist loaded as dependencies will be loaded outset, before the named package is loaded
Notation: Practice not put the package proper name in quotes!
Some packages produce messages when they are loaded (merely some don't)

Loading R Packages

After loading a bundle, the functions exported by that package will be attached to the elevation of the search() list (after the workspace)

              library(ggplot2) search()

              ##  [i] ".GlobalEnv"         "package:kernlab"    "package:caret"      ##  [4] "parcel:lattice"    "parcel:ggplot2"    "packet:makeslides" ##  [7] "bundle:knitr"      "package:slidify"    "tools:rstudio"      ## [10] "package:stats"      "parcel:graphics"   "bundle:grDevices"  ## [13] "package:utils"      "parcel:datasets"   "package:methods"    ## [16] "Autoloads"          "bundle:base"

Summary

R packages provide a powerful mechanism for extending the functionality of R
R packages tin can be obtained from CRAN or other repositories
The install.packages() tin exist used to install packages at the R console
The library() function loads packages that accept been installed so that you may access the functionality in the package