1. R Package Management
By Toni Lee McCreash

2. What, exactly is an R package?
Packages are collections of R functions, data, and compiled code in a well-defined format.
Two or more functions together
Based on a single topic or theme (e.g., biology, physics, finance, etc.)
Documentation regarding the package
The directory where packages are stored is called the library. 
R comes with a standard set of packages.
Others are available for download and installation. Once installed, they have to be loaded into the session to be used.
Source:

3. What are the components of a package?
content/uploads/2015/06/devtools-cheatsheet.pdf

4. Finding Your Library Folder(s) There are 2!
System Folder
C:\Program Files\R\R.3.2.2\library
Local Folder
C:\Users\user.name\Docume nts\R\win-library\3.2

5. Viewing Installed Packages in RStudio

6. How are packages managed?
What packages do I already have?
installed.packages()
Source:

7. installed.packages() installed.packages() installed.packages()[1,]

8. Check if installed? Did I already install a specific package?
a<-installed.packages()
packages<-a[,1]
is.element(‘boot’,packages)
Source:

9. Stop If Version Not High Enough
Do I have a new enough version or can I add logic to my code to make sure that others have a new enough version?
packageVersion("stats")[1,1]
packageVersion("stats")[1,2]
packageVersion("stats")[1,3]
# this will stop the script if the stats package is not major version 3 or greater
stopifnot(packageVersion("stats")[1,1] >= 3)

10. How are packages managed?
How can I add or delete packages?
Add = install.packages(“<package name>”)
Delete = remove.packages(“<package name>”)
Source:

11. How are packages managed?
What packages are available?
p<-available.packages()
dim(p)
P[1:5,]
Source:

12. The Many Arguments of “install.packages()”
install.packages(pkgs, lib, repos = getOption("repos"),
contriburl = contrib.url(repos, type),
method, available = NULL, destdir = NULL,
dependencies = NA, type = getOption("pkgType"),
configure.args = getOption("configure.args"),
configure.vars = getOption("configure.vars"),
clean = FALSE, Ncpus = getOption("Ncpus", 1L),
verbose = getOption("verbose"),
libs_only = FALSE, INSTALL_opts, quiet = FALSE,
keep_outputs = FALSE, ...)
Source:

13. Walking Through “install.packages()”
A Simple Download from Mirror
install.packages(pkgs='dplyr')
Specify Your Destination Library
install.packages(pkgs='dplyr', lib='/usr/local/lib/R/site-library')
Specify a Mirror
install.packages(pkgs='dplyr', repos='
Use a Local Package to Install From
install.packages('~/dplyr_0.4.3.tar.gz', repos=NULL, type='source')
Only Install 64-bit Compatible Version
install.packages(pkgs='dplyr', INSTALL_opts="--no-multiarch")
(helpful with database drivers which sometimes are hard to install 32 & 64-bit)

14. Installing a Package from “Source” (.tar.gz file)
Find your desired package as a .tar.gz file
For example, search “CRAN dplyr”
Save to your computer (your desktop), then install from that file using:
install.packages('~/dplyr_0.4.3.tar.gz', repos=NULL, type='source')

15. What is the role of CRAN?
CRAN stands for “Comprehensive R Archive Network.”
CRAN is a network of ftp and web servers around the world that store identical, up-to-date, versions of code and documentation for R.

16. What are the criteria for packages to be carried on CRAN?
project.org/web/packages/policies.html

17. What is Packrat for Package Management?
Creating a packrat enabled project in Rstudio
It’s completely isolated!!! Install anything you need
Do a weird install:
install.packages(pkgs='dplyr', INSTALL_opts="--no-multiarch")
# snapshot it
packrat::snapshot()
# check the status of packages in our project
packrat::status()
# remove any packages we don’t actually use
packrat::clean()

18. Packrat and Colleague Collaboration
If you’re collaborating using a version control system, Packrat will help keep your private libraries in sync. RStudio watches for changes to your Packrat lockfile. When a change from a version control system updates your Packrat lockfile, RStudio will prompt you to apply that change to your private library.
For instance, let’s say your collaborator adds a package called argparser as part of a commit. When the packrat.lockfile is updated by the version control system, RStudio will prompt you to bring your library in sync.