15 Using R in real life

15.1 Organizing work

Usually, work is organized into a directory with:

  • A folder containing R scripts (scripts/BRFSS-visualize.R)
  • ‘External’ data like the csv files that we’ve been working with, usually in a separate folder (extdata/BRFSS-subset.csv)
  • (sometimes) R objects written to disk using saveRDS() (.rds files) that represent final results or intermediate ‘checkpoints’ (extdata/ALL-cleaned.rds). Read the data into an R session using readRDS().
  • Use setwd() to navigate to folder containing scripts/, extdata/ folder
  • Source an entire script with source("scripts/BRFSS-visualization.R").

R can also save the state of the current session (prompt when choosing to quit() R), and to view and save the history() of the the current session; I do not find these to be helpful in my own work flows.

15.2 R Packages

All the functionality we have been using comes from packages that are automatically loaded when R starts. Loaded packages are on the search() path.

search()
##  [1] ".GlobalEnv"           "package:RColorBrewer" "package:stats"       
##  [4] "package:graphics"     "package:grDevices"    "package:utils"       
##  [7] "package:datasets"     "package:methods"      "Autoloads"           
## [10] "package:base"

Additional packages may be installed in R’s libraries. Use `installed.packages() or the RStudio interface to see installed packages. To use these packages, it is necessary to attach them to the search path, e.g., for survival analysis

library("survival")

There are many thousands of R packages, and not all of them are installed in a single installation. Important repositories are

Packages can be discovered in various ways, including CRAN Task Views and the Bioconductor web and Bioconductor support sites.

To install a package, use install.packages() or, for Bioconductor packages, instructions on the package landing page, e.g., for GenomicRanges. Here we install the ggplot2 package.

install.packages("ggplot2", repos="https://cran.r-project.org")

A package needs to be installed once, and then can be used in any R session.