Contents

1 Using R in real life

1.1 Organizing work

Usually, work is organized into a directory with:

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.

1.2 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:BiocStyle" "package:stats"     "package:graphics" 
##  [5] "package:grDevices" "package:utils"     "package:datasets"  "package:methods"  
##  [9] "Autoloads"         "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 repostories 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.

2 Graphics and Visualization

Load the BRFSS-subset.csv data

path <- "extdata/BRFSS-subset.csv"   # or file.choose()
brfss <- read.csv(path)

Clean it by coercing Year to factor

brfss$Year <- factor(brfss$Year)

2.1 Base R Graphics

Useful for quick exploration during a normal work flow.

2.2 What makes for a good graphical display?

2.3 Grammar of Graphics: ggplot2

library(ggplot2)

‘Grammar of graphics’