R startup procedures
library(tidyverse)
set.seed(1234)
theme_set(theme_minimal())
R offers the ability to customize its startup procedures. That is, every time an R process is initiated, users can define custom R code to evaluate before the session begins. This custom code is generally stored in one of two locations:
.Renviron- which contains environment variables to be set in R sessions..Rprofile- which contains R code to be run in each session.
.Renviron
The .Renviron file is most useful for defining sensitive information such as API keys (such as GitHub or Twitter) as well as R specific environment variables like the history size (R_HISTSIZE=100000) and default library locations R_LIBS_USER.
The .Renviron file contains lists of environment variables to set. This is not R code, it uses a format similar to that used on the command line shell.
The easiest way to edit .Renviron is by running usethis::edit_r_environ().
A simple example of a .Renviron file is
R_HISTSIZE=100000
GITHUB_PAT=abc123
R_LIBS_USER=~/R/%p/%v
You will not typically need to edit this file manually. For example, rtweet automatically stores your Twitter API authentication information in .Renviron.
.Rprofile
The .Rprofile file contains R code to be run when R starts up. It is run after the .Renviron file is sourced. You generally have only a single .Renviron file on your computer. However you can have multiple .Rprofile files stored on a single computer.
- Typically
.Rprofileis located in the users’ home directory (~/.Rprofileon MacOS/Linux). This.Rprofileis run whenever you start up R. - Each R Project folder can also contain a separate
.Rprofile. This.Rprofileis specific to that project and will only be run if you open that R Project in RStudio.
The easiest way to edit .Rprofile is by running usethis::edit_r_profile().
Some common things people often add to their .RProfile
- Set a default CRAN mirror
- Write a welcome message
- Customize their R prompt
- Change options, screen width, numeric display
- Store API keys/tokens that are necessary for only a single project
Git tracking of .Rprofile
You can commit .Rprofile inside of a Git repository, however you should only do this for a private repository or if .Rprofile does not contain API keys. If you commit .Rprofile to a public repo, anybody can access and view the file. If it contains an API key, anyone can use it to access that API (which is typically a violation of your user agreement, not to mention if it is a paid API you will be charged for these queries).
Reproducibility
A good rule of thumb is you should only put things in your .Rprofile that you run interactively in the R terminal. If it ever appears in a R script or R Markdown file it should not be in your .Rprofile.
If you set these options in your .Rprofile, then try to run one of your scripts on another system without your .Rprofile it will no longer be reproducible. Some problematic examples are loading packages used in analysis (such as dplyr or ggplot2) or changing default options which change the value of outputs, such as options(stringsAsFactors = FALSE).
In addition because the .Rprofile is run by every R process (including those started by R itself) it is important to guard most of the code with interactive(), so it is only run in interactive sessions (sessions you are controlling with a terminal).
A simple example of a .Rprofile is
options(repos = c(CRAN = "https://cran.rstudio.org"))
if (interactive()) {
options(width = 120)
}
Acknowledgments
- Substantial material drawn from What They Forgot To Teach You About R by Jenny Bryan and Jim Hester. Licensed under the licensed under the CC BY-SA 4.0 Creative Commons License.
Session Info
sessioninfo::session_info()
## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.2.1 (2022-06-23)
## os macOS Monterey 12.3
## system aarch64, darwin20
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/New_York
## date 2022-08-22
## pandoc 2.18 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown)
##
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