running-r

Running R

Rule: load R explicitly, restore packages deliberately, and never let package installs happen inside large job arrays.

Tooling defaults

Slightly opinionated picks for new R projects on the cluster:

• Cluster R module for the R executable. Load it explicitly in every job script, and pin the version for reproducibility — pick one from module spider r and module load r/<version>, rather than bare module load r, which follows the moving default.
• The base R module ships essentially no add-on packages — not even renv. optparse, data.table, arrow, tidyverse, here, fixest, etc. are all absent until you install them. Your very first setup step is bootstrapping a project library (see "Use renv carefully"); a job that library(optparse) without that step will fail with there is no package called 'optparse'.
• renv for project libraries. renv.lock is the R analogue of uv.lock — it is what makes runs reproducible from login node to compute node.
• pak as the installer behind renv for fast parallel installs.
• lintr + styler for static checks and formatting; testthat for tests. Install once at project setup.
• optparse for CLI scripts (one-file batch entry points like the pattern below).
• Native pipe |> unless you specifically need magrittr's %>% placeholders.

Style defaults

For the audience that is new to R — these are not stylistic preferences, they are the conventions that will make your code readable to anyone who comes after you (including future-you):

• snake_case for variables and functions; reserve CamelCase for S4/R6 classes.
• <- for assignment, not =. (Reserve = for named function arguments.)
• All library() calls at the top of the script.
• File paths via here::here() or explicit project paths; do not hardcode laptop paths.
• Always set set.seed() for stochastic work.
• Always use named arguments where the meaning is not obvious: mean(x, na.rm = TRUE), not mean(x, T).
• Smoke test on a small slice of real data before submitting a full cluster job. This is genuinely the fastest debugging loop you have.