Coding In R

Coding in R

Rule: renv, portable paths, script as source of truth. Never rely on the global workspace.

For cluster execution, also load [running R](../running-r/SKILL.md).

Defaults

• renv for package versions. Commit renv.lock and .Rprofile.
• On SOM HPC: module load r; no rig or mise default.
• pak for fast installs when available.
• styler for formatting.
• lintr for linting.
• here::here() for paths. No setwd() in tracked scripts.
• readr::read_csv() over base read.csv().

install.packages("renv")
renv::init()
renv::install(c("tidyverse", "data.table", "here", "fs", "styler", "lintr"))
renv::snapshot()

Restore with:

renv::restore()

On HPC, restore once before arrays. Do not let many workers install packages concurrently.

Layout

project/
├── renv.lock
├── .Rprofile
├── README.md
├── scripts/       # entry points
├── R/             # shared helpers
├── notebooks/     # .Rmd / .qmd
├── data/raw/      # immutable; usually ignored
├── data/derived/  # rebuildable
└── results/       # figures/tables/logs

Paths

Never commit setwd() or personal absolute paths.

library(here)
counts_path ` unless `%>%` materially helps.
- 2-space indentation; aim for 80-char lines, max 120.
- Named arguments: `mean(x, na.rm = TRUE)`, not `mean(x, T)`.
- `library()` at top.
- Never `attach()` or `<<-`.
- `set.seed(42)` before stochastic work.

## Data

Default to tidyverse for clarity. Use data.table when data are large, joins/grouping dominate, or in-place mutation matters. Benchmark before rewriting clear code for speed.

## CLI skeleton

```r
#!/usr/bin/env Rscript
suppressPackageStartupMessages({
  library(optparse)
})

option_list <- list(
  make_option(c("-i", "--input"), type = "character"),
  make_option(c("-o", "--output"), type = "character")
)
opt <- parse_args(OptionParser(option_list = option_list))
if (is.null(opt$input) || is.null(opt$output)) {
  stop("--input and --output are required", call. = FALSE)
}

set.seed(42)

Checklist

• [ ] styler::style_dir(".") run
• [ ] lintr::lint_dir(".") clean or justified
• [ ] No setwd() or personal paths
• [ ] set.seed() where needed
• [ ] renv::snapshot() if deps changed
• [ ] Small smoke test run
• [ ] HPC uses module load r + renv, not rig/mise

Further reading

• Tidyverse style guide
• renv
• data.table
• here

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: yale-som-hpc
• Source: yale-som-hpc/claude-code-marketplace
• License: Unlicense

Install and usage instructions live in the source repository linked above.