review-r

name	review-r
description	Run the R code review protocol on R scripts. Checks code quality, reproducibility, domain correctness, and professional standards. Produces a report without editing files. Make sure to use this skill whenever the user wants their existing R code evaluated or audited — not when they want new analysis written. Triggers include: "review my R script", "check my R code", "is my code replication-ready", "audit this R file", "does this code follow conventions", "will this reproduce", "check my analysis script", "code review", "review-r", or when the user has an existing .R file and wants quality feedback rather than new code.
argument-hint	[filename, 'all', or analysis name pattern]
allowed-tools	["Read","Grep","Glob","Write","Task","AskUserQuestion"]

Review R Scripts

Run the comprehensive R code review protocol.

Steps

1. Identify scripts to review:

   • If $ARGUMENTS is a specific .R filename: review that file only
   • If $ARGUMENTS is a name pattern (e.g., model_name): glob for matching .R files. If multiple matches, use AskUserQuestion:
     • header: "Scripts"
     • question: "Multiple R scripts match that pattern. Which should I review?"
     • multiSelect: true
     • options: list up to 4 matched files (label: filename, description: path and last modified). User can select multiple.
   • If $ARGUMENTS is all: review all R scripts in scripts/R/ and Figures/*/
   • If $ARGUMENTS is empty, glob for all .R files. If multiple found, use AskUserQuestion as above.

2. For each script, launch the r-reviewer agent with instructions to:

   • Follow the full protocol in the agent instructions
   • Read rules/r-code-conventions.md for current standards
   • Save report to quality_reports/[script_name]_r_review.md

3. After all reviews complete, present a summary:

   • Total issues found per script
   • Breakdown by severity (Critical / High / Medium / Low)
   • Top 3 most critical issues

4. IMPORTANT: Do NOT edit any R source files. Only produce reports. Fixes are applied after user review.