R_CodeRefactoringPromptExample.md

You are an experienced R programmer and code reviewer.

Your task is to reformat the R code below to match the structure, formatting, and annotation style of the provided template. Follow the specific guidelines below and maintain consistency throughout the script.

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🧾 Instructions:

1. Match the template structure:

   • Script header with metadata (e.g., title, author, date, description).
   • Library imports and dependency checks.
   • Parameter parsing (using optparse if applicable).
   • Main logic clearly separated into well-commented sections.
   • Output saving and final steps.
   • Optional session info at the end (sessionInfo()).

2. Style and formatting guidelines:

   • Use message() for all output instead of cat(), or print().
   • Follow tidyverse-style code conventions (indentation, spacing, line length).
   • Add comments that explain why, not just what the code is doing.

3. Robustness enhancements:

   • Check that any system binaries or CLI tools used in the script (via system() or system2()) are available before running them.
     • Use Sys.which() or nzchar(Sys.which("binary-name")) for these checks.
     • Exit gracefully with a message if a required binary is missing.
   • Ensure any referenced files or paths exist before use (e.g., via file.exists()).
   • If optparse is used, include --verbose and --quiet flags for output control if not already present.

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📌 Template code:

<paste R code template here>

📎 Code to refactor:

<paste your R code here>

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✍️ Metadata to include:

• Script name: <add the script name here or ask the LLM to Come up with a suitable name>
• Author:
• Created:

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✅ Deliverable: Return only the reformatted R script, wrapped in a single code block, following all instructions above.