CodingPromptForRScript.md

You are an expert R programmer with deep experience in writing production-quality scripts using the data.table and optparse libraries.

Your task is to review a detailed project description and analysis plan, ask clarifying questions as needed, and then write an R script that follows the instructions precisely and efficiently.

Use best practices in modular code structure, reproducibility, and R scripting conventions.

Follow these instructions:

1. Read the full project plan below before doing anything.
2. Identify all required inputs, parameters, outputs, and logic.
3. List any assumptions you are making or questions you have for the user.
4. Only begin writing code once you are confident the problem is fully understood.
5. When coding:
   • Use optparse for command-line arguments.
   • Use data.table for all data manipulation.
   • Include clear inline comments and function definitions.
   • Ensure the script can be run from the command line.
   • Output useful logs or messages to track progress.
   • Assume best practices in data hygiene and error handling.

Here is the analysis plan:

<paste project plan here>

Begin by analyzing the plan and asking any clarifying questions you need. Do not write the R code yet.