Running R Analysis in Existing Projects

This skill operates inside an already structured R project. It helps extend, debug, or enhance existing analyses without recreating the project from scratch.

Use this skill when the user wants to:

• Continue analysis in an existing R project
• Modify or extend R scripts
• Add new statistical models or tests
• Update plots or figures
• Regenerate reports after data or code changes
• Debug R errors in a project

What This Skill Does

When activated, this skill will:

1. Understand the project structure
• Detect folders like data/, scripts/, results/, reports/
• Identify .Rproj, .Rmd, .qmd, or .R files

1. Inspect existing analysis
• Read current scripts and reports
• Identify which packages and methods are being used
• Avoid rewriting working components unnecessarily

1. Extend or modify analysis
• Add new models or statistical tests
• Introduce new plots using ggplot2
• Add new data processing steps
• Improve code structure or reproducibility

1. Re-run and update outputs
• Recompute results
• Overwrite or version new outputs in results/
• Re-render R Markdown or Quarto reports

1. Debug issues
• Fix missing packages
• Resolve file path problems
• Handle common R errors and warnings

Example User Requests That Should Trigger This Skill

• "Add a survival analysis to this R project"
• "Update the plots in my report"
• "This R Markdown file throws an error, fix it"
• "Extend this analysis with a mixed-effects model"
• "Re-run everything after I updated the data"

Example Workflow

User: Add a logistic regression model and update the report.

Skill actions:

• Locate main analysis script
• Add logistic regression using glm()
• Save model summary to results/
• Update report with new section and plot
• Re-render HTML/PDF report

Tools & Packages Commonly Used

Notes

• Respect the existing project structure and style
• Do not delete user code unless explicitly requested
• Prefer incremental updates over full rewrites
• Always regenerate reports after modifying analysis