running-r-analysis-in-existing-projects

# 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 2. **Inspect existing analysis** - Read current scripts and reports - Identify which packages and methods are being used - Avoid rewriting working components unnecessarily 3. **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 4. **Re-run and update outputs** - Recompute results - Overwrite or version new outputs in `results/` - Re-render R Markdown or Quarto reports 5. **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 | Purpose | R Packages | |--------|------------| | Data wrangling | tidyverse, dplyr | | Modeling | stats, lme4, glmnet | | Visualization | ggplot2 | | Reporting | rmarkdown, quarto | | Project management | here, renv | --- ## 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