Run R Analysis

A specialized sub-skill for executing R analyses in existing research projects and generating comprehensive outputs.

Overview

This sub-skill runs R scripts, RMarkdown documents, and Quarto reports within an existing R project structure. It captures all outputs including console results, plots, tables, and rendered reports.

Use this sub-skill when the user wants to:

• Execute an R script in a project
• Generate an R Markdown or Quarto report
• Run parameterized analyses with different inputs
• Capture and return analysis outputs

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What This Sub-Skill Does

When invoked, this sub-skill will:

1. Activate project environment

   • Load renv environment if present
   • Set working directory to project root
   • Source .Rprofile if available

2. Execute analysis script

   • Run specified R script
   • Capture console output
   • Track generated files
   • Monitor for errors and warnings

3. Generate reports

   • Render R Markdown to HTML/PDF
   • Render Quarto documents
   • Include all figures and tables
   • Return rendered report path

4. Return results

   • Console output and messages
   • Paths to generated files
   • Summary statistics
   • Error messages if any

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Example User Requests

• "Run analysis.R and show me the results"
• "Execute the differential expression analysis in my RNA-seq project"
• "Render the report and return the HTML file"
• "Run the analysis with different parameters"
• "Generate all plots from my analysis script"

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Supported File Types

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Execution Workflow

1. Verify project structure exists
   ↓
2. Activate renv environment (if present)
   ↓
3. Load required packages
   ↓
4. Execute analysis script
   ↓
5. Capture outputs
   ↓
6. Return results summary

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Output Handling

Console Output

All print statements, messages, and warnings are captured and returned.

Generated Files

• Figures: results/figures/*.pdf, *.png, *.svg
• Tables: results/tables/*.csv, *.tsv
• Models: results/models/*.rds
• Reports: reports/*.html, *.pdf

Error Handling

• Script errors are reported with line numbers
• Missing packages are identified
• File path issues are diagnosed
• Suggestions for fixes are provided

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Parameters

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Example Usage

Basic Script Execution

User: Run the analysis script in my project.

Skill actions:

# Set working directory
setwd("my-project")

# Activate renv
renv::activate()

# Source analysis script
source("scripts/01_analysis.R")

# Report outputs
# - results/tables/statistics.csv created
# - results/figures/pca_plot.pdf created
# - results/models/regression_model.rds created

Parameterized Report

User: Run the report with dataset='variant2'.

Skill actions:

rmarkdown::render(
  "reports/report.Rmd",
  params = list(dataset = "variant2"),
  output_format = "html_document"
)
# Output: reports/report_variant2.html

Quarto Report

User: Render the Quarto document to PDF.

Skill actions:

quarto::quarto_render(
  "reports/analysis.qmd",
  output_format = "pdf"
)
# Output: reports/analysis.pdf

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Common Output Patterns

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Notes

• Working directory is always set to project root
• Relative paths in scripts work correctly
• renv ensures correct package versions
• All outputs are tracked and reported
• Long-running scripts show progress updates

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Related Sub-Skills

• create-project: Set up new projects before running analyses
• debug-env: Troubleshoot environment issues before execution