When to Use

User asks for any statistical analysis, hypothesis testing, group comparison, prediction, association, survival analysis, meta-analysis, causal inference, power/sample size, or mentions R statistical packages.

What This Skill Does NOT Do

• Claim causality from observational data (use "associated with")
• Run large exploratory fishing without clear user intent
• Silently ignore assumption violations
• Report only p-values (always include effect sizes and CIs)

Pre-Flight (Mandatory)

• Confirm dataset exists and is readable
• Run schema inspection: bash {baseDir}/scripts/run-rstats.sh schema --data
• Report: rows, columns, types, missing values
• If missing > 5%, warn. If n < 30, warn small sample.

Environment Setup

First time or errors: bash {baseDir}/scripts/run-rstats.sh doctor

Install by profile (only when needed):

Workflow

• Determine analysis type (see references/METHOD_TABLE.md)
• Inspect dataset schema
• Build JSON spec:

{
  "dataset_path": "",
  "analysis_type": "",
  "outcome": "",
  "predictors": [""],
  "hypothesis": "",
  "alpha": 0.05,
  "seed": 42,
  "output_dir": ""
}

• Save as .json, run: bash {baseDir}/scripts/run-rstats.sh analyze --spec
• Read summary.json + report.md
• Present: Summary → Statistics → Interpretation → Plots → Assumptions → Caveats

Analysis Selection

For the complete 82-method table with user intent mapping, see references/METHOD_TABLE.md.

Quick lookup — most common:

Automatic Method Switching

• Non-normal + n < 30 → wilcoxon over ttest
• Unequal variance → Welch t-test (equal_var: false)
• Expected cells < 5 → fisher over chisq
• Overdispersion in Poisson → suggest negative binomial
• Heteroscedastic residuals → robust SE warning

Reporting Rules (Non-Negotiable)

Every analysis MUST include:

• Sample size (n) and missing data handling
• Method name and rationale
• Point estimates with confidence intervals
• Effect sizes (Cohen's d, η², R², OR, HR, etc.)
• Assumption check results
• Limitations

Language: "associated with" / "evidence suggests" — NEVER "proves" / "causes"

Spec Field Reference

See references/SPEC_REFERENCE.md for required/optional fields per analysis_type.