verify-r-command

name	verify-r-command
description	Execute the frozen validation cases in an independent R implementation and emit normalized, reproducible results. Use as the R leg of Python-Stata-R validation after command specification, or when R package versions, mappings, defaults, or output extraction need verification.

Verify R Command

Run R as an independent result engine. Execution and normalization are the only responsibilities of this skill.

Inputs

• Frozen manifest.yaml and cases.yaml.
• validation/commands/<command>/r/run.R or permission to create it.
• Identical input data and expected SHA256 values.
• Project renv.lock and required R package/function mappings.
• Run ID and current Git commit.

Outputs

Write only inside the run directory:

• validation/runs/<command>/<run_id>/r/results.json
• validation/runs/<command>/<run_id>/r/environment.json
• validation/runs/<command>/<run_id>/r/raw/ for logs or package-native artifacts

The normalized JSON must include schema version, command, case ID, engine, sample hash, included-row hash, convergence state, warnings, coefficient names/order, every required metric, missing metrics, elapsed time, and error details. Preserve full numeric precision.

Workflow

1. Check Rscript, renv.lock, required package versions, and package availability without changing the environment.
2. Verify input bytes and row IDs against the frozen hash before fitting.
3. Invoke explicit R functions and options from the manifest; never accept package defaults unless the manifest records them.
4. Capture warnings, convergence codes, rank, omitted parameters, sample membership, and all required statistics.