/research-analysis

Role: Principal Investigator (analysis) Pipeline position: mid-chain

Analyzes the raw data per the preregistered plan — runs the planned statistical tests, reports effect sizes with confidence intervals (not p-values alone), applies multiple-comparison correction where applicable, runs robustness / sensitivity checks, and discloses every deviation from preregistration.

Canonical invocation

/research-analysis

With arguments:

/research-analysis [path/to/research-suite/]

Inputs

The raw data at the host-natural location the experiment stage recorded, plus _inputs/preregistration.md (the frozen analysis plan).

Outputs

_outputs/analysis.md (the preregistered tests with effect sizes and CIs, the multiple-comparison correction, the robustness checks, and disclosed deviations) + figures / tables at a host-natural location.

Downstream

/research-paper (downstream consumer)

Workflow phases

The command follows the standard /research pipeline workflow:

1. Load context — Read the raw data and the preregistration.
2. Verify the Sequence Gate — Confirm the experiment outputs exist; otherwise halt with Blocked: run /research-experiment first.
3. Analyze — Run the preregistered tests; report effect sizes + CIs; correct for multiple comparisons; run robustness / sensitivity checks.
4. Disclose deviations — Record every departure from the preregistered plan.
5. Update the handoff manifest — Record the analysis path and the figures / tables.
6. Emit the analysis — _outputs/analysis.md + figures / tables.

Rigor floor

Stochastic results are reported as best, mean, median, standard deviation, and worst across repetitions, with convergence curves and distribution plots. Comparisons use nonparametric tests — a paired signed-rank test pairwise, an omnibus rank test with post-hoc correction across methods — reported with a stochastic-superiority effect size and a critical-difference diagram. A result advances to the paper only when it clears the advancement gate: it beats its comparators convincingly and significantly, and the clearance is logged in an auditable runbook.

Failure modes

Examples

# Analyze the raw data per the preregistered plan
/research-analysis path/to/research-suite/

Cross-references

• Pipeline overview
• Commands reference