executing-analysis

name	executing-analysis
description	Use when you have a pre-registered analysis plan to execute inline in this session with review checkpoints, on a platform without subagents

Executing the Analysis

Overview

Load the pre-registered plan, review it critically, execute all steps exactly as registered, report when complete.

Announce at start: "I'm using the executing-analysis skill to run this analysis."

Note: Tell your human partner that Science Superpowers works much better with access to subagents — the protocol-compliance and rigor reviews catch more when run by fresh agents. If subagents are available, use science-superpowers:subagent-driven-analysis instead.

Prerequisite

The plan MUST be pre-registered and frozen (science-superpowers:preregistering-analysis) and the workspace set up (science-superpowers:setting-up-reproducible-analysis). If either is missing, stop and do it first. Executing before freezing turns the analysis exploratory.

The Process

Step 1: Load and Review

1. Read the analysis plan and the frozen pre-registration.
2. Review critically — any concern about the design, the decision rule, or feasibility?
3. If concerns: raise them with your human partner before starting. A change to the registered analysis is a documented deviation and renders that part exploratory.
4. If no concerns: create a TodoWrite with all steps and proceed.

Step 2: Execute Steps

For each step:

1. Mark in_progress.
2. For nontrivial estimators: validate the pipeline on known/simulated data first.
3. Run the step exactly as registered. Keep the seed. Read immutable raw / named derived; write a new artifact.
4. Validate the output (shape, ranges, counts) — nothing changes silently.
5. Apply the registered decision rule as written; do not re-decide it after seeing the number.