Subagent-Driven Analysis

Execute a pre-registered analysis plan by dispatching a fresh subagent per analysis step, with two-stage review after each: protocol-compliance review first (did it run exactly what was pre-registered, nothing more), then statistical-rigor review (assumptions, leakage, correctness, reproducibility).

Why subagents: You delegate steps to specialized agents with isolated context. By precisely crafting their instructions, you keep them focused and prevent them from improvising analyses you didn't pre-register. They never inherit your session's history — you construct exactly what they need. This also preserves your own context for coordination.

Core principle: Fresh subagent per step + two-stage review (protocol then rigor) = trustworthy, reproducible results.

Continuous execution: Do not pause to check in between steps. Execute the whole plan. The only reasons to stop: a BLOCKED status you cannot resolve, an anomaly that needs science-superpowers:investigating-anomalous-results, a genuine ambiguity, or all steps complete.

Prerequisite

The analysis plan MUST be pre-registered and frozen (science-superpowers:preregistering-analysis) before any step runs. If it is not frozen, stop and pre-register first. Executing before freezing turns the whole thing exploratory.

When to Use

dot
digraph when_to_use {
    "Pre-registered plan?" [shape=diamond];
    "Steps mostly independent?" [shape=diamond];
    "Stay in this session?" [shape=diamond];
    "subagent-driven-analysis" [shape=box];
    "executing-analysis" [shape=box];
    "Pre-register first" [shape=box];

    "Pre-registered plan?" -> "Steps mostly independent?" [label="yes"];
    "Pre-registered plan?" -> "Pre-register first" [label="no"];
    "Steps mostly independent?" -> "Stay in this session?" [label="yes"];
    "Stay in this session?" -> "subagent-driven-analysis" [label="yes"];
    "Stay in this session?" -> "executing-analysis" [label="no - parallel session"];
}

The Process

dot
digraph process {
    rankdir=TB;

    "Set up reproducible workspace" [shape=box];
    "Read plan + frozen prereg, extract all steps, create TodoWrite" [shape=box];
    "Dispatch analyst subagent (./analyst-prompt.md)" [shape=box];
    "Analyst asks questions?" [shape=diamond];
    "Answer, provide context" [shape=box];
    "Analyst runs step, validates, commits, self-reviews" [shape=box];
    "Dispatch protocol-compliance reviewer (./protocol-compliance-reviewer-prompt.md)" [shape=box];
    "Ran exactly the pre-registered analysis?" [shape=diamond];
    "Analyst fixes deviations" [shape=box];
    "Dispatch rigor reviewer (./rigor-reviewer-prompt.md)" [shape=box];
    "Rigor reviewer approves?" [shape=diamond];
    "Analyst fixes rigor issues" [shape=box];
    "Mark step complete" [shape=box];
    "More steps?" [shape=diamond];
    "Use requesting-red-team-review on whole result" [shape=box style=filled fillcolor=lightgreen];
    "Use reporting-and-archiving-findings" [shape=box style=filled fillcolor=lightgreen];

    "Set up reproducible workspace" -> "Read plan + frozen prereg, extract all steps, create TodoWrite";
    "Read plan + frozen prereg, extract all steps, create TodoWrite" -> "Dispatch analyst subagent (./analyst-prompt.md)";
    "Dispatch analyst subagent (./analyst-prompt.md)" -> "Analyst asks questions?";
    "Analyst asks questions?" -> "Answer, provide context" [label="yes"];
    "Answer, provide context" -> "Dispatch analyst subagent (./analyst-prompt.md)";
    "Analyst asks questions?" -> "Analyst runs step, validates, commits, self-reviews" [label="no"];
    "Analyst runs step, validates, commits, self-reviews" -> "Dispatch protocol-compliance reviewer (./protocol-compliance-reviewer-prompt.md)";
    "Dispatch protocol-compliance reviewer (./protocol-compliance-reviewer-prompt.md)" -> "Ran exactly the pre-registered analysis?";
    "Ran exactly the pre-registered analysis?" -> "Analyst fixes deviations" [label="no"];
    "Analyst fixes deviations" -> "Dispatch protocol-compliance reviewer (./protocol-compliance-reviewer-prompt.md)" [label="re-review"];
    "Ran exactly the pre-registered analysis?" -> "Dispatch rigor reviewer (./rigor-reviewer-prompt.md)" [label="yes"];
    "Dispatch rigor reviewer (./rigor-reviewer-prompt.md)" -> "Rigor reviewer approves?";
    "Rigor reviewer approves?" -> "Analyst fixes rigor issues" [label="no"];
    "Analyst fixes rigor issues" -> "Dispatch rigor reviewer (./rigor-reviewer-prompt.md)" [label="re-review"];
    "Rigor reviewer approves?" -> "Mark step complete" [label="yes"];
    "Mark step complete" -> "More steps?";
    "More steps?" -> "Dispatch analyst subagent (./analyst-prompt.md)" [label="yes"];
    "More steps?" -> "Use requesting-red-team-review on whole result" [label="no"];
    "Use requesting-red-team-review on whole result" -> "Use reporting-and-archiving-findings";
}

Model Selection

Use the least powerful model that can handle each role.

• Mechanical steps (load data, apply a fixed transform, produce a planned figure): fast, cheap model.
• Integration/judgment steps (fitting the primary model, handling missingness per plan): standard model.
• Rigor review and anomaly judgment: most capable model.

Handling Analyst Status

DONE: Proceed to protocol-compliance review.

DONE_WITH_CONCERNS: Read the concerns. If about correctness or an unexpected data issue, address before review (may need science-superpowers:investigating-anomalous-results). If an observation ("this file is getting large"), note and proceed.

NEEDS_CONTEXT: Provide the missing information and re-dispatch.

BLOCKED: Assess. Context problem → provide more and re-dispatch. Needs more reasoning → more capable model. Step too large → split. Plan itself is wrong → escalate to your human partner. A wrong plan may require re-opening the pre-registration, which must be documented as a deviation.

Never silently let a subagent change the registered analysis to make a step "work." A deviation is documented and renders that analysis exploratory.

Prompt Templates

• ./analyst-prompt.md — dispatch the analyst subagent
• ./protocol-compliance-reviewer-prompt.md — did it match the pre-registration?
• ./rigor-reviewer-prompt.md — is the statistics correct, reproducible, leak-free?

Red Flags

Never:

• Execute before the pre-registration is frozen
• Skip either review (protocol OR rigor)
• Let a subagent add an unregistered analysis and report it as confirmatory
• Run rigor review before protocol compliance is green (wrong order)
• Accept a silently dropped outlier or changed cutoff (route to anomaly investigation instead)
• Dispatch multiple analyst subagents on the same artifacts in parallel (conflicts)
• Make the subagent read the whole plan (provide the step's full text + the relevant pre-registration excerpt)

If a reviewer finds issues: the same analyst subagent fixes them, then the reviewer reviews again. Repeat until approved.

Integration

Required workflow skills:

• science-superpowers:setting-up-reproducible-analysis — isolated, seeded, reproducible workspace (run first)
• science-superpowers:preregistering-analysis — must be frozen before execution
• science-superpowers:investigating-anomalous-results — when a step's output is surprising or impossible
• science-superpowers:requesting-red-team-review — adversarial review of the whole result
• science-superpowers:reporting-and-archiving-findings — after all steps complete

Subagents should use:

• science-superpowers:verifying-results-before-claiming — before any subagent reports a step as done

Alternative:

• science-superpowers:executing-analysis — inline execution for harnesses without subagents