# Pre Analysis Plan

> Use BEFORE running a confirmatory analysis, an experiment readout, an A/B test, a policy evaluation, or any study whose credibility depends on not having fished for the result — especially causal/econometric work. Locks the hypotheses, estimand, primary specification, sample and exclusions, and the robustness suite while the outcomes are still unseen, so the analysis is confirmatory rather than a specification search. Use whenever the user says "evaluate whether X worked", "test this hypothesis", "did the experiment move the metric" (outcomes still unseen — already-unblinded results route to causal-identification and analysis-review), "register this analysis", or is about to estimate an effect they have a stake in — and use it to clearly separate pre-registered confirmatory claims from exploratory findings.

- Skill: `lancegui/pre-analysis-plan` (Agent Skill)
- Install (CLI): `npx skillmds@latest add lancegui/pre-analysis-plan`
- Raw SKILL.md: https://api.skillmd.com/api/skills/lancegui/pre-analysis-plan/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: lancegui (https://skillmd.com/u/lancegui)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/lancegui/pre-analysis-plan

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# Pre-Analysis Plan

## Overview

If you can run a hundred reasonable specifications and report the one you like, you haven't measured an effect — you've measured your own preferences with extra steps. A pre-analysis plan (PAP) is the commitment that stops this: write down what you will do, and what would count as the answer, *before the outcomes are visible*. It's the analytics counterpart of writing a spec before code — decide the contract first — but the stakes are higher: the temptation to retrofit the plan to the result is enormous and almost invisible after the fact.

**Core principle:** A specification chosen after seeing the outcome is not evidence. Decide the analysis while you are still ignorant of how it will turn out.

## When you actually need this

Not every exploration needs a PAP — forcing one onto genuine EDA is theater (see `question-framing` and the exploration regime in `data-contracts`). It earns its weight when:

- The result will be used to **make or defend a decision** (ship the feature, keep the policy, publish the finding).
- You or the requester **have a stake** in the result coming out a particular way.
- The analysis is **causal** — identification claims are exactly where specification search does the most damage.
- The work will be **scrutinized** — a referee, a regulator, a skeptical exec, a replication.

If none of those hold, you're exploring; label it exploratory and move on.

## What the plan locks (before seeing outcomes)

1. **Hypotheses.** Stated directionally and ranked: primary vs. secondary. Test the primary one; treat everything else as secondary or exploratory. **Pre-commit the multiple-comparisons correction** for secondary tests (Bonferroni / Benjamini–Hochberg / etc.) — uncorrected, they reintroduce the forking-paths problem the PAP exists to stop.
2. **Estimand.** The exact quantity (ATE/ATT/LATE/ITT), on the exact population, over the exact window. Reuse the `question-framing` brief.
3. **Primary specification.** One pre-committed model: functional form, controls, fixed effects, SE structure (and clustering level), inference method — *the* number you will report. Robustness specs support it; they don't replace it when you like them better. Write the primary specification to the presentation standard in `causal-identification` — equation with subscripts defined, level of variation, intuition, literature precedent — not an estimator name-drop.
4. **Sample and exclusions.** Inclusion criteria, exclusion rules, and how outliers and missing data are handled — decided now, by rule, not later by eye. "Drop obvious outliers" after seeing the data is a degree of freedom; "drop values beyond 3 IQR, pre-committed" is a rule.
5. **Robustness suite.** The alternative specs, placebo/falsification tests, and sensitivity analyses you commit to run *regardless of whether the primary result survives them* — you can't quietly drop the ones that disagree. Keep it **small and targeted**: two or three checks that probe the load-bearing assumption, not a catalogue; a pre-registered buffet is still a buffet. (`causal-identification`'s design-specific diagnostics are **mandatory and separate** from this discretionary suite; "small" governs the discretionary specs only.)
6. **Decision rule and power.** What result leads to what action, and what counts as the effect being absent — define the null outcome so a null is a finding, not a prompt to keep digging. Commit too to the **minimum detectable effect / power** the design has: a null from an underpowered test isn't evidence of no effect, and saying so up front stops a noisy null from being read as a clean one.

## Write it down and get sign-off before touching outcome data

**The PAP's trigger line is stricter than the shared gate's** (`analysis-checkpoints` owns the write→sign-off mechanics): sign-off fires at touching outcome data, not merely at "estimation." Loading the outcomes, plotting their distribution, or peeking at the treatment–outcome relationship *is itself* the blinding violation — once seen, every later "choice" is contaminated, so the user signs off while everyone is still blind. Persist the PAP to a file (e.g. `docs/pre-analysis-plan.md`) and register it in `docs/analysis/index.yaml` via `analysis-state-management`; don't write it and proceed on your own reading.

## Confirmatory vs. exploratory — keep the line bright

You will discover interesting things you didn't pre-register. That's good — it's where new hypotheses come from. The sin is *laundering* them as confirmatory. Report them, clearly flagged as exploratory and hypothesis-generating, with the understanding that they need fresh data to confirm. A finding that has been both used to form a hypothesis and to test it has been counted twice.

## The garden of forking paths

Even with no conscious cheating, the sheer number of defensible choices — which controls, which window, which subgroup, how to handle outliers — means *somewhere* in that garden is a significant result, and you'll tend to wander toward it. The PAP prunes the garden to one path chosen in advance. When the data surprises you and a departure seems warranted, that is a **checkpoint, not a judgment call you make on your own**: stop, bring the proposed deviation and its rationale to the user, and report both the pre-registered and the revised analysis once they agree (see **`analysis-checkpoints`**). Deviation approved and disclosed is science; deviation taken silently — even with good intentions — is fishing.

## Red flags — STOP

- You've seen the outcomes and *now* you're deciding which controls to include or which subgroup to feature.
- The robustness checks reported are exactly the ones that agreed with the headline — you can't say what happened to the others.
- "We'll know the right specification once we see the data" — for a confirmatory claim, that's the forking-paths trap.
- An exploratory finding is about to be presented with the confidence of a pre-registered test.
- No stated null — no result that would have counted as "no effect."

## Common rationalizations

| Excuse | Reality |
|---|---|
| "Pre-registration is for academics, this is just an internal readout." | An exec's ship decision deserves the same protection against a fished result as a journal submission. |
| "I'll just try a few specs and report the robust one." | The "robust one" selected after seeing results is selection. Pre-commit the suite; report all of it. |
| "The data will tell me the right model." | The data will fit a model to its own noise. The question decides the model — commit it first. |
| "We don't have time to write a plan." | The plan is a few lines. Re-running after someone catches the forking-paths problem costs far more. |
| "I found something better than I planned." | Report it as exploratory and confirm on fresh data — don't relabel it as the test you ran. |

## The Process

1. **Lock the six items** — hypotheses (+ comparisons correction), estimand, primary spec, sample/exclusion rules, robustness suite, decision rule/power — using the `question-framing` brief and the sample rules `data-contracts` enforces.
2. **Persist the PAP to a file and get explicit sign-off before touching outcome data** — mandatory, not rhetorical: once outcomes are seen, the lock is gone.
3. **Route to exactly one next step.** Structural/counterfactual work → *invoke `structural-estimation`* for the model card. Otherwise → *invoke `executing-analysis-plans`* to carry out the locked plan (`causal-identification` runs the design diagnostics there).
4. **If the outcomes surprise you and a departure tempts → STOP and invoke `analysis-checkpoints`** — report pre-registered and revised analyses; never deviate silently.

## The bottom line

```
Confirmatory claim  →  hypotheses, estimand, primary spec, sample rules, robustness suite, decision rule — all fixed before outcomes seen
Otherwise           →  exploratory; label it so, and confirm on fresh data
```