RES: Generate and run reproducible data cleaning, harmonization, reshaping, and merging scripts. Preserves raw data. Produces cleaned datasets, cleaning report, and merge report. Trigger: clean data, merge data, process data, harmonize data. Do NOT load for: audit, analysis, review, release, setup.
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RES: Generate and run reproducible data cleaning, harmonization, reshaping, and merging scripts. Preserves raw data. Produces cleaned datasets, cleaning report, and merge report. Trigger: clean data, merge data, process data, harmonize data. Do NOT load for: audit, analysis, review, release, setup.
description-en
RES: Generate and run reproducible data cleaning, harmonization, reshaping, and merging scripts. Preserves raw data. Produces cleaned datasets, cleaning report, and merge report. Trigger: clean data, merge data, process data, harmonize data. Do NOT load for: audit, analysis, review, release, setup.
kind
workflow
purpose
Generate and run reproducible data cleaning and merging scripts while preserving raw data integrity
trigger
clean data, merge data, process data, harmonize data, /research-harness-clean
shape
workflow
role
executor
pair
research-harness-plan
owner
research-harness-core
since
2026-05-29
allowed-tools
["Read","Write","Edit","Bash","Glob","Grep"]
argument-hint
[--plan PATH] [--dry-run] [--task TASK-ID]
user-invocable
true
effort
high
Research Harness Clean
Generate and run reproducible data cleaning, harmonization, reshaping, and merging scripts.
Raw data is never modified. Every cleaning decision is documented in the cleaning report.
This skill runs after /research-harness-audit and before /research-harness-plan.
Quick Reference
Input
Action
/research-harness-clean
Run all cleaning tasks in reports/data_cleaning_plan.md
/research-harness-clean --task 3
Run only cleaning task 3 from the plan
/research-harness-clean --dry-run
Write scripts but do not execute them; report what would run
/research-harness-clean --plan PATH
Use a cleaning plan at a custom path
Pre-flight Checks
Before writing any script:
Read reports/data_audit_report.md. If it does not exist, stop — audit must run first.
Read reports/data_cleaning_plan.md. If it does not exist, stop. Tell the user to fill in templates/data_cleaning_plan.md and save it as reports/data_cleaning_plan.md.
Confirm all source files listed in the cleaning plan exist under data/raw/.
Confirm all target output paths are under data/processed/ or data/intermediate/, not data/raw/.
If any pre-flight check fails: report which check failed and stop. Do not write scripts around the failure.
Procedure
Step 1 — Review the cleaning plan
Read reports/data_cleaning_plan.md in full.
Identify:
All cleaning tasks (renaming, type conversion, date parsing, missing-value coding, duplicates, unit harmonization, reshaping, winsorization flags)
All merge tasks (in execution order)
All derived variable definitions
All sample restriction filters
The final analysis-ready dataset name and path
If any merge task has unknown merge keys or unknown expected match rate: stop before writing any merge script. Report the ambiguity and ask the user for clarification.
Step 2 — Write the cleaning script
Write a single cleaning script (or one script per major task if the cleaning plan is large).
Script requirements:
Language: R, Stata, or Python — use whichever the user specifies or whichever is appropriate given the data format. Default to R if unspecified.
* Project: <study name>
* Task: data cleaning
* Date: YYYY-MM-DD
* Analyst: Claude Code
log using "logs/clean_YYYYMMDD.log", replace text
use "data/raw/filename.dta", clear
display "Loaded: `c(N)' rows"
* Filter
count
keep if ...
display "Remaining after filter: `c(N)'"
save "data/processed/analysis_ready.dta", replace
log close
Step 3 — Handle each cleaning task from the plan
Implement each task in the cleaning plan in order:
Renaming: rename variables exactly as specified in the plan. Do not rename variables not in the plan.
Type conversion: convert types as specified. Log any values that cannot be converted.
Date parsing: parse dates to ISO 8601 (YYYY-MM-DD). Log any unparseable dates.
Missing-value coding: recode non-standard missing codes to NA / .. Log the count of values recoded.
Duplicate check: identify and handle duplicates per the plan (drop first / drop last / flag / stop). Log duplicates found.
ID consistency: verify IDs are consistent per the plan. Log any inconsistencies.
Unit harmonization: apply conversion factors as specified. Do not guess conversion factors not in the plan.
Winsorization / outlier flags: apply only if explicitly specified in the plan. Log bounds and count of affected observations.
Reshaping: reshape as specified. Log the row count before and after.
Derived variables: generate each derived variable per the formula in the plan. Log the count of non-missing values produced.
Step 4 — Handle each merge task
For each merge task in the cleaning plan, in execution order:
Before merging:
Confirm merge keys exist in both files
Count rows in each file
Check for duplicate keys in each file
Log pre-merge counts
Merge:
Perform the merge using the specified keys and merge type
Log post-merge row count
Count and log matched, unmatched-left, unmatched-right
After merging:
If match rate is far below the expected rate in the plan: stop, report the discrepancy, and ask the user whether to continue
If variable conflicts exist (same variable name, different values): do not silently choose one. Report the conflict and stop unless the plan specifies a resolution
Handle unmatched observations per the plan (keep / drop / flag)
Write merge_report.md entry:
For every merge, copy the templates/merge_report.md block and fill in all fields. Append to reports/merge_report.md.
If merge keys are ambiguous or missing from the plan: stop. Do not guess. Document the problem and ask for clarification.
Step 5 — Run the script
Run the cleaning script. Capture the exit code.
If exit code is 0: proceed
If exit code is non-zero: read the log, identify the error, fix the script, and re-run (up to 2 retries)
If the script fails after 3 attempts: stop. Write the error to the cleaning report under "Unresolved Issues." Mark the task cc:blocked in analysis_plan.md. Do not fabricate output.
Step 6 — Verify output
After the script runs:
Confirm the output file exists at the path specified in the plan
Confirm the row count in the output matches the cleaning report
Confirm data/raw/ was not modified (check that file sizes match or use git status data/raw/)
Step 7 — Write the cleaning report
Copy templates/data_cleaning_report.md to reports/data_cleaning_report.md and fill in all sections.
All of these must be present:
Input file row counts
Output file row count
Every filter step with obs dropped
Every rename, recode, and derived variable
Merge summary (with reference to reports/merge_report.md)
Verification checklist: all items checked PASS or documented as FAIL
Forbidden Actions
Do not write to or modify any file under data/raw/
Do not silently drop observations — every filter must be logged with a count
Do not guess merge keys — stop and ask if ambiguous
Do not silently resolve variable conflicts across source files — report and stop
Do not claim a cleaned dataset was created unless the script ran successfully (exit code 0) and a log exists
Do not use absolute file paths in scripts
Do not winsorize or flag outliers unless explicitly specified in the cleaning plan
Evidence Requirements
Cleaning script exists at documented path
logs/clean_YYYYMMDD.log exists
data/processed/ output file exists
reports/data_cleaning_report.md exists with all sections populated
reports/merge_report.md exists with one entry per merge (if any merges occurred)
No files in data/raw/ were modified
Completion Criteria
Pre-flight checks passed
Cleaning script wrote and ran without error
Log file exists
Output file exists with expected row count
All observations dropped are documented with reason and count
All merges have a merge_report.md entry with pre/post counts and match rates
