Ma Publication Quality

Ma Publication Quality

Overview

Add high-impact-journal quality controls: reporting checklists, robustness diagnostics, GRADE SoF outputs, and manuscript consistency audits.

Inputs

• 06_analysis/ outputs
• 07_manuscript/ Quarto files
• 08_reviews/grade_summary.csv
• 02_search/round-01/search_report.md
• 02_search/round-01/search_audit.json

Outputs

• 06_analysis/tables/hakn_summary.txt
• 06_analysis/tables/prediction_intervals.csv
• 06_analysis/figures/baujat_*.png
• 06_analysis/figures/influence_*.png
• 06_analysis/tables/grade_summary.html
• 07_manuscript/prisma_checklist.md
• 07_manuscript/moose_checklist.md (if observational)
• 09_qa/claim_audit.md
• 09_qa/crossref_report.md
• 09_qa/reporting_checklist_audit.md
• 09_qa/claim_table_check.md

Workflow

1. Initialize reporting checklists with scripts/init_reporting_checklists.py.
   • Use scripts/init_reporting_checklists.py
   • Copy references/prisma2020-checklist-template.md → 07_manuscript/prisma_checklist.md
   • Copy references/moose-checklist-template.md → 07_manuscript/moose_checklist.md (if observational)
2. Copy R templates from assets/r/ into 06_analysis/ and run after the primary model scripts.
   • Copy assets/r/10_robust_diagnostics.R → 06_analysis/10_robust_diagnostics.R
   • Write to 06_analysis/tables/hakn_summary.txt, 06_analysis/tables/prediction_intervals.csv
   • Write to 06_analysis/figures/baujat_*.png, 06_analysis/figures/influence_*.png
3. Generate GRADE Summary of Findings table from 08_reviews/grade_summary.csv.
   • Read from 08_reviews/grade_summary.csv
   • Write to 06_analysis/tables/grade_summary.html
4. Run claim audit on Abstract vs Results and save to 09_qa/claim_audit.md.
   • Use scripts/claim_audit.py
   • Read from 07_manuscript/00_abstract.qmd and 07_manuscript/03_results.qmd
   • Write to 09_qa/claim_audit.md
5. Run reporting checklist completion audit and save to 09_qa/reporting_checklist_audit.md.
   • Use scripts/check_reporting_completion.py
   • Read from 07_manuscript/prisma_checklist.md
   • Write to 09_qa/reporting_checklist_audit.md
6. Run claim-to-table check and save to 09_qa/claim_table_check.md.
   • Use scripts/claim_table_check.py
   • Read from 07_manuscript/03_results.qmd and 06_analysis/tables/*.csv
   • Write to 09_qa/claim_table_check.md
7. Run cross-reference check to ensure figures/tables are referenced in manuscript.
   • Use scripts/crossref_check.py
   • Read from 07_manuscript/*.qmd and 06_analysis/figures/, 06_analysis/tables/
   • Write to 09_qa/crossref_report.md
8. Update checklists and re-run final_qa_report.py.
   • Use ma-end-to-end/scripts/final_qa_report.py
   • Write to 09_qa/final_qa_report.md

Resources

• assets/r/ contains robust diagnostics and SoF scripts.
• scripts/claim_audit.py checks numeric claims in Abstract vs Results.
• scripts/check_reporting_completion.py checks PRISMA/MOOSE completion.
• scripts/claim_table_check.py checks Results numeric claims vs tables.
• scripts/crossref_check.py checks for unreferenced figures/tables.
• scripts/init_reporting_checklists.py copies PRISMA/MOOSE templates.
• references/prisma2020-checklist-template.md
• references/moose-checklist-template.md

Validation

• Do not render final manuscript until PRISMA/MOOSE checklists are filled.
• Ensure all figures/tables are referenced in Results.

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