Baseline gut Fusobacterium predicts ustekinumab non-remission in CERTIFI: archived statistical analysis plans

This project is a public archive of the statistical analysis plans (SAPs) for a microbiome study of the ustekinumab induction cohort in the CERTIFI trial (NCT00771667; BioProject PRJNA418765, MGnify MGYS00005191) in Crohn's disease. It archives the four locked SAPs together with the timestamp evidence showing that each plan was finalized before its corresponding analysis was run. IMPORTANT: this page was created after the analyses were completed. It is a public archive and timestamp voucher, not a pre-registration. The plan was finalized ("locked") in four modules: Module 1 - baseline Fusobacterium (2026-09-20); Module 2 - genus-wide longitudinal modeling (2026-09-21); Module 3 - PICRUSt2 predicted functional pathways (main plan 2026-09-21, prior-pathway addendum 2026-09-24); Module 4 - MIMt species-level assignment (2026-09-25). The evidence for each lock date is the script header comments and decision records rather than file timestamps. The SAP documents themselves were archived retrospectively, so their file-system timestamps (09-27/09-29) are archive dates, not lock dates. Transparency note: on 2026-09-26 the Module 3 statistics script was corrected for a baseline-coefficient matching bug affecting three pathways whose names begin with a digit; all three were non-significant and no conclusion changed. All documents are in Chinese, the language of the locked plans and therefore the reference version; an English translation will be added before submission, stating that the Chinese version prevails in case of any discrepancy. Also archived at OSF: https://osf.io/dm8vq