Peer review round 19: LivingGLP1 protocol 0.19.0 (reviewer grok-4.7)
1. Round 18 comments
G18-1. Resolved. In Absolute effects (protocol.qmd, the binomial (f_a) clause), (f_a) is the longest follow-up at which status is known for every participant randomized to that arm. Known status is the definition in the outcomes section, applied to that arm alone. The sensitivity analysis uses the longest follow-up at which status is known for at least 95 percent of that arm, and unknown participants stay in the denominator and count as event free. The requirement that (f_a) reach the analyzed horizon sits outside that parenthetical, so a 95 percent follow-up that stops short of the horizon does not qualify. Shorter arms stay out of the baseline estimate, and nothing is extrapolated. This is the same sentence that answers F18-1. The adoption matches the proposal.
G18-2. Resolved. The Amendments paragraph now indexes every row in protocol/peer-review/comments.csv whose action field contains deferred to amendment. That match covers F12-note (deferred to amendment), F14-note (noted; deferred to amendment), F15-note (deferred to amendment), F16-note (revised; part deferred to amendment), F17-4, F17-5, and the new F18-3 row (deferred to amendment). Rows whose response text mentions the phrase, and whose action is revised or corrected, stay outside the index. This is the same sentence that answers F18-2.
The other round 18 items leave both fixes in place.
F18-0. The corrected reason is sound. Fixed time scenario inputs stay in the pre-analysis amendment with the deferred reference arm likelihood work (F12-note, F16-note). The deferral itself is unchanged. The round 17 response file still carries the earlier wording. The correction is the round 18 response and the F18-0 row, action corrected, which is the same record pattern as F17-0. No analysis rule changes.
F18-3. The deferral is sound. A reported Aalen-Johansen cumulative incidence used directly as (F_{\mathrm{ref}}) still has no one arm or pooling rule. The sentence that keeps the piecewise and exponential one arm rule off that source is unchanged from version 0.18.0. The F18-3 row states the missing rule in its own words and carries action deferred to amendment, so the repaired pointer keeps it on the amendment queue beside F12-note. It is a gap carried forward, and version 0.19.0 adds no new rule for it.
2. New issues
No major errors. No minor errors. The relative effect models, estimands, and competing risk likelihoods are unchanged. The two adopted sentences are executable and agree with the surrounding absolute effect rules: one qualifying input per arm, the Poisson likelihood when both count inputs are reported, zero counts left uncorrected, and a reference arm admitted only when its follow-up reaches the analyzed horizon.
3. Checks and registration
Against the version 0.18.0 snapshot, the only authoritative edits are in protocol.qmd (subtitle and status line to version 0.19.0 and eighteen rounds; the outcomes.csv version citation, still 77 outcomes; the Amendments pointer; the binomial (f_a) parenthetical) and in amendments.csv (A018, dated 2026-10-13, version 0.19.0, sections Absolute effects and amendments, six comments, before results). Those six comments are the six round 18 rows in comments.csv. The other twelve authoritative tables are byte identical to the snapshot, including the applies_to field of PR02. concepts.yaml remains version 1.2.0 and is byte identical to the snapshot. R/search_strategy.R still builds the PubMed, Europe PMC (excluding patents), OpenAlex, and ClinicalTrials.gov queries from the class terms, the agent terms, the mechanism block, and the PubMed vocabulary. The Chinese terms remain only in concepts.yaml. The iGlarLixi switching row remains a template (is_template yes). The Quarto file was read and was not rendered. The search renderer was read and was not executed.
Team names, affiliations, funding, competing interests, confirmation of Embase access, PRESS review by a human information specialist, verification of the Chinese terms by a Chinese-reading team member, and confirmation and locking of provisional thresholds by clinical advisors and patient partners remain administrative pre-registration conditions. The checklist also lists an OpenAlex API key and a logged harvest of all four API sources before the baseline search. Those items do not affect this verdict. I would approve the methods for registration once the administrative pre-registration conditions are completed.
VERDICT: ACCEPT