LivingGLP1
Round 12 · protocol version 0.12.0

Peer review round 12

GPT-6 Astra

accept

Read the verbatim review

Fable 5.1

accept

Read the verbatim review

Grok 4.7

major revision

Read the verbatim review

Version 0.12.0 as reviewedFiles on GitHubPrevious roundNext round

Round 12: response to reviewers

Protocol version reviewed: 0.12.0. Revised version: 0.13.0.

Verdicts: GPT-6 Astra ACCEPT; Fable 5.1 ACCEPT; Grok 4.7 MAJOR REVISION (one item, also raised as minor by Fable 5.1). GPT-6 Astra raised no comments. Every comment is answered below and recorded in ../comments.csv.

Summary of main changes

  • Curve inversion uncertainty: the Jacobian of the map to log hazards; one multivariate random effects model across arms with joint predictive draws, so copied grid intervals stay one draw.
  • Author supplied covariances paired with the authors own ordinate estimates; data items wording.

Grok 4.7 (grok-4.7)

G12-M1 (major; Competing risks). The Jacobian was of the hazards, not the log hazards; per interval pooling dropped the shared draw.

Response (revised). Agreed; your replacement passage adopted. J is the Jacobian of the map from ordinates to log hazards; reported counts give independent log hazards with variance 1/d_k; copies of one reported interval are one coordinate; the arms are pooled in one multivariate random effects model, the reference hazard per grid interval is the median of its marginal predictive distribution, and integrated risks and scenarios use joint predictive draws. fable-5.1 (F12-1) raised the same dependence point.

Fable 5.1 (fable-5.1)

F12-1 (minor; Competing risks). How per interval pooling preserves within arm dependence.

Response (revised). Agreed; see G12-M1 (one multivariate model with joint predictive draws).

F12-2 (minor; Data items). Self contradictory where published wording.

Response (revised). Agreed; where published now qualifies the curves, and covariances are requested from authors with their ordinate estimates when not published.

F12-3 (minor; Competing risks). Ordinates paired with an author supplied covariance.

Response (revised). Agreed; author supplied covariances are paired with the authors own ordinate estimates, and digitized values are inverted only with a published covariance at the same times.

F12-note (note; Absolute effects; priors). Reported Aalen-Johansen values rarely sit at the analyzed horizon; no heterogeneity prior row for the reference arm meta-analysis.

Response (deferred to amendment). Noted as pre-existing matters to settle by amendment before the first analysis, as the reviewer suggests; they are recorded here so that they are not lost.

GPT-6 Astra (gpt-6-astra)

No comments; verdict ACCEPT.

The brief every reviewer received

Peer review round 12: protocol version 0.12.0

You reviewed versions 0.1.0 to 0.11.0 (rounds 1 to 11) of this protocol as reviewer {REVIEWER}. Do NOT edit, create or delete any file.

Read, in the repository root:

  • protocol/peer-review/round-11/review-{REVIEWER}.md (your round 11 review)
  • protocol/peer-review/round-11/response.md (point by point responses to all three reviewers in round 11; yours are the {PREFIX}11- items)
  • protocol/protocol.qmd (version 0.12.0) and the tables it declares authoritative: protocol/populations.csv, outcomes.csv, windows.csv, agents.csv, nodes.csv, node_classes.csv, effect_modifiers.csv, harms_nrs.csv, priors.csv, reference_sd.csv, turner_map.csv, registry_dose_candidates.csv, amendments.csv
  • search/strategies/concepts.yaml (version 1.2.0) and R/search_strategy.R

Tasks:

  1. For each of your round 11 comments, state whether the response and revision resolve it (resolved, partly resolved, not resolved), with a short reason. Where a response declines or partly adopts your proposal with a stated reason, judge the reason.
  2. List any new errors, inconsistencies or non-executable rules introduced by the revision, ordered by severity (major, then minor), with the exact file, section or row, and concrete replacement text or values.
  3. Administrative items that only the review owner can supply (team names, affiliations, funding, competing interests, confirmation of Embase access, PRESS review by a human information specialist, verification of Chinese terms by a Chinese-reading team member, confirmation and locking of provisional thresholds by clinical advisors and patient partners) are tracked as pre-registration conditions in the administrative checklist. Do not withhold acceptance for their absence alone; judge whether the methods are acceptable for registration once they are completed.

Use American English and do not use dashes as sentence punctuation. Keep under 1,500 words.

End with exactly one line: VERDICT: ACCEPT or VERDICT: MINOR REVISION or VERDICT: MAJOR REVISION ACCEPT means you would approve the methods of this protocol for registration once the administrative pre-registration conditions are completed.