LivingGLP1
Round 14 · protocol version 0.14.0

Peer review round 14

GPT-6 Astra

accept

Read the verbatim review

Fable 5.1

accept

Read the verbatim review

Grok 4.7

minor revision

Read the verbatim review

Version 0.14.0 as reviewedFiles on GitHubPrevious roundNext round

Round 14: response to reviewers

Protocol version reviewed: 0.14.0. Revised version: 0.15.0.

Verdicts: GPT-6 Astra ACCEPT; Fable 5.1 ACCEPT; Grok 4.7 MINOR REVISION. GPT-6 Astra raised no comments. Every comment is answered below and recorded in ../comments.csv.

Summary of main changes

  • Competing risk pooling: explicit one arm draw, exponentiation of log hazard draws, and the definition of y_a and V_a for counts.
  • A single shared interval from 0 to the horizon is the exponential approximation, with its support judgment and label.
  • Absolute effects: PR16 cited for competing risk routes; Kaplan-Meier values and rates pooled on the log cumulative hazard under PR17.

Grok 4.7 (grok-4.7)

G14-1 (minor; Competing risks). The one arm rule contradicted the predictive draw, and exponentiation was not stated.

Response (revised). Agreed; your text adopted: with one covering arm u_new is not drawn and each draw is from N(y_a, V_a); with two or more, mu + Z u_new at that draw tau_k; hazards are the exponentials of the log hazards, integrated jointly; scenario draws are exponentiated before integration. fable-5.1 (F14-3) raised the one arm point too.

G14-2 (minor; Competing risks). y_a and V_a not assigned for counts.

Response (revised). Agreed; y_a is the vector of estimated log hazards, one coordinate per event and common interval, in that order, and for counts V_a is diagonal with variances approximately 1/d_k.

G14-3 (minor; Competing risks). A single shared interval skipped the constant hazard gate; d_k ambiguous.

Response (revised). Agreed; your text adopted: when the identical boundaries are the single interval from 0 to the horizon, the piecewise fit is the exponential approximation, with its support judgment and label; the separate exponential route applies only when the piecewise route is unavailable and every arm supplies counts and person time from 0 to the horizon; d_k is the count from 0 to the horizon. fable-5.1 (F14-1) raised the same overlap.

Fable 5.1 (fable-5.1)

F14-1 (minor; Competing risks). One interval per arm belonged to two routes.

Response (revised). Agreed; resolved with the wording of G14-3, which also settles arms whose totals cover different follow-up: only counts from 0 to the horizon qualify for the single interval.

F14-2 (minor; Absolute effects). PR17 cited where PR16 applies.

Response (revised). Agreed; now "heterogeneity prior PR17; PR16 for the competing risk routes".

F14-3 (minor; Competing risks). One arm distribution implicit.

Response (revised). Agreed; see G14-1.

F14-4 (minor; Absolute effects). Pooling scale for mixed Kaplan-Meier and rate inputs.

Response (revised). Agreed; your text adopted: both enter one model on the log cumulative hazard at the horizon (log{-log(1-F)} with delta method variance; log(lambda t) with variance approximately 1/d) under PR17.

F14-note (note; Priors; absolute effects). PR16 scale 1 versus 0.5 without stated reason; reported Aalen-Johansen values that miss the horizon remain deferred.

Response (noted; deferred to amendment). PR16 uses Half-normal(0; 1^2) to match PR17 and the weakly informative log scale used for baseline risks, with 0.5 and 2 as sensitivity priors; the horizon matter stays deferred to the pre-analysis amendment, as agreed in round 12.

GPT-6 Astra (gpt-6-astra)

No comments; verdict ACCEPT.

The brief every reviewer received

Peer review round 14: protocol version 0.14.0

You reviewed versions 0.1.0 to 0.13.0 (rounds 1 to 13) of this protocol as reviewer {REVIEWER}. Do NOT edit, create or delete any file.

Read, in the repository root:

  • protocol/peer-review/round-13/review-{REVIEWER}.md (your round 13 review)
  • protocol/peer-review/round-13/response.md (point by point responses to all three reviewers in round 13; yours are the {PREFIX}13- items)
  • protocol/protocol.qmd (version 0.14.0) 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 13 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.