Peer review round 3: LivingGLP1 protocol 0.3.0 (reviewer fable-5.1)

What I verified on 2026-10-12: the rendered 1.2.0 PubMed query runs with no field errors (28,673 records; the six phrases PubMed reports as not found are development codes kept by design); IDegLira[nm] returns 57; the mechanism block still adds 185 records the rest of the strategy misses, as the text says; a script over the tables finds no overlapping windows for any outcome and population, exactly one primary window for every pair except O120, every binary, time to event and count outcome mapped once in turner_map.csv, every continuous outcome in reference_sd.csv, and 76 outcomes as stated; source_pubmed.R (lines 148 to 149) and source_ctgov.R (lines 108 to 112) now write the reconciliation into the run log, so that claim in the response is true.

1. Round 2 comments

2. New errors and inconsistencies

Major

1. windows.csv W22 (P14A to P14E, lower limit 12 weeks). The only randomized trial of semaglutide in alcohol use disorder (Hendershot 2025, PMID 39937469) treated for 9 weeks, and the exenatide smoking cessation trial (Yammine 2021, PMID 33831213) assessed abstinence after 6 weeks of treatment; neither falls in any window, so the P14A and P14B primary outcome networks lose eligible trials. This is the error class of round 1 item 1 and round 2 item 2. Replacement: add "W33, O110A;O110B;O111;O111B;O112;O113;O114, P14A;P14B;P14C;P14D;P14E, secondary, nearest_target, 8, 4, 12", which keeps the 12 to 40 week primary network for trials with a maintenance phase, gives short phase 2 trials a network of their own, and preserves both invariants (upper exclusive 12 against W22's inclusive 12; still one primary window per pair). If the owner would rather have them in the primary network, lower W22's lower_week_inclusive to 4 instead and let nearest_target choose.

Minor

2. priors.csv PR04 and PR08; protocol.qmd line 477. O24C is an SMD outcome (reference_sd.csv already lists "O24B;O24C"), but PR04 and PR08 apply to O24B only and the text says "standardized mean differences only for O24B". Replacement: applies_to "O24B; O24C" in both rows; "standardized mean differences only for O24B and O24C".

3. outcomes.csv O22C. Defined as "as in O22 or O22B plus cardiovascular death", so it pools the 40 and 50 percent eGFR thresholds that O22 and O22B keep apart. Replacement mapping_rules: "The eGFR decline threshold (40 or 50 percent) is recorded per trial; when both appear in one network, the 50 percent trials form the primary network and the 40 percent trials are added in a sensitivity analysis. Never pooled with O22; O22B or O22D."

4. windows.csv and the Time windows text (line 431). O120 has no window, so "each outcome and population has exactly one primary window" is false. Replacement: append to the longest_follow_up sentence "O120 is synthesized from nonrandomized studies only, per pregnancy, and has no window."

5. outcomes.csv O04B; Absolute effects; CINeMA imprecision. O04B is the one relative threshold with rare_outcome = no, while the text ties relative thresholds to the rare flag. It is right in practice (no baseline rate is modeled) but unstated. Replacement, in Absolute effects after the rare outcome sentence: "Count outcomes synthesized only from reported rate ratios (O04B) have no modeled baseline rate; their threshold is the rate ratio range 1/1.25 to 1.25." Add "or rate outcomes on reported rate ratios" to the parenthesis in the imprecision rule.

6. Outcomes and prioritization, line 443. "Percent weight change (O10) uses 40 to 104 weeks ... except P12 and P15 (12 to 52 weeks)": O10 does not apply to P12 or P15; O10B does. Replacement: "Percent weight change (O10) uses 40 to 104 weeks (target 68); its short trial version O10B, used in P12 and P15, uses 12 to 52 weeks (target 24)."

7. nodes.csv OTHER_ACTIVE_<name>; Networks and nodes text. The note says a numeric dose replaces "<dose>", but the placeholder is <name>, and the text describes templates as "agents whose doses are not yet known". Replacement note: "Template, not a node: a molecule level comparator node named at extraction replaces <name>." Text: "Rows marked is_template = yes (agents whose doses are not yet known, and the other active comparator placeholder)".

Conclusion

The methods are sound, the search claims reproduce and the round 2 fixes are complete. Every item above is a row or sentence edit; item 1 removes eligible trials from two primary outcome networks, which is the one reason I do not accept today. A version carrying these replacements, with the administrative conditions and the logged four source harvest tracked in the checklist, would receive ACCEPT from me without further methods review.

VERDICT: MINOR REVISION