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D53: landmark on baseline covariates (month-5 version as landmark_m5), NCO-1 depends on PVI-free severity, physician-cluster bootstrap script

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Co-Authored-By: Claude Opus 5.5 <[email protected]>
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chendun1995
2026-10-28 07:20:32 -04:00
co-authored by Claude Opus 5.5
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@@ -109,3 +109,4 @@ Each decision is listed with the date and the reason for it. Settled decisions a
| # | Decision | Why |
|---|---|---|
| 52 | **Draft run done:** 8 worlds × 3 scenarios × 100 replicates of 50,000 patients; 9.4 h on 11 cores; 0 errors. 16 of 288,000 estimates are NA (sequential trials, V4, 4 replicates) and are dropped. Summary: `simulations/04_summarise.R` writes `results/summary/`. Report: `reports/draft-report.Rmd`. Two open questions: (Q1) the landmark propensity model adjusts for month-5 severity, a post-PVI mediator, which drives the landmark question gap (W1 own truth about 20 pp vs a reference of 7.2 pp); with baseline covariates only, the 20-replicate oracle mean is 8.1. (Q2) NCO-1 has no severity term in the DGP, contrary to D32, so it cannot detect W5/WR bias. The bootstrap check (D28) waits on Q1/Q2. | Surfaced by the draft results. |
| 53 | **Answers to D52 (user, 2026-10-28).** (Q1) **The primary landmark propensity score uses baseline covariates only** (diagnosis covariates and month-0 severity). The version that also adjusts for month-5 severity becomes `landmark_m5` (supplement). It conditions on a mediator, because a PVI in months 0–5 has already changed that severity. Both versions get their own oracle. (Q2) **NCO-1 now depends on severity (coefficient 0.3)**, using the patient's **PVI-free severity path** (the same baseline, rate and monthly noise, with no relief and no kappa). That way NCO-1 shares the confounder but still cannot be affected by PVI (only through death as a competing risk, D46). Intercept −6.75 keeps 5-year NCO-1 incidence at about 9.3%. This is the best case for a patient-level negative control, and the paper says so. **Bootstrap (D28, reduced):** W0 and WR × null and harm, replicates 1–20 of the main run, 50 physician-cluster resamples each, V1 point estimates, about 8 s per resample. Compare the bootstrap SD with the model SE (patient and cluster) and the empirical SE. **The rerun goes to `results/main/n50k_v2`;** the first draft stays in `n50k`. Truths are recomputed (NCO-1 changed). | Landmark analyses in practice adjust for baseline covariates. D32 intended NCO-1 to share severity. |