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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]>
This commit is contained in:
chendun1995
2026-10-28 07:20:32 -04:00
co-authored by Claude Opus 5.5
parent fbc417662c
commit 5304c89316
10 changed files with 86 additions and 18 deletions
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pvisim/R/estimators.R
+9 -4
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@@ -197,6 +197,9 @@ run_designs <- function(rec, designs, variant, outcomes = c(male = "t_male", dis
cbind(contrast = "early_none", est_naive(rec, outcomes[[o]], variant), outcome = o))),
landmark = rbindlist(lapply(names(outcomes), function(o)
cbind(contrast = "early_none", est_landmark(rec, outcomes[[o]], variant, extra_covs = rec$extra_covs), outcome = o))),
landmark_m5 = rbindlist(lapply(names(outcomes), function(o)
cbind(contrast = "early_none", est_landmark(rec, outcomes[[o]], variant, extra_covs = rec$extra_covs,
at_landmark = TRUE), outcome = o))),
ccw = est_ccw(rec, outcomes, variant, rs = copy(rs), phat = phat, comparators = cmp),
seq = cbind(contrast = "now_not", est_seq(rec, outcomes, variant, rs = copy(rs), phat = phat)))
r[, `:=`(design = design, variant = variant, n = nrow(rec$patients))]
@@ -239,9 +242,11 @@ fit_pvi_ps <- function(p, variant, covs = c(BASE_COVS, "sev_obs", "sev0")) {
}
#' Landmark at month W (D13): patients alive and MALE-free at the start of month W;
#' exposure = PVI in months 0..W-1; covariates at diagnosis and at month W-1;
#' outcome counted in months W..horizon-1.
est_landmark <- function(rec, outcome = "t_male", variant = "V1_ignore", horizon = 60L, extra_covs = NULL) {
#' exposure = PVI in months 0..W-1; covariates at diagnosis; outcome counted in months
#' W..horizon-1. With at_landmark = TRUE the propensity score also uses severity at month
#' W-1, which a PVI has already changed (supplement, D53).
est_landmark <- function(rec, outcome = "t_male", variant = "V1_ignore", horizon = 60L, extra_covs = NULL,
at_landmark = FALSE) {
W <- rec$par$size$window
p <- copy(rec$patients)[(is.na(t_death) | t_death >= W) & (is.na(t_male) | t_male >= W)]
p[, `:=`(t_out = get(outcome), arm = ifelse(!is.na(t_pvi) & t_pvi < W, "early", "none"))]
@@ -249,7 +254,7 @@ est_landmark <- function(rec, outcome = "t_male", variant = "V1_ignore", horizon
p <- merge(p, rec$pm[t == W - 1L, .(id, sev_obs)], by = "id")
p <- merge(p, rec$pm[t == 0, .(id, sev0 = sev_obs)], by = "id")
p[, pvi := as.integer(arm == "early")]
ps <- fit_pvi_ps(p, variant, covs = c(BASE_COVS, "sev_obs", "sev0", extra_covs))
ps <- fit_pvi_ps(p, variant, covs = c(BASE_COVS, "sev0", if (at_landmark) "sev_obs", extra_covs))
p[, w := ifelse(arm == "early", 1 / ps, 1 / (1 - ps))]
d <- expand_followup(p[!is.na(w)], W, horizon)
rd_from_aj(aj_cif(d, horizon), "early", "none")