Validation, NCE analysis, per-replicate oracle for landmark/naive, RCT truths script, resumable experiment runner
- W0 harm validation (40 reps): CCW and sequential ITT unbiased for their truths (|z| <= 0.7) - PVI models fitted separately inside and after the window - experiments.yml grid (8 worlds x 3 scenarios; designs x V1-V4; NCE; RCTs); smoke run clean Co-Authored-By: Claude Opus 5.5 <[email protected]>
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Claude Opus 5.5
+31
-12
@@ -21,13 +21,15 @@ VARIANTS <- c("V1_ignore", "V2_cluster", "V3_random", "V4_within")
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#' MALE and no PVI before the decision in month t: the risk set of the PVI model.
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pvi_risk_set <- function(rec) {
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p <- rec$patients
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pm <- merge(rec$pm, p[, c("id", "phys_id", BASE_COVS, "t_pvi", "pvi_elective", "t_male", "t_death"),
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extra <- intersect("t_pvi_orig", names(p))
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pm <- merge(rec$pm, p[, c("id", "phys_id", BASE_COVS, "t_pvi", "pvi_elective", "t_male", "t_death", extra),
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with = FALSE], by = "id")
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pm <- pm[(is.na(t_death) | t_death > t) & (is.na(t_male) | t_male > t) & (is.na(t_pvi) | t_pvi >= t)]
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pm[, pvi := as.integer(!is.na(t_pvi) & t_pvi == t)]
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sev0 <- rec$pm[t == 0, .(id, sev0 = sev_obs)]
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pm <- merge(pm, sev0, by = "id")
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pm[, `:=`(win = as.integer(t < rec$par$size$window), tt = pmin(t, 12))]
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if (length(extra)) pm[, pvi_before := as.integer(!is.na(t_pvi_orig) & t_pvi_orig < t)]
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pm[]
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}
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@@ -41,7 +43,7 @@ pvi_risk_set <- function(rec) {
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#' variant: V1/V2 no physician terms; V3 physician random intercept (glmer, nAGQ = 0);
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#' V4 physician fixed effects (fixest). Under V4 a physician with no PVI in a phase has
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#' no estimable intercept for it; the maximum-likelihood probability there is 0.
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fit_pvi <- function(data, newdata, variant) {
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fit_pvi <- function(data, newdata, variant, extra_covs = NULL) {
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out <- numeric(nrow(newdata))
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for (w in c(1L, 0L)) {
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i_new <- newdata$win == w
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@@ -49,13 +51,14 @@ fit_pvi <- function(data, newdata, variant) {
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d <- data[win == w]
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nd <- newdata[i_new]
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tt_levels <- if (w == 1L) "factor(tt)" else "splines::ns(t, df = 4)"
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out[i_new] <- fit_pvi_phase(d, nd, variant, tt_levels)
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# no exposure at all in a phase (the NCE after the window): probability 0
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out[i_new] <- if (sum(d$pvi) == 0) 0 else fit_pvi_phase(d, nd, variant, tt_levels, extra_covs)
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}
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out
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}
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fit_pvi_phase <- function(d, nd, variant, time_terms) {
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covs <- c(BASE_COVS, "sev_obs", "sev0")
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fit_pvi_phase <- function(d, nd, variant, time_terms, extra_covs = NULL) {
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covs <- c(BASE_COVS, "sev_obs", "sev0", extra_covs)
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if (variant == "V4_within") covs <- setdiff(covs, "obl")
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rhs <- paste(c(covs, time_terms), collapse = " + ")
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if (variant %in% c("V1_ignore", "V2_cluster")) {
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@@ -161,12 +164,13 @@ run_design <- function(rec, design, variant, outcomes = c(male = "t_male", disea
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nco1 = "t_nco1", nco2 = "t_nco2")) {
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rec <- restrict_variant(rec, variant)
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rs <- if (design %in% c("ccw", "seq")) pvi_risk_set(rec) else NULL
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phat <- if (design == "ccw") fit_pvi(rs, rs, variant) else NULL
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phat <- if (design == "ccw") fit_pvi(rs, rs, variant, rec$extra_covs) else NULL
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cmp <- if (is.null(rec$comparators)) c("B1", "B2") else rec$comparators
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out <- lapply(names(outcomes), function(o) {
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r <- switch(design,
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naive = cbind(contrast = "early_none", est_naive(rec, outcomes[[o]], variant)),
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landmark = cbind(contrast = "early_none", est_landmark(rec, outcomes[[o]], variant)),
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ccw = est_ccw(rec, outcomes[[o]], variant, rs = copy(rs), phat = phat),
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landmark = cbind(contrast = "early_none", est_landmark(rec, outcomes[[o]], variant, extra_covs = rec$extra_covs)),
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ccw = est_ccw(rec, outcomes[[o]], variant, rs = copy(rs), phat = phat, comparators = cmp),
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seq = cbind(contrast = "now_not", est_seq(rec, outcomes[[o]], variant, rs = copy(rs))))
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r[, `:=`(outcome = o, design = design, variant = variant, n = nrow(rec$patients))]
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use_patient <- variant == "V1_ignore"
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@@ -178,13 +182,13 @@ run_design <- function(rec, design, variant, outcomes = c(male = "t_male", disea
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#' Naive "ever early PVI" design: exposure = PVI in months 0..W-1, follow-up from month 0,
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#' baseline propensity score. Immortal time is present by construction.
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est_naive <- function(rec, outcome = "t_male", variant = "V1_ignore", horizon = 60L) {
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est_naive <- function(rec, outcome = "t_male", variant = "V1_ignore", horizon = 60L, extra_covs = NULL) {
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W <- rec$par$size$window
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p <- copy(rec$patients)
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p[, `:=`(t_out = get(outcome), arm = ifelse(!is.na(t_pvi) & t_pvi < W, "early", "none"))]
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p <- merge(p, rec$pm[t == 0, .(id, sev_obs)], by = "id")
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p[, pvi := as.integer(arm == "early")]
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ps <- fit_pvi_ps(p, variant, covs = c(BASE_COVS, "sev_obs")) # sev_obs is the month-0 value here
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ps <- fit_pvi_ps(p, variant, covs = c(BASE_COVS, "sev_obs", extra_covs)) # sev_obs is the month-0 value here
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p[, w := ifelse(arm == "early", 1 / ps, 1 / (1 - ps))]
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d <- expand_followup(p[!is.na(w)], 0L, horizon)
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rd_from_aj(aj_cif(d, horizon), "early", "none")
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@@ -212,7 +216,7 @@ fit_pvi_ps <- function(p, variant, covs = c(BASE_COVS, "sev_obs", "sev0")) {
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#' Landmark at month W (D13): patients alive and MALE-free at the start of month W;
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#' exposure = PVI in months 0..W-1; covariates at diagnosis and at month W-1;
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#' outcome counted in months W..horizon-1.
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est_landmark <- function(rec, outcome = "t_male", variant = "V1_ignore", horizon = 60L) {
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est_landmark <- function(rec, outcome = "t_male", variant = "V1_ignore", horizon = 60L, extra_covs = NULL) {
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W <- rec$par$size$window
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p <- copy(rec$patients)[(is.na(t_death) | t_death >= W) & (is.na(t_male) | t_male >= W)]
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p[, `:=`(t_out = get(outcome), arm = ifelse(!is.na(t_pvi) & t_pvi < W, "early", "none"))]
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@@ -220,7 +224,7 @@ est_landmark <- function(rec, outcome = "t_male", variant = "V1_ignore", horizon
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p <- merge(p, rec$pm[t == W - 1L, .(id, sev_obs)], by = "id")
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p <- merge(p, rec$pm[t == 0, .(id, sev0 = sev_obs)], by = "id")
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p[, pvi := as.integer(arm == "early")]
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ps <- fit_pvi_ps(p, variant)
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ps <- fit_pvi_ps(p, variant, covs = c(BASE_COVS, "sev_obs", "sev0", extra_covs))
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p[, w := ifelse(arm == "early", 1 / ps, 1 / (1 - ps))]
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d <- expand_followup(p[!is.na(w)], W, horizon)
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rd_from_aj(aj_cif(d, horizon), "early", "none")
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@@ -300,3 +304,18 @@ est_seq <- function(rec, outcome = "t_male", variant = "V1_ignore", horizon = 60
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data.table(est = sum(res$wt * res$est), se_patient = sqrt(sum(pi$inf^2)),
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se_cluster = sqrt(sum(tapply(pi$inf, pi$phys_id, sum)^2)), risk1 = NA_real_, risk0 = NA_real_)
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}
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#' Negative-control exposure (D32, D36): the early low-value procedure (NCE, months
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#' 0..W-1) takes the place of early PVI as the exposure; early-PVI status is adjusted
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#' for (time-varying "PVI before t" in CCW, "PVI in the window" at the landmark).
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#' Only the landmark and CCW (A vs B1) designs are run.
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nce_records <- function(rec, adjust_pvi = TRUE) {
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W <- rec$par$size$window
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p <- copy(rec$patients)
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p[, `:=`(t_pvi_orig = t_pvi, pvi_before = as.integer(!is.na(t_pvi) & t_pvi < W))]
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p[, `:=`(t_pvi = t_nce, pvi_elective = !is.na(t_nce))]
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rec$patients <- p
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rec$extra_covs <- if (adjust_pvi) "pvi_before" else NULL
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rec$comparators <- "B1"
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rec
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}
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