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

Co-Authored-By: Claude Opus 5.5 <[email protected]>
2026-10-28 07:20:32 -04:00
parent fbc417662c
commit 5304c89316
10 changed files with 86 additions and 18 deletions
@@ -0,0 +1,35 @@
+# Physician-cluster bootstrap check of the model-based SEs (D28, reduced in D53).
+# Usage: Rscript simulations/05_bootstrap.R [reps] [B] [cores]
+# Writes results/bootstrap/<world>_<scenario>_rep<k>.csv: the estimate and the
+# bootstrap SD for each design, contrast and outcome (V1 point estimates).
+
+pkgload::load_all("pvisim", quiet = TRUE)
+suppressPackageStartupMessages(library(data.table))
+a <- commandArgs(TRUE)
+reps <- if (length(a) >= 1) as.integer(a[1]) else 20L
+B <- if (length(a) >= 2) as.integer(a[2]) else 50L
+cores <- if (length(a) >= 3) as.integer(a[3]) else 11L
+cfg <- yaml::read_yaml("simulations/config/experiments.yml")
+n <- cfg$scales$draft$n_patients
+outdir <- "results/bootstrap"; dir.create(outdir, showWarnings = FALSE, recursive = TRUE)
+designs <- c("naive", "landmark", "landmark_m5", "ccw", "seq")
+outs <- c(male = "t_male", disease = "t_disease")
+
+jobs <- CJ(world = c("W0", "WR"), scenario = c("null", "harm"), rep = seq_len(reps), sorted = FALSE)
+jobs[, file := file.path(outdir, sprintf("%s_%s_rep%03d.csv", world, scenario, rep))]
+todo <- jobs[!file.exists(file)]
+cat(sprintf("bootstrap: %d jobs, %d to do, B = %d, %d cores\n", nrow(jobs), nrow(todo), B, cores))
+res <- parallel::mclapply(seq_len(nrow(todo)), function(i) tryCatch({
+  j <- todo[i]
+  par <- load_params(j$world, j$scenario)
+  rec <- simulate_records(par, rep = j$rep, n = n)          # the same data as the main run's replicate
+  bs <- rbindlist(lapply(seq_len(B), function(b)
+    cbind(b = b, run_designs(bootstrap_records(rec, seed = 1e6 * j$rep + b), designs, "V1_ignore", outs))), fill = TRUE)
+  out <- bs[, .(boot_se = sd(est, na.rm = TRUE), boot_mean = mean(est, na.rm = TRUE), B = sum(!is.na(est))),
+            by = .(design, contrast, outcome)]
+  fwrite(out[, `:=`(world = j$world, scenario = j$scenario, rep = j$rep)], j$file)
+  NULL
+}, error = function(e) sprintf("%s/%s/%d: %s", todo$world[i], todo$scenario[i], todo$rep[i], conditionMessage(e))),
+mc.cores = cores, mc.preschedule = FALSE)
+err <- unlist(res[!vapply(res, is.null, TRUE)])
+cat(sprintf("done; %d errors\n", length(err))); if (length(err)) cat(head(err, 3), sep = "\n")