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Speed-ups (shared PVI fit, clones once, case-control sampled deferred model); final scale 200 reps extending the draft (D51)

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Co-Authored-By: Claude Opus 5.5 <[email protected]>
This commit is contained in:
chendun1995
2026-10-27 09:31:03 -04:00
co-authored by Claude Opus 5.5
parent e1457ccc1e
commit cfc9da2c87
6 changed files with 288 additions and 65 deletions
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simulations/run_experiment.R
+10 -18
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@@ -10,7 +10,7 @@ cores <- as.integer(opt("--cores", "10"))
cfg <- yaml::read_yaml("simulations/config/experiments.yml")
g <- cfg[[grid_name]]; sc <- cfg$scales[[scale]]
worlds <- if (is.null(opt("--worlds", NULL))) g$worlds else strsplit(opt("--worlds", NULL), ",")[[1]]
outdir <- file.path("results", grid_name, scale)
outdir <- file.path("results", grid_name, if (is.null(sc$dir)) scale else sc$dir)
jobs <- CJ(world = worlds, scenario = unlist(g$scenarios), rep = seq_len(sc$reps), sorted = FALSE)
jobs[, file := file.path(outdir, world, scenario, sprintf("rep%03d.csv", rep))]
todo <- jobs[!file.exists(file)]
@@ -21,25 +21,17 @@ one_job <- function(i) {
par <- load_params(j$world, j$scenario)
rec <- simulate_records(par, rep = j$rep, n = sc$n_patients)
out <- list()
with_v2 <- function(r) if (r$variant[1] == "V1_ignore") # same fit, two SEs
rbind(r, copy(r)[, `:=`(variant = "V2_cluster", se = se_cluster)]) else r
nce_out <- c(male = "t_male", disease = "t_disease")
for (v in g$variants) {
for (d in g$designs) {
r <- run_design(rec, d, v)
if (v == "V1_ignore") { # same fit, two SEs
r2 <- copy(r)[, `:=`(variant = "V2_cluster", se = se_cluster)]
r <- rbind(r, r2)
}
out[[length(out) + 1]] <- r[, analysis := "main"]
}
if (isTRUE(g$nce)) for (d in c("landmark", "ccw")) {
r <- run_design(nce_records(rec), d, v, outcomes = c(male = "t_male", disease = "t_disease"))
if (v == "V1_ignore") r <- rbind(r, copy(r)[, `:=`(variant = "V2_cluster", se = se_cluster)])
out[[length(out) + 1]] <- r[, analysis := "nce"]
}
}
for (d in c("landmark", "ccw")) { # unadjusted NCE (supplement, D36), V1/V2 only
r <- run_design(nce_records(rec, adjust_pvi = FALSE), d, "V1_ignore", outcomes = c(male = "t_male", disease = "t_disease"))
out[[length(out) + 1]] <- r[, analysis := "nce_unadjusted"]
out[[length(out) + 1]] <- with_v2(run_designs(rec, unlist(g$designs), v))[, analysis := "main"]
if (isTRUE(g$nce))
out[[length(out) + 1]] <- with_v2(run_designs(nce_records(rec), c("landmark", "ccw"), v, nce_out))[, analysis := "nce"]
}
# unadjusted NCE (supplement, D36), V1/V2 only
out[[length(out) + 1]] <- with_v2(run_designs(nce_records(rec, adjust_pvi = FALSE), c("landmark", "ccw"),
"V1_ignore", nce_out))[, analysis := "nce_unadjusted"]
out[[length(out) + 1]] <- run_oracle(rec)[, analysis := "main"] # own estimand of landmark / naive
for (dz in g$rct) {
r <- run_rct(par, dz, rep = j$rep)