Report: bootstrap SE section (Table 6)

Co-Authored-By: Claude Opus 5.5 <[email protected]>

reports/draft-report.Rmd

@@ -276,6 +276,28 @@ W5/WR bias.
 are near 1 for CCW (0.96–1.07, except WR 0.87). They are 0.83–0.92 for landmark and sequential trials
 in W0, and 0.58 for landmark in W1.
 
+# 7. Standard errors: physician-cluster bootstrap check (D28, D53)
+
+```{r boot}
+bf <- list.files(file.path(root, "results", "bootstrap"), pattern = "\\.csv$", full.names = TRUE)
+if (length(bf)) {
+  bt <- rbindlist(lapply(bf, fread))
+  mv <- reps[analysis == "main" & variant == "V1_ignore" & rep %in% unique(bt$rep),
+             .(world, scenario, rep, design, contrast, outcome, se_patient, se_cluster)]
+  bt <- merge(bt, mv, by = c("world", "scenario", "rep", "design", "contrast", "outcome"))
+  emp <- perf[analysis == "main" & variant == "V2_cluster", .(world, scenario, design, contrast, outcome, emp_se)]
+  x <- bt[, .(reps = .N, boot = sqrt(mean(boot_se^2)), patient = sqrt(mean(se_patient^2)),
+              cluster = sqrt(mean(se_cluster^2))), by = .(world, scenario, design, contrast, outcome)]
+  x <- merge(x, emp, by = c("world", "scenario", "design", "contrast", "outcome"))
+  x <- x[outcome == "disease" & contrast != "A_B2"]
+  knitr::kable(x[order(world, scenario, design), .(World = world, Scenario = scenario, Design = design,
+    `Empirical SE (100 reps)` = pp(emp_se, 2), `Bootstrap SE` = pp(boot, 2), `Model SE, cluster` = pp(cluster, 2),
+    `Model SE, patient` = pp(patient, 2), `Bootstrap / empirical` = round(boot / emp_se, 2),
+    `Cluster / empirical` = round(cluster / emp_se, 2))],
+    caption = "Table 6. Disease composite. Bootstrap: 50 physician-cluster resamples on each of replicates 1-20.")
+} else cat("Bootstrap results not yet available.")
+```
+
 # Supplement: full performance table
 
 ```{r supp}