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]>

pvisim/R/records.R

@@ -68,3 +68,24 @@ replicate_seed <- function(world, scenario, rep) {
   h <- sum(utf8ToInt(key) * seq_along(utf8ToInt(key))^2)
   as.integer((h * 2654435761) %% 2147483647)
 }
+
+#' Physician-cluster bootstrap resample of a replicate's records (D28): physicians are
+#' drawn with replacement and each draw brings all of its patients, with new patient and
+#' physician ids so repeated physicians count as separate clusters.
+bootstrap_records <- function(rec, seed) {
+  set.seed(seed)
+  phys <- unique(rec$patients$phys_id)
+  draw <- data.table(phys_id = sample(phys, length(phys), replace = TRUE), new_phys = seq_along(phys))
+  map <- rec$patients[, .(id, phys_id)][draw, on = "phys_id", allow.cartesian = TRUE]
+  map[, new_id := seq_len(.N)]
+  remap <- function(x) {
+    x <- x[map[, .(id, new_id)], on = "id", allow.cartesian = TRUE]
+    x[, id := new_id][, new_id := NULL][]
+  }
+  out <- rec
+  out$patients <- remap(rec$patients)[map[, .(new_id, new_phys)], on = c(id = "new_id"), phys_id := i.new_phys]
+  out$pm <- setkey(remap(rec$pm), id, t)
+  out$hidden <- remap(rec$hidden)
+  out$hidden_pm <- remap(rec$hidden_pm)
+  out
+}