ready set go

2026-06-03 11:28:14 -08:00
commit 097f88f85d
22 changed files with 8793 additions and 0 deletions
@@ -0,0 +1,71 @@
+suppressPackageStartupMessages(library(dplyr))
+
+simulate_icu_cohort <- function(n_patients = 1000, seed = 20260531) {
+  set.seed(seed)
+
+  tibble(
+    patient_id = seq_len(n_patients),
+
+    age = round(rnorm(n_patients, mean = 65, sd = 14)) |>
+      pmin(95) |>
+      pmax(18),
+
+    sex = sample(c("female", "male"), size = n_patients, replace = TRUE, prob = c(0.45, 0.55)),
+
+    sofa_score = rpois(n_patients, lambda = 7) |>
+      pmin(20),
+
+    lactate = round(rlnorm(n_patients, meanlog = log(3), sdlog = 0.5), 1) |>
+      pmin(15),
+
+    map = round(rnorm(n_patients, mean = 62, sd = 10)) |>
+      pmin(95) |>
+      pmax(35),
+
+    suspected_sepsis = rbinom(n_patients, size = 1, prob = 0.90)
+  ) |>
+    mutate(
+      hypotension_at_baseline = as.integer(map < 65),
+      elevated_lactate_at_baseline = as.integer(lactate >= 2),
+      eligible = as.integer(
+        suspected_sepsis == 1 &
+          hypotension_at_baseline == 1 &
+          elevated_lactate_at_baseline == 1
+      ),
+      severity_score = 0.04 * (age - 65) +
+        0.18 * (sofa_score - 7) +
+        0.25 * (lactate - 3) -
+        0.04 * (map - 62),
+      prob_early_vasopressor = plogis(-0.2 + severity_score),
+      early_vasopressor = rbinom(n(), size = 1, prob = prob_early_vasopressor),
+      time_to_vasopressor_hours = ifelse(
+        early_vasopressor == 1,
+        runif(n(), min = 0, max = 2),
+        runif(n(), min = 2, max = 24)
+      ) |>
+        round(2),
+      mortality_linear_predictor = -1.4 +
+        0.03 * (age - 65) +
+        0.20 * (sofa_score - 7) +
+        0.28 * (lactate - 3) -
+        0.05 * (map - 62) -
+        0.25 * early_vasopressor,
+      prob_death_28d = plogis(mortality_linear_predictor),
+      death_28d = rbinom(n(), size = 1, prob = prob_death_28d)
+    ) |>
+    select(
+      patient_id,
+      age,
+      sex,
+      sofa_score,
+      lactate,
+      map,
+      suspected_sepsis,
+      hypotension_at_baseline,
+      elevated_lactate_at_baseline,
+      eligible,
+      early_vasopressor,
+      time_to_vasopressor_hours,
+      death_28d
+    )
+}