From 5e006b9021d18a66d1fe5884a8966ba02ca417f8 Mon Sep 17 00:00:00 2001
From: Daniel Sabanes Bove <daniel.sabanes_bove@roche.com>
Date: Mon, 8 Apr 2024 11:26:14 +0200
Subject: [PATCH] add naive method

---
 simulations/naive.R | 34 ++++++++++++++++++++++++++++++++++
 simulations/run.R   |  1 +
 2 files changed, 35 insertions(+)
 create mode 100644 simulations/naive.R

diff --git a/simulations/naive.R b/simulations/naive.R
new file mode 100644
index 00000000..39fca2f4
--- /dev/null
+++ b/simulations/naive.R
@@ -0,0 +1,34 @@
+# Method for a single data set.
+naive_method <- function(df) {
+  df$arm <- factor(df$arm)
+  model <- naive(
+    resp = "tt_pfs",
+    trt = "arm",
+    subgr = c("x_1", "x_2", "x_3", "x_4", "x_5", "x_6", "x_7", "x_8", "x_9", "x_10"),
+    data = df,
+    resptype = "survival",
+    status = "ev_pfs"
+  )
+  s <- summary(model)
+  s
+}
+
+# Analysis of a single scenario.
+naive_analysis <- function(scenario) {
+  assert_list(scenario)
+  results <- lapply(scenario, naive_method)
+}
+
+# Results across all scenarios.
+naive_file <- "results/naive.rds"
+naive_results <- if (file.exists(naive_file)) {
+  readRDS(naive_file)
+} else {
+  res <- lapply(
+    scenarios,
+    function(x) naive_analysis(x$scenario)
+  )
+  saveRDS(res, file = naive_file)
+  res
+}
+# todo: modify results format once target is clear
diff --git a/simulations/run.R b/simulations/run.R
index dd1eb0b3..38f5cb8d 100644
--- a/simulations/run.R
+++ b/simulations/run.R
@@ -28,5 +28,6 @@ source("functions.R")
 # Run analyses ----
 
 source("naivepop.R") # fast.
+source("naive.R")
 source("ridge.R")    # takes a few minutes.
 source("lasso.R")    # takes a few minutes.