From 725a325b1357d5b6747653d7e883771403724f2a Mon Sep 17 00:00:00 2001
From: Dan Chaltiel <15105152+DanChaltiel@users.noreply.github.com>
Date: Sat, 24 Aug 2024 14:30:43 +0200
Subject: [PATCH] survival POC

---
 tests/testthat/_snaps/quick_surv.md | 24 +++++++++++++++++
 tests/testthat/test-quick_surv.R    | 41 +++++++++++++++++++++++++++++
 2 files changed, 65 insertions(+)
 create mode 100644 tests/testthat/_snaps/quick_surv.md
 create mode 100644 tests/testthat/test-quick_surv.R

diff --git a/tests/testthat/_snaps/quick_surv.md b/tests/testthat/_snaps/quick_surv.md
new file mode 100644
index 00000000..c99a21c3
--- /dev/null
+++ b/tests/testthat/_snaps/quick_surv.md
@@ -0,0 +1,24 @@
+# survival POC
+
+    Code
+      df = data.frame(time = c(71.1, 75.7, 78.7, 79, 95.1, 108, 120.1, 120.3, 121,
+        140.8, 145, 146.7, 160, 160, 167.6, 167.6, 225, 258, 275.8, 275.8, 275.8, 301,
+        304, 318, 350, 351, 360, 360, 400, 440, 460, 472), event = rep(rep(c(1, 0), 6),
+      c(6L, 1L, 2L, 1L, 1L, 1L, 2L, 7L, 1L, 3L, 1L, 6L)), group = rep(c("B", "A", "B",
+        "A", "B", "A", "B", "A", "B", "A", "B"), c(9L, 1L, 1L, 1L, 2L, 3L, 1L, 1L, 7L,
+        2L, 4L)))
+      df$surv = survival::Surv(df$time, df$event)
+      fit = survival::survfit(surv ~ group, data = df)
+      times = sort(fit$time)
+      a = summary(fit, times = times, extend = TRUE, data.frame = TRUE)
+      a %>% dplyr::filter(strata == "group=B") %>% dplyr::filter(time > 120 & time <
+        150) %>% dplyr::select(strata, time, n.risk, n.event, surv)
+    Output
+         strata  time n.risk n.event      surv
+      1 group=B 120.1     18       0 0.7500000
+      2 group=B 120.3     17       1 0.7058824
+      3 group=B 121.0     16       1 0.6617647
+      4 group=B 140.8     15       1 0.6617647
+      5 group=B 145.0     15       1 0.6176471
+      6 group=B 146.7     14       1 0.6176471
+
diff --git a/tests/testthat/test-quick_surv.R b/tests/testthat/test-quick_surv.R
new file mode 100644
index 00000000..b9e4530f
--- /dev/null
+++ b/tests/testthat/test-quick_surv.R
@@ -0,0 +1,41 @@
+test_that("survival POC", {
+
+  # mtcars3 %>%
+  #   transmute(time=as.numeric(disp), event=as.numeric(factor(am))-1,
+  #             group=ifelse(is.na(dummy2), "A", "B")) %>%
+  #   arrange(time) %>% as.data.frame() %>%
+  #   # filter(time<150) %>%
+  #   constructive::construct()
+
+  expect_snapshot({
+
+    df = data.frame(
+      time = c(71.1, 75.7, 78.7, 79, 95.1, 108, 120.1, 120.3, 121, 140.8, 145, 146.7, 160,
+               160, 167.6, 167.6, 225, 258, 275.8, 275.8, 275.8, 301, 304, 318, 350, 351,
+               360, 360, 400, 440, 460, 472),
+      event = rep(rep(c(1, 0), 6), c(6L, 1L, 2L, 1L, 1L, 1L, 2L, 7L, 1L, 3L, 1L, 6L)),
+      group = rep(c("B", "A", "B", "A", "B", "A", "B", "A", "B", "A", "B"),
+                  c(9L, 1L, 1L, 1L, 2L, 3L, 1L, 1L, 7L, 2L, 4L))
+    )
+
+    df$surv = survival::Surv(df$time, df$event)
+    fit = survival::survfit(surv~group, data=df)
+    times = sort(fit$time)
+
+    a = summary(fit, times=times, extend=TRUE, data.frame=TRUE)
+    a %>%
+      dplyr::filter(strata=="group=B") %>%
+      dplyr::filter(time>120 & time<150) %>%
+      dplyr::select(strata, time, n.risk, n.event, surv)
+
+  })
+
+
+  #t=140.8
+  #on local 4.3 : 1/15
+  #on local 4.4 : 1/15
+  #on ubuntu-devel : 1/15
+  #on 4.4.1 : 0/15
+  #on release : 0/15
+
+})