From 465ce64487a938779d3c2d2f33feb28c1bf8ef60 Mon Sep 17 00:00:00 2001
From: Jens Sauer <jsauer65@gmail.com>
Date: Sun, 17 Jan 2021 11:43:34 +0100
Subject: [PATCH] Add cox time dependend analysis for death and sm

Simple analysis of influence of relapse and sm on death.

The SM part is not working currently (due to limited events).
---
 cox-time.R | 53 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100644 cox-time.R

diff --git a/cox-time.R b/cox-time.R
new file mode 100644
index 0000000..4c09f78
--- /dev/null
+++ b/cox-time.R
@@ -0,0 +1,53 @@
+# Cox time-depended hazard models for death and sm
+#
+# License: GPL version 3
+# Jens Mathis Sauer (c) 2020
+
+sma_cox_time_death_setup <- function() {
+	data <- tmerge(data1 = secmal %>% select(uuid),
+		       data2 = secmal,
+		       id = uuid,
+		       tstop = event_time_asct)
+	data <- tmerge(data, secmal, id = uuid, death = event(event_time_asct,
+				event_status))
+	data <- tmerge(data, secmal, id = uuid, relapse = tdc(
+				event_time_asct - event_time_relapse))
+	data <- tmerge(data, secmal, id = uuid, sm = tdc(
+				event_time_asct - event_time_sm))
+
+	return(data)
+}
+
+# Calculate HR of death with time dependend relapse status
+sma_cox_death_relapse <- function() {
+	data <- sma_cox_time_death_setup()
+	cox <- coxph(Surv(tstart, tstop, death) ~ relapse + cluster(uuid), data)
+
+	return(cox)
+}
+
+sma_cox_death_sm <- function() {
+	data <- sma_cox_time_death_setup()
+	cox <- coxph(Surv(tstart, tstop, death) ~ sm + cluster(uuid), data)
+
+	return(cox)
+}
+
+sma_cox_time_sm_setup <- function() {
+	data <- tmerge(data1 = secmal %>% select(uuid),
+		       data2 = secmal,
+		       id = uuid,
+		       tstop = time_at_risk)
+	data <- tmerge(data, secmal, id = uuid, sm = event(event_time_sm))
+	data <- tmerge(data, secmal, id = uuid, relapse = tdc(
+				event_time_asct - event_time_relapse))
+
+	return(data)
+}
+
+sma_cox_sm_rel <- function() {
+	data <- sma_cox_time_sm_setup()
+	cox <- coxph(Surv(tstart, tstop, sm) ~ relapse + cluster(uuid), data)
+
+	return(cox)
+}