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

@@ -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)
+}