# 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)
}