From 63c2883c7e4cb015e357a2c276f0937433dae0cb Mon Sep 17 00:00:00 2001
From: Jens Sauer <jsauer65@gmail.com>
Date: Mon, 18 Jan 2021 01:46:49 +0100
Subject: [PATCH] coxph: Adjust for cause-specific analysis

Since the data specifies death as a competing risk, the cox analysis
must be adjusted. Death will now, as it was before, treated as a censor.
---
 coxph.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/coxph.R b/coxph.R
index 3ccf4fb..5393f31 100644
--- a/coxph.R
+++ b/coxph.R
@@ -44,7 +44,7 @@ sma_cox_res <- function(m) {
 #
 sma_coxph_univ <- function() {
 	univ_formulas <- sapply(covariates, function(x) as.formula(
-				paste('Surv(time_at_risk, time_at_risk_status) ~ ',
+				paste('Surv(time_at_risk, ifelse(time_at_risk_status == 1, 1, 0)) ~ ',
 				x)))
 	univ_models <- lapply(univ_formulas,
 			      function(x) {coxph(x, data = secmal)})