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coxph: Adjust coxph summary output

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Split HR and CI, print logrank values.
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Jens Sauer 2021-01-17 11:21:05 +01:00
parent 351b26368d
commit a3c816ad64
1 changed files with 8 additions and 7 deletions
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15
coxph.R
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@ -21,20 +21,21 @@ covariates <- c("dx_age", "asct_age", "time_dx_to_asct", "sex",
# #
# Extract data from Cox PH results # Extract data from Cox PH results
# #
sma_cox_res <- function(x) { sma_cox_res <- function(m) {
x <- summary(x) x <- summary(m)
p.value<-signif(x$wald["pvalue"], digits=2) p.value<-signif(x$wald["pvalue"], digits=2)
wald.test<-signif(x$wald["test"], digits=2) wald.test<-signif(x$wald["test"], digits=2)
beta<-signif(x$coef[1], digits=2);#coeficient beta beta<-signif(x$coef[1], digits=2);#coeficient beta
HR <-signif(x$coef[2], digits=2);#exp(beta) HR <-signif(x$coef[2], digits=2);#exp(beta)
HR.confint.lower <- signif(x$conf.int[,"lower .95"], 2) HR.confint.lower <- signif(x$conf.int[,"lower .95"], 2)
HR.confint.upper <- signif(x$conf.int[,"upper .95"],2) HR.confint.upper <- signif(x$conf.int[,"upper .95"],2)
HR <- paste0(HR, " (", HR.confint <- paste0(HR.confint.lower, "-", HR.confint.upper)
HR.confint.lower, "-", HR.confint.upper, ")") logtest <- signif(x$logtest["test"], digits = 2)
logtest.pvalue <- x$logtest["pvalue"]
res<-c(beta, HR, wald.test, p.value) res<-c(beta, HR, HR.confint, wald.test, p.value, logtest, logtest.pvalue)
names(res)<-c("beta", "HR (95% CI for HR)", "wald.test", names(res)<-c("beta", "HR", "95% CI for HR", "wald test",
"p.value") "p value", "logtest", "logtest p value")
return(res) return(res)
} }