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coxph: First commit of coxph models

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First univariate with covariates coxph models.
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Jens Sauer 2020-11-25 17:26:18 +01:00
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# Cox proportional hazard models
#
# License: GPL version 3
# Jens Mathis Sauer (c) 2020
source("utils.R")
sma_init()
covariates <- c("dx_age", "asct_age", "time_dx_to_asct", "sex",
"asct_n", "relapse_status", "nicotin_history","pre_rt", "post_rt",
"pre_alkylating_agents", "pre_alkylating_agents_n",
"pre_topoisomerase", "pre_topoisomerase_n",
"pre_anthracyclines", "pre_anthracyclines_n",
"peri_alkylating_agents", "peri_alkylating_agents_n",
"peri_topoisomerase", "peri_topoisomerase_n",
"peri_anthracyclines", "peri_anthracyclines_n",
"post_alkylating_agents", "post_alkylating_agents_n",
"post_topoisomerase", "post_topoisomerase_n",
"post_anthracyclines", "post_anthracyclines_n")
#
# Extract data from Cox PH results
#
sma_cox_res <- function(x) {
x <- summary(x)
p.value<-signif(x$wald["pvalue"], digits=2)
wald.test<-signif(x$wald["test"], digits=2)
beta<-signif(x$coef[1], digits=2);#coeficient beta
HR <-signif(x$coef[2], digits=2);#exp(beta)
HR.confint.lower <- signif(x$conf.int[,"lower .95"], 2)
HR.confint.upper <- signif(x$conf.int[,"upper .95"],2)
HR <- paste0(HR, " (",
HR.confint.lower, "-", HR.confint.upper, ")")
res<-c(beta, HR, wald.test, p.value)
names(res)<-c("beta", "HR (95% CI for HR)", "wald.test",
"p.value")
return(res)
}
#
# Univariate Cox ph analysis with multiple covariates.
#
sma_coxph_univ <- function() {
univ_formulas <- sapply(covariates, function(x) as.formula(
paste('Surv(time_at_risk, time_at_risk_status) ~ ',
x)))
univ_models <- lapply(univ_formulas,
function(x) {coxph(x, data = secmal)})
univ_results <- lapply(univ_models, sma_cox_res)
res <- t(as.data.frame(univ_results, check.names = FALSE))
print("Univariate coxph with multiple covariates:")
print(as.data.frame(res))
}
#
# Stratified univariate Cox ph analysis with multiple covariates.
# The strata is "diagnosis"
#
sma_coxph_univ_strata <- function() {
univ_formulas <- sapply(covariates, function(x) as.formula(
paste('Surv(time_at_risk, time_at_risk_status) ~ ',
x, ' + strata(diagnosis)')))
univ_models <- lapply(univ_formulas,
function(x) {coxph(x, data = secmal)})
univ_results <- lapply(univ_models, sma_cox_res)
res <- t(as.data.frame(univ_results, check.names = FALSE))
print("Univariate coxph with multiple covariates, stratified by diagnosis:")
print(as.data.frame(res))
}