R version 4.4.0 RC (2024-04-16 r86458 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(survival) > # > # Check that the survival curves from a Cox model with beta=0 > # match ordinary survival > # > # Aalen > surv1 <- survfit(Surv(time,status) ~ sex, data=lung, stype=2) > fit1 <- coxph(Surv(time, status) ~ age + strata(sex), data=lung, iter=0, + ties='breslow') > fit1$var <- 0*fit1$var #sneaky, causes the extra term in the Cox variance > # calculation to be zero > surv2 <- survfit(fit1, stype=2) > surv3 <- survfit(fit1) > > arglist <- c('n', 'time', 'n.risk','n.event', 'n.censor', 'surv', 'strata', + 'std.err', 'upper', 'lower') > all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist]) [1] TRUE > all.equal(unclass(surv1)[arglist], unclass(surv3)[arglist]) [1] TRUE > > > # Efron method > surv1 <- survfit(Surv(time,status) ~ sex, data=lung, stype=2, ctype=2) > surv2 <- survfit(fit1, ctype=2) > all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist]) [1] TRUE > > # Kaplan-Meier > surv1 <- survfit(Surv(time,status) ~ sex, data=lung) > surv2 <- survfit(fit1, stype=1) > all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist]) [1] TRUE > > > # Now add some random weights > rwt <- runif(nrow(lung), .5, 3) > surv1 <- survfit(Surv(time,status) ~ sex, data=lung, stype=2, weight=rwt, + robust=FALSE) > fit1 <- coxph(Surv(time, status) ~ age + strata(sex), data=lung, iter=0, + ties='breslow', weight=rwt, robust=FALSE) > fit1$var <- 0*fit1$var #sneaky > surv2 <- survfit(fit1, stype=2, ctype=1) > surv3 <- survfit(fit1) > > all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist]) [1] TRUE > all.equal(unclass(surv1)[arglist], unclass(surv3)[arglist]) [1] TRUE > > > # Efron method > surv1 <- survfit(Surv(time,status) ~ sex, data=lung, stype=2, ctype=2, + weight=rwt, robust=FALSE) > surv2 <- survfit(fit1, ctype=2, robust=FALSE) > all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist]) [1] TRUE > > # Kaplan-Meier > surv1 <- survfit(Surv(time,status) ~ sex, data=lung, weight=rwt, robust=FALSE) > surv2 <- survfit(fit1, stype=1, robust=FALSE) > all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist]) [1] TRUE > > > proc.time() user system elapsed 0.84 0.09 0.92