R Under development (unstable) (2023-08-12 r84939 ucrt) -- "Unsuffered Consequences" Copyright (C) 2023 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) > > # Strata by covariate interactions, a case pointed out in early 2011 > # by Frank Harrell, which as it turns out had never been computed > # correctly by any version of the package. Which shows how often this > # case arises in practice. > # > aeq <- function(x, y, ...) all.equal(as.vector(x), as.vector(y)) > fit1 <- coxph(Surv(time, status) ~ wt.loss + age*strata(sex) + strata(ph.ecog), + data=lung) > tdata <- data.frame(wt.loss=c(10,5,0,10, 15,20,25), + age =c(50,60,50,60,70,40,21), + sex =c(1,1,2,2,1,1,1), + ph.ecog=c(0,0,1,1,2,2,2)) > surv1 <- survfit(fit1, newdata=tdata) > > fit2 <- coxph(Surv(time, status) ~ wt.loss + age + I(age*0), data=lung, + init=fit1$coef, iter=0, subset=(sex==1 & ph.ecog==0)) > fit2$var <- fit1$var > > surv2 <- survfit(fit2, newdata=list(wt.loss=c(10,5), age=c(50,60))) > s1 <- surv1[1:2] > aeq(s1$surv, surv2$surv) #first a vector, second a matrix [1] TRUE > aeq(s1$std.err, surv2$std.err) [1] TRUE > aeq(s1[1]$time, surv2$time) [1] TRUE > aeq(s1[1]$n.event, surv2$n.event) [1] TRUE > > fit3 <- coxph(Surv(time, status) ~ wt.loss + age + I(age*1), + data=lung, init=fit1$coef, iter=0, + subset=(sex==2 & ph.ecog==1)) > fit3$var <- fit1$var > surv3 <- survfit(fit3, newdata=list(wt.loss=c(0,10), age=c(50,60))) > aeq(surv1[3:4]$surv, surv3$surv) [1] TRUE > aeq(surv1[3:4]$std, surv3$std) [1] TRUE > > fit4 <- coxph(Surv(time, status) ~ wt.loss + age + I(age*0), + data=lung, init=fit1$coef, iter=0, + subset=(sex==1 & ph.ecog==2)) > fit4$var <- fit1$var > surv4 <- survfit(fit4, newdata=list(wt.loss=c(15,20,25), age=c(70,40,21))) > > aeq(surv1[5:7]$surv, surv4$surv) [1] TRUE > aeq(surv1[5:7]$std.err, surv4$std.err) [1] TRUE > aeq(surv1[5]$n.risk, surv4$n.risk) [1] TRUE > > > proc.time() user system elapsed 1.35 0.12 1.48