R Under development (unstable) (2024-02-13 r85898 ucrt) -- "Unsuffered Consequences" 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. > options(na.action=na.exclude) # preserve missings > options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type > library(survival) > > # > # Trivial test of stratified residuals > # Make a second strata = replicate of the first, and I should get the > # exact same answers > test1 <- data.frame(time= c(9, 3,1,1,6,6,8), + status=c(1,NA,1,0,1,1,0), + x= c(0, 2,1,1,1,0,0)) > test2 <- data.frame(start=c(1, 2, 5, 2, 1, 7, 3, 4, 8, 8), + stop =c(2, 3, 6, 7, 8, 9, 9, 9,14,17), + event=c(1, 1, 1, 1, 1, 1, 1, 0, 0, 0), + x =c(1, 0, 0, 1, 0, 1, 1, 1, 0, 0) ) > > temp <- as.matrix(test1) > n <- nrow(temp) > ndead<- sum(test1$status[!is.na(test1$status)]) > temp <- data.frame(rbind(temp, temp)) #later releases of S have rbind.data.frame > tstrat <- rep(1:2, c(n,n)) > > fit1 <- coxph(Surv(time, status) ~x, test1) > fit2 <- coxph(Surv(time, status) ~x + strata(tstrat), temp) > > all.equal(resid(fit1) , (resid(fit2))[1:n]) [1] TRUE > all.equal(resid(fit1, type='score') , (resid(fit2, type='score'))[1:n]) [1] TRUE > all.equal(resid(fit1, type='schoe') , (resid(fit2, type='schoe'))[1:ndead]) [1] TRUE > > > #AG model > temp <- as.matrix(test2) > n <- nrow(temp) > ndead<- sum(test2$event[!is.na(test2$event)]) > temp <- data.frame(rbind(temp, temp)) > tstrat <- rep(1:2, c(n,n)) > > fit1 <- coxph(Surv(start, stop, event) ~x, test2) > fit2 <- coxph(Surv(start, stop, event) ~x + strata(tstrat), temp) > > all.equal(resid(fit1) , (resid(fit2))[1:n]) [1] TRUE > all.equal(resid(fit1, type='score') , (resid(fit2, type='score'))[1:n]) [1] TRUE > all.equal(resid(fit1, type='schoe') , (resid(fit2, type='schoe'))[1:ndead]) [1] TRUE > > proc.time() user system elapsed 0.82 0.10 0.92