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. > options(na.action=na.exclude) # preserve missings > options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type > library(survival) > > # Create a "counting process" version of the simplest test data set > # > 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)) > > test1b<- list(start= c(0, 3, 0, 0, 5, 0, 6,14, 0, 0, 10,20,30, 0), + stop = c(3,10, 10, 5,20, 6,14,20, 30, 10,20,30,40, 10), + status=c(0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0), + x= c(1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, NA), + id = c(3, 3, 4, 5, 5, 6, 6, 6, 7, 1, 1, 1, 1, 2)) > > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) > # > # Check out the various residuals under an Efron approximation > # > fit0 <- coxph(Surv(time, status)~ x, test1, iter=0) > fit <- coxph(Surv(time, status) ~x, test1) > fit0b <- coxph(Surv(start, stop, status) ~ x, test1b, iter=0) > fitb <- coxph(Surv(start, stop, status) ~x, test1b) > fitc <- coxph(Surv(time, status) ~ offset(fit$coef*x), test1) > fitd <- coxph(Surv(start, stop, status) ~ offset(fit$coef*x), test1b) > > aeq(fit0b$coef, fit0$coef) [1] TRUE > > aeq(resid(fit0), resid(fit0b, collapse=test1b$id)) [1] TRUE > aeq(resid(fit), resid(fitb, collapse=test1b$id)) [1] TRUE > aeq(resid(fitc), resid(fitd, collapse=test1b$id)) [1] TRUE > aeq(resid(fitc), resid(fit)) [1] TRUE > > aeq(resid(fit0, type='score'), resid(fit0b, type='score', collapse=test1b$id)) [1] TRUE > aeq(resid(fit, type='score'), resid(fitb, type='score', collapse=test1b$id)) [1] TRUE > > aeq(resid(fit0, type='scho'), resid(fit0b, type='scho', collapse=test1b$id)) [1] TRUE > aeq(resid(fit, type='scho'), resid(fitb, type='scho', collapse=test1b$id)) [1] TRUE > > # The two survivals will have different censoring times > # nrisk, nevent, surv, and std should be the same > temp1 <- survfit(fit, list(x=1), censor=FALSE) > temp2 <- survfit(fitb, list(x=1), censor=FALSE) > all.equal(unclass(temp1)[c(3,4,6,8)], unclass(temp2)[c(3,4,6,8)]) [1] TRUE > > > > proc.time() user system elapsed 1.23 0.04 1.28