
R version 2.7.1 (2008-06-23)
Copyright (C) 2008 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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)
Loading required package: splines
> 
> #
> # 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
> 
