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