69 lines
2.3 KiB
Plaintext
69 lines
2.3 KiB
Plaintext
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R version 2.7.1 (2008-06-23)
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Copyright (C) 2008 The R Foundation for Statistical Computing
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ISBN 3-900051-07-0
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R is free software and comes with ABSOLUTELY NO WARRANTY.
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You are welcome to redistribute it under certain conditions.
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Type 'license()' or 'licence()' for distribution details.
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R is a collaborative project with many contributors.
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Type 'contributors()' for more information and
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'citation()' on how to cite R or R packages in publications.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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'help.start()' for an HTML browser interface to help.
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Type 'q()' to quit 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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Loading required package: splines
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>
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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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>
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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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>
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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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>
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> all.equal(resid(fit1) , (resid(fit2))[1:n])
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[1] TRUE
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> all.equal(resid(fit1, type='score') , (resid(fit2, type='score'))[1:n])
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[1] TRUE
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> all.equal(resid(fit1, type='schoe') , (resid(fit2, type='schoe'))[1:ndead])
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[1] TRUE
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>
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>
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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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>
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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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>
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> all.equal(resid(fit1) , (resid(fit2))[1:n])
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[1] TRUE
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> all.equal(resid(fit1, type='score') , (resid(fit2, type='score'))[1:n])
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[1] TRUE
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> all.equal(resid(fit1, type='schoe') , (resid(fit2, type='schoe'))[1:ndead])
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[1] TRUE
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>
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