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R version 2.11.1 (2010-05-31)
Copyright (C) 2010 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
>
> #
> # Test out the revised model.matrix code
> #
> 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),
+ z= factor(c('a', 'a', 'b', 'b', 'c', 'c', 'a')))
>
> fit1 <- coxph(Surv(time, status) ~ z, test1, iter=1)
> fit2 <- coxph(Surv(time, status) ~z, test1, x=T, iter=1)
> all.equal(model.matrix(fit1), fit2$x)
[1] TRUE
>
> # This has no level 'b', make sure dummies recode properly
> test2 <- data.frame(time= c(9, 3,1,1,6,6,8),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0),
+ z= factor(c('a', 'a', 'a', 'a', 'c', 'c', 'a')))
>
> ftest <- model.frame(fit1, data=test2)
> all.equal(levels(ftest$z), levels(test1$z))
[1] TRUE
>
> # xtest will have one more row than the others, since it does not delete
> # the observation with a missing value for status
> xtest <- model.matrix(fit1, data=test2)
> dummy <- fit2$x
> dummy[,1] <- 0
> all.equal(xtest[-2,], dummy, check.attributes=FALSE)
[1] TRUE
>
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