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R Under development (unstable) (2018-04-09 r74565) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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
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Type 'q()' to quit R.
> options(na.action=na.exclude) # preserve missings
> options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
> library(survival)
>
> #
> # A simple test of an overdetermined system
> # Should give a set of NA coefficients
> #
> test1 <- data.frame(time= c(4, 3,1,1,2,2,3),
+ status=c(1,NA,1,0,1,1,0),
+ x= c(0, 2,1,1,1,0,0))
>
> temp <- rep(0:3, rep(7,4))
>
> stest <- data.frame(start = 10*temp,
+ stop = 10*temp + test1$time,
+ status = rep(test1$status,4),
+ x = c(test1$x+ 1:7, rep(test1$x,3)),
+ epoch = rep(1:4, rep(7,4)))
>
> # Will create a warning about a singular X matrix
> fit1 <- coxph(Surv(start, stop, status) ~ x * factor(epoch), stest)
> fit1$coef # elements 2:4 should be NA
x factor(epoch)2 factor(epoch)3 factor(epoch)4
0.1041579 NA NA NA
x:factor(epoch)2 x:factor(epoch)3 x:factor(epoch)4
1.5726996 1.5726996 1.5726996
> all.equal(is.na(fit1$coef), c(F,T,T,T,F,F,F), check.attributes=FALSE)
[1] TRUE
>
> proc.time()
user system elapsed
0.668 0.040 0.704
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