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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$coef # elements 2:4 should be NA
all.equal(is.na(fit1$coef), c(F,T,T,T,F,F,F), check.attributes=FALSE)
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