R Under development (unstable) (2024-02-13 r85898 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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) > > # > # 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 0.81 0.10 0.92