Hi,
I am experimenting with the function predict() in two versions of R and the R
extension package "survival".
library(survival)
set.seed(123)
testdat=data.frame(otime=rexp(10),event=rep(0:1,each=5),x=rnorm(10))
testfm=as.formula('Surv(otime,event)~x')
testfun=function(dat,fm)
{
predict(coxph(fm,data=dat),type='lp',newdata=dat)
}
# Under R 2.11.1 and survival_2.35-8
testfun(testdat,testfm)
> testfun(testdat,testfm)
[,1]
1 -0.34786190
2 0.53622182
3 0.07861553
4 0.10030148
5 -0.05329258
6 -0.40619876
7 0.83422564
8 0.15170217
9 -1.15316613
10 0.25945273
> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-pc-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] survival_2.35-8
# Under R 2.12.2 and survival_2.36-5
> testfun(testdat,testfm)
Error in model.frame(formula = fm, data = dat) : object 'fm' not found
> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] survival_2.36-5
Any enlightenment on what might be causing the different performance?
Regards
Ivo
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