On Jan 11, 2013, at 5:35 PM, Katie Anweiler wrote:
Hello all,
I am trying to understand how to specify nested factors when using
coxph(), and if it is appropriate to nest these factors in my
situation.
In the simplest form, I am testing two different temperatures, with
each temperature being performed twice in different experimental
periods (e.g. Temp5 performed in Period A and C, Temp4 performed in
Period B and D)
I am trying to see if survival time is affected by the treatment
temperature. To do this I am using temperature and experimental
period nested within temperature as factors.
LOEtempmod.5days=coxph(LOE.stable.5days~Temp+Temp/
Period,data=goodstable)
Warning message:
In coxph(LOE.stable.5days ~ Temp + Temp/Period, :
X matrix deemed to be singular; variable 2 5 6 7
1. Is this an appropriate way of nesting?
Have you looked at the coxme package?
http://cran.r-project.org/web/packages/coxme/index.html
2. Can this error message be ignored?
Sometimes R packages correctly drop variables that are exactly
collinear: other times the correct solution is not clear. I would
think the answer in this case would be "no", but do not have a lot to
go on at this point.
--
David Winsemius, MD
Alameda, CA, USA
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