Katie:
You need to get local statistical help. What you are doing makes no
sense. See inline below.
-- Bert
On Sat, Jan 12, 2013 at 1:03 PM, David Winsemius <dwinsemius at comcast.net> wrote:
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)
Period is confounded with temperature. That is the source of the
singularity. in the message received below.
You can estimate the C-A and the D-B differences.
As I said, get statistical help. These are not R questions.
-- Bert
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?
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