[R] Multilevel Survival Analysis - Cox PH Model
gunter.berton at gene.com
Fri Jul 1 17:31:20 CEST 2011
Is there any right censoring?
If not, then plain old lme, lmer, gam (in mgcv), ... etc. would seem
to me do just fine for time to waking = ORIENTATION as a response --
or are you thinking of this as interval-censored data, which it would
appear to be since you've binned the response? I strongly suspect
that the simpler approach would work pretty well, anyway, but ...
For FULLY ORIENTED, which is binary, glmm, glmer, etc. would seem to
do if there's no censoring.
I'd be happy doing this even for a "small" amount of right censoring
(uh-oh) and the usual hack cheats --replacing the censoring time with
something slightly bigger than the censoring time, for example. But
here I'd be getting by knuckles slapped -- whack whack! -- for
statistical hackery, probably justifiably, so you probably need to
retreat to the original approach if that's the case.
I would welcome criticism/correction on this suggestion if I'm all wet
-- or even just damp.
On Fri, Jul 1, 2011 at 7:32 AM, David Winsemius <dwinsemius at comcast.net> wrote:
> On Jul 1, 2011, at 10:22 AM, David Winsemius wrote:
>> On Jul 1, 2011, at 10:10 AM, dunner wrote:
>>> Hello all, thanks for your time and patience.
>>> I'm looking for a method in R to analyse the following data:
>>> Time to waking after anaesthetic for medical procedures repeated on the
>>> labelled [1:740, 1:2] 20 20 15 20 30+ 40+ 50 30 15 10 ...
>>> - attr(*, "dimnames")=List of 2
>>> ..$ : NULL
>>> ..$ : chr [1:2] "time" "status"
>>> - attr(*, "type")= chr "right"
>>> - attr(*, "units")= chr "Day"
>>> - attr(*, "time.label")= chr "ORIENTATION"
>>> - attr(*, "event.label")= chr "FullyOrientated"
>>> mysurv is constructed from the following data:
>>> head(data.frame(MRN, ORIENTATION, FullyOrientated))
>>> MRN ORIENTATION FullyOrientated
>>> 1 0008291 20 2
>>> 2 0008469 20 2
>>> 3 0008469 15 2
>>> 4 0010188 20 2
>>> 5 0013664 30 1
>>> 6 0014217 40 1
>>> I had planned to use a Cox PH model to analyse time to waking
>>> (ORIENTATION =
>>> 10, 15, 20 mins ....... 50 mins) and whether or not people (MRN) are
>>> awake within an hour (FullyOrientated). I've put GENDER, etc. into the
>>> model but I have the following bias:
>>> The procedure is repeated weekly on each individual (MRN), so each
>>> individual has 5-9 cases associated with them. Currently I am including
>>> these in the model as if they were independent.
>>> Is there a way to account for the non-independence of these waking times?
>>> I'm thinking of something similar to the NLMER package and Multilevel /
>>> Mixed Effects analysis as described in Pinheiro and Bates.
>> Have you looked at the coxme package?
> As an initial strata()-gem, as it were, perhaps just adding strata(MRN) may
> parcel out the intra-individual variability and degrees of freedom, so that
> they are not inappropriately included in the IV's. My initial suggestion of
> coxme may be overkill.
>> David Winsemius, MD
>> West Hartford, CT
>> R-help at r-project.org mailing list
>> PLEASE do read the posting guide
>> and provide commented, minimal, self-contained, reproducible code.
> David Winsemius, MD
> West Hartford, CT
> R-help at r-project.org mailing list
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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-- Maimonides (1135-1204)
Genentech Nonclinical Biostatistics
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