Suggestions? -- Yes.
1) Wrong list.. Post on R-sig-mixed-models, not here.
2) Follow the posting guide and provide the modelformula, which may
well be the source of the difficulties (overfitting).
-- Bert
On Fri, Dec 16, 2011 at 1:56 PM, Scott Raynaud <scott.raynaud at
yahoo.com> wrote:> I'm using an R program (which I did not write) to simulate multilevel
data
> (subjects in locations) used in power calculations. It uses lmer to fit a
> mixed logistic model to the simulated data based on inputs of means,
> variances, slopes and proportions:
>
> (fitmodel <- lmer(modelformula,data,family=binomial(link=logit),nAGQ=1))
>
> where modelformula is set up in another part of the program.? Locations are
> treated as random and the model is random intercept only.? The program is
> set?to run 1000 simulations.
>
> I have temperature, five levels of gestational age (GA), birth wieght (BW)
and?four
> other categorical pedictors, all binary.? I scaled everything so that all
my slopes are in the
> range of -5.2 to 1.6 and?variances from .01 to .08.? I have a couple of
categories
> of GA that have small probabilities (<.10).? I'm using a structured
sampling approach
> looking at 20, 60, 100, and 140 locations with a total?n=75k.? The first
looks like this:
>
> ????????????# groups?? n
> ????????????5???????????? 800
> ????????????4?????????????2239
> ????????????3?????????????3678
> ????????????3?????????????5117
> ????????????3?????????????6557
> ????????????2?????????????7996
> Total ????20???????????75000
>
> As the level 2 sizes increase, the cell sizes decrease.? When I run this
model in
> the simulation I get:
>
> Warning: glm.fit: algorithm did not converge
>
> every time the model is fit (I killed this long before it ran 1000 times).
>
> I tried increasing the number of iterations to no avail.? I suspected
linear
> dependencies among the predictors, so I took out GA (same result), put
> GA back and took out BW (same result) and then took out both GA and
> BW.? This ran about half the time with th other half passing warnings
> such as:
>
> Warning: glm.fit: algorithm did not converge
> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
>
> or
>
> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
>
> in addition to some like the original warning.
>
> If I leave everything in but temperature, then it runs fine.? I also tested
the full
> model separately at 50 and 75 level 2 units each with total n=75k.? Nothing
converged.
>
> I want to include temperature, but I'm not sure what else to try.? Any
> suggestions?
>
> ______________________________________________
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
Bert Gunter
Genentech Nonclinical Biostatistics
Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm