Dear R-users,
I have a frustrating problem that I am hoping has a simple fix. I am running a
series of lmer models from the lme4 package of the general form:
model<-lmer(y~x1 + x2 ..... + xn +
(1|site),data=dataframe,family=poisson,method="Laplace",control=list(usePQL=FALSE,msVerbose=TRUE))
where the same model is executed multiple times on a bootstrapped dataframe.
For each bootstrapped model run the resulting model object is used to return
the AIC (and models are then compared using a bootstrapped weight - frequency
of runs a given model had the lowest AIC).
This works just fine when running interactively on my windows machine (so there
is nothing the matter with the code, hence I have not bored you with the
details here).... however when I submit the job as a batch to a UNIX system it
usually (but not always) fails and the execution is halted after an error
message is produced:
Error in objective (.par,...): Leading minor of order 1 in downdated X'X is not
positive definite
In addition: There were 12 warnings (use warnings() to see them)
Error in logLik(model) : no applicable method for "logLik"
Execution halted
On windows when the execution of a single model run fails to estimate the
logLik (an unstable model...) R just continues past the error and still runs to
the end of the script (i.e. runs through all the bootstraps), and I can then
inspect the output and any errors at the end.
My question, then is when using UNIX on batch mode, how can I get the job to
NOT halt it's execution on the production of an unstable model (not positive
definite) and continue running? If the models are not bootstrapped then the
script is executed without any problem in UNIX (so the script is successfuly
submitted as a batch job), so it seems that some of the bootstrap runs are
producing unstable models in rare instances, but just one is sufficient to halt
the execution of the script.
I am running R.2.3.1 on both Windows and UNIX,
Many thanks in advance,
Toby Gardner
School of Environmental Sciences
University of East Anglia
Norwich, NR4 7TJ
United Kingdom
Email: [EMAIL PROTECTED]
Website: www.uea.ac.uk/~e387495
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