[ADMB Users] ADMB versus R
bbolker at gmail.com
Thu Nov 15 17:34:36 PST 2012
Before I forget and this subsides into the depths of my inbox, I also
wanted to thank Dave for working on this (he sent a private e-mail to me
saying that he had reconciled his TPL file with the results of glmmADMB
with the random effect specified as ~time-1|group and allowing for an
unstructured correlation matrix (corstruct="full")).
It is true that the terseness of the glmmADMB formulae can make it
harder to figure out what's actually going on under the hood.
On 12-11-08 12:54 PM, Seth W. Bigelow wrote:
> Dear Dave & admb users:
> When I recently began using the glmmADMB package I picked up from R forge, I
> noticed right away that 1) the thing was awesome and let me cleanly do an
> analysis that other R packages didn't seem to be able to and 2) that there
> was some missing functionality, e.g., some of the usual R 'methods' didn't
> work. After I asked the R mixed models listserv about the lack of change in
> likelihood when I changed the variance structure, I got suspicious that
> there was something wrong with the analysis (because of the huge, many
> orders of magnitude differences in the error variances) but I didn't pursue
> it further on the R listserv because the basic analysis seemed fine. I just
> assumed that the translation of more advanced variance structures from R to
> ADMB had not been done yet.
> I appreciated Dave's analysis in ADMB, using the more complicated variance
> structure; it confirmed my intuition that the complicated variance structure
> was not necessary, and gave me a little more insight into ADMB. I'm not sure
> I'm going to skip the R interface and learn to program ADMB directly, but
> for the moment I'm continuing to use glmmADMB--cautiously--and it has been a
> So, many thanks to Dave and other ADMB (& glmmADMB) developers!
> Seth W. Bigelow
> -----Original Message-----
> From: dave fournier [mailto:davef at otter-rsch.com]
> Sent: Thursday, November 08, 2012 12:00 PM
> To: users at admb-project.org
> Cc: Seth W. Bigelow
> Subject: Re: [ADMB Users] ADMB versus R
> I think you a re missing the point.
> This all began because a guy asked a question about a seeming
> contradiction in
> his model fits on the R list. He got the usual runaround about his data
> not being good
> enough or whatever.
> Now after years of watching this stuff my general opinion is that people
> who trust
> the R gurus for information more or less deserve what they get.
> However in this case glmmadmb is something that I am partly responsible
> for so
> I react when I think someone is getting bad advice. I took a fair
> amount of time
> and R pain to recreate his analysis and discovered that glmmadmb is not
> doing what one
> might assume in this case.
> I quickly hacked together what I assume is the model the guy wanted and
> it did
> produce a better fit as one would expect. However the improvement was
> not significant.
> Then Ben modified the R code to produce what he assumed was the correct
> and posted the results, noting that they were different from mine with the
> implication that I must be doing something wrong.
> However he never checked the log-likelihood for his new model. It is a
> lot worse
> than the original user's LL so the model is not what he thinks it is.
> I ran my model on the glmmadmb.dat file that Ben's model produced and
> got the
> same LL as he got. I agree with him that the design matrix Z appears to be
> correct, but there must be something wrong with the dat file. I wonder
> if it is the II's.
> Anyway this is neither convenient or quick and I have more interesting
> things to work on.
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