[ADMB Users] ADMB versus R

Ben Bolker bbolker at gmail.com
Thu Nov 8 11:35:01 PST 2012

On 12-11-08 11:59 AM, dave fournier wrote:
> I think you are 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 model and posted the results, noting that they were
> different from mine with the implication that I must be doing
> something wrong.

  I hope I didn't imply that.  In any case, I didn't mean to, and
apologize if I gave offense.

> 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.


  I have other things to do too; I will work on this if I get a chance.

   Ben Bolker

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