[R-sig-ME] glmmadmb - problems understanding the output when run in cmd console

Ben Bolker bbolker at gmail.com
Wed Jan 13 01:01:18 CET 2016

  In the long run it would probably be better to figure out why
glmmADMB isn't running in RStudio ... it might also be interesting to
see whether the glmmTMB (aka the New Hotness,
https://github.com/glmmTMB/glmmTMB) might work.

  In the short run, what you need to know is probably documented in

if you want to try running the ADMB model outside of R,
              use ‘run=FALSE’ and set ‘save.dir’ in the ‘glmmADMB’
              arguments.  This will result in a saved directory
              containing the ‘glmmadmb’ executable (on systems other
              than Windows) as well as ‘glmmadmb.pin’ and
              ‘glmmadmb.dat’ files.  You can then run the ‘glmmadmb’
              executable with appropriate command-line arguments in a
              command shell or terminal window.  If you run the same R
              command again (i.e. still with ‘run=FALSE’ and with the
              same ‘save.dir’) ‘glmmADMB’ will find any output files
              that have been produced and read them into a ‘glmmadmb’

In other words, if you run


after running the ADMB executable manually from the shell, then the
function should automatically locate the output files and read them
into a well-set-up object for you.

  Ben Bolker

On Tue, Jan 12, 2016 at 4:31 PM, Diego Pavon
<diego.pavonjordan at gmail.com> wrote:
> Hello all
> I am trying to run GLMM, ZIP and ZINB using glmmadmb package. I have count
> data and I want to see whether there is an effect of temperature on the
> counts of 12 species over a period of 29 years (counts in ca. 2000 sites).
> I am having troubles getting the models converged when running them in
> RStudio. For some reason, they do run nicely when I use the windows command
> line (cmd).
> Then I get all these files with the results (.eval, .par, .std, etc...).
> My question is, how do I read those? I can open them in R or a text editor,
> but I can't understand what is what. In the glmmadmb website there is a
> small description but I can't really understand. for instance, the betas
> that I get in the .par file are not the actual estimates. In the website,
> It says:
> "BETA: fixed-effect parameter estimates: note that these are the versions
> of the parameters fitted internally, using an orthogonalized version of the
> original design matrix, not the original coefficients (if this means
> nothing to you, as it might well, just accept that these are transformed
> versions of the parameters)."
> So, could someone help me understanding these "results files" that I get
> when running glmmadmb outside R, and how to get the estimates, SE and
> significance of the covariates?
> Thank you very much.
> Diego
> --
> *Diego Pavón Jordán*
> *Finnish Museum of Natural History*
> *PO BOX 17 *
> *Helsinki. Finland*
> *0445061210https://tuhat.halvi.helsinki.fi/portal/en/persons/diego-pavon-jordan%288d5db37c-eddd-4fca-92cd-9c9956a42b4a%29.html
> <https://tuhat.halvi.helsinki.fi/portal/en/persons/diego-pavon-jordan%288d5db37c-eddd-4fca-92cd-9c9956a42b4a%29.html>http://www.linkedin.com/profile/view?id=170617924&trk=nav_responsive_tab_profile
> <http://www.linkedin.com/profile/view?id=170617924&trk=nav_responsive_tab_profile>https://helsinki.academia.edu/DiegoPavon
> <https://helsinki.academia.edu/DiegoPavon>*
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