[R-sig-ME] Questions - next steps in GLMM analysis on nested ecological dataset

Ben Bolker bbolker at gmail.com
Sun Nov 7 19:42:12 CET 2010

Hash: SHA1

On 10-11-07 11:14 AM, Shawn McCracken wrote:
> Shawn McCracken <smccracken at ...> writes:
>> Dear Mixed-models group,
>> I am working with a dataset containing fixed and nested random effects. I
>> have
>> one fixed effect that I am most interested in and the others were collected
>> to
>> see if they also might have an influence. I apologize for the novel but
>> hopefully discussion of this will help others in the future who are as
>> intimidated as I was/am.
>> The data consist of total counts of anuran individuals from a particular
>> species
>> of epiphytic phytotelm plant found in tree canopies at two sites. The site
>> difference (if any) is my main interest. At each site all trees with
>> suitable
>> #¹s of this epiphyte species for sampling were located within a
>> predetermined
>> size area. 16 trees were randomly selected from those available at each site
>> and
>> 5 epiphytes were then randomly sampled for all anurans within them. So, 2
>> sites
>> -> 16 trees (at each site) -> 5 epiphytes (in each tree), which equals 80
>> samples from each site for a total of 160........................
>> 	[[alternative HTML version deleted]]
> Update: The install problem with glmmADMB has been fixed on my Mac. Thanks to
> Dave. Details below. I could still use some feedback on what I have done so far
> still.

  Update: I have been working on the glmmADMB package a bit.  The
current version on R-forge installs OK on my MacOS X.6 machine. It
contains 32-bit binaries which it automatically puts in the correct
location, so that you shouldn't have to mess around with doing this
stuff manually.  Dave F. has sent me compiled 64-bit OS X binaries, but
I haven't gotten around to incorporating them yet (the 32-bit binaries
do work on my system, although presumably the 64-bit ones would be
faster in general).
should work on MacOS.
  It would be helpful to get reports of trouble from list members who
try it.

  To follow up on some of your other questions with my own opinions:
* as I recommend on <http://glmm.wikidot.com/faq> (I have just added a
few words to make my personal opinions clearer), I would recommend
glmm.admb or glmer with individual-level random effects over the various
quasi- options.
 * glmm.admb currently only works with a single random effect, so you
can't do nested random effects that way.  You could build a more
complete model in AD Model Builder, or revert to glmer.
 * Your model specification


  looks reasonable.  If you say
ecpad2$indiv <- 1:nrow(ecpad2)
and add +(1|indiv) to your model specification you will have an
individual-level random effect.

 * Is 'treat' your site variable?  In any case, if you are trying to do
a statistical comparison between only two sites you have a major
pseudo-replication problem (Hurlbert 1984).

  * The p-values that you get from summary(lmer) are Wald Z statistics,
they assume large data sets and are possibly unreliable for
moderate-sized data sets ...

 * Opinions differ on the value of backward stepwise model reduction. It
is standard practice in many ecological contexts and is suggested for
moderate model complexity by many respected practicing
(eco)statisticians (Bates, Wood, Zuur ...) but is vehemently decried by
others (Harrell).  I would probably base inference on your full model
rather than doing backward elimination.

> The solution that worked for me:
> I used the binaries Dave sent in admbfiles.zip over in the post in the
> admb-users group: http://groups.google.com/group/admb-users/t/df5779586e45b9b
> First, I copied them to my desktop and unzipped.
> Opened Terminal and typed the following to direct it to run nbmm in the expanded
> folder and confirm it would run:
> ShawnMBP:$ /Users/Shawn/Desktop/admbfiles/nbmm     #of course you will need to
> change this to navigate to where it is on your computer#
> Error trying to open data input file /users/shawn/desktop/admbfiles/nbmm.dat
>  Error trying to read in model data
>  This is usual caused by a missing DAT file
> Dave said the error message comes from ndmm looking for the data file to use but
> it is running.
> I then located where glmmADMB had originally placed these same named files when
> I did the install of glmmADMB. I can’t remember how I found where they were and
> spotlight won’t show them either. I think I did a search just for “R” and found
> an R.framework folder in the Library folder. I looked through there and found
> them in a folder called admb here:
> MBP_SFM>Library>Frameworks>R.framework>Versions>2.11>Resources>library>glmmADMB>
> admb
> I then replaced the nbmm and bvprobit files that were there with the ones
> provided by Dave.
> Started up R, loaded glmmADMB, viewed the epil2 dataset, and then ran the
> example model and it ran fine!
> My system: Macbook Pro, Mac OSX 10.6.4, R 64-bit
> Hope this helps.
> Shawn
> _______________________________________________
> R-sig-mixed-models at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

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