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

Shawn McCracken frocga at gmail.com
Sun Nov 7 17:14:58 CET 2010

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

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:


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.


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