GLMM and R issues

December 4, 2010

(This article was first published on Quantitative Ecology, and kindly contributed to R-bloggers)

I have been trying to run a Generalized Linear Mixed Model (GLMM) for some count data with repeated measures on sub-sampled sites and fixed effects at the site level with covariates at both the sub-plot and time levels.  Plus there are different numbers of sub-plots within each site and not all sub-plots are sampled the same number of times.  It’s quite the gnarly dataset.  I tried to use binomial-mixture models for the analysis to account for differences in detection probability but unfortunately I didn’t have a sufficient number of independent sites to differentiate between detection and abundance.  Plus the sampling may have violated assumptions of closure.  So, anyway, I am back to GLMM and the troubles with that will have to wait for another day.

I use Mac OS 10.5.8 (Leopard) to run R unless I need to run WinBUGS (via R2WinBUGS).  Unfortunately, the R package “lme4” won’t load on R for Macs.  It works fine on my Windows shell.  I have been looking up solutions.  I think the problem is that I need a fortran add-on for Xcode.  Now the problem is that I don’t understand anything about compiling R or Fortran or any of the other things on this website.  It does look like it might be part of the solution (maybe?) to my problems with running WinBUGS through Wine on my Mac.  So here is the solution I’ve found:

This is the specific part that I hope will work:
GNU Fortran 4.2.4 for Mac OS X 10.5 (Leopard):
Download: gfortran-42-5577.pkg (for Xcode 3.1.4 only!)
This package adds GNU Fortran 4.2.4 to Apple’s Xcode 3.1.4 gcc 4.2 (build 5577) compilers on Mac OS X 10.5 (Leopard). It does NOT work on Snow Leopard. This binary has been built the Apple way with the gcc_42 (build 5577) sources (by adding the Fortran directories from gcc 4.2.4 release), so it features full Apple driver (i.e. all special flags work) and works directly with the gcc 4.2 system compiler. You have to install Xcode 3.1.4 first (from ADC). 

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