glmmADMB

The glmmADMB package, built on the open-source AD Model Builder platform, is an R package for fitting generalized linear mixed models (GLMMs).

Its capabilities include:

• a wide range of families (response distributions), including non-exponential families such as negative binomial (type 1 and 2), Beta, logistic, and truncated Poisson and negative binomial distributions as well as the standard exponential families (binomial, Poisson, Gamma, Gaussian).
• a wide range of link functions: log, logit, probit, complementary log-log, identity, inverse.
• Zero-inflation (currently only as a single constant term across all groups)
• Single or multiple random effects, including both nested and crossed effects
• Markov chain Monte Carlo (MCMC) summaries of uncertainty

In order to use glmmADMB effectively you should already be reasonably familiar with GLMMs, which in turn requires familiarity with (i) generalized linear models (e.g. the special cases of logistic, binomial, and Poisson regression) and (ii) 'modern' mixed models (those working via maximization of the marginal likelihood rather than by manipulating sums of squares).

Please visit the following webpages for more information about the glmmADMB package (please note the latter is somewhat out of date, although it may still contain useful information):

• R-Forge (current development)
• ADMB Project (recent homepage)

Installation

1. First try

   install.packages("glmmADMB", repos="http://r-forge.r-project.org")
   

2. If this fails (because you don't have the very latest version of R, or because R-forge is having a bad day), try

   install.packages("glmmADMB", repos="http://r-forge.r-project.org",type="source")

3. If this fails, you may have an internet connection problem. Go to the R-forge packages page for the glmmADMB project and download the source package (search for the link labeled "Package source (.tar.gz)") to your computer. Put this file (which will be called glmmADMB_xxxx.tar.gz, where xxxx is the version number) in your R working directory and try

   install.packages("glmmADMB_xxxx.tar.gz",repos=NULL, type="source")
   

4. If the most recent build of glmmADMB is messed up (usually the maintainers' fault), you may be able to find/install a fairly recent version via

   install.packages("glmmADMB", repos="http://www.math.mcmaster.ca/bolker/R",type="source")
   

   or by navigating to http://www.math.mcmaster.ca/bolker/R/src/contrib and downloading the appropriate file, and following step #3 above.
5. You can use the following helper function to see which versions of glmmADMB are available at a given repository:

   favail <- function(repos="r-forge.r-project.org",
                      pkg="glmmADMB",
                      ...) {
       hdr <- "http://"
       if (!substr(repos,1,8)==hdr) repos <- paste(hdr,repos,sep="")
       a <- available.packages(contriburl=contrib.url(repos),...)
       if (length(grep(pkg,rownames(a)))==0)
           stop(sprintf("%s unavailable at repos %s",pkg,repos))
       a[pkg,"Version"]
   }
   

   You can use type="source" if you want to check for source packages rather than for the binaries for your OS. For example:

   favail()              ## r-forge, automatic build (default)
   favail(type="source") ## r-forge, source (the same, for Linux)
   favail("glmmadmb.r-forge.r-project.org/repos")  ## r-forge, alternative location
   

6. If all else fails, contact the package maintainers.
7. Note that recent versions of glmmADMB (>=0.7) require the R2admb package as well; under normal circumstances this should be installed automatically when you install glmmADMB, but if you run into trouble you should try solutions similar to those listed above.
8. At present the binaries included in the glmmADMB will not run on MacOS 10.5 (Leopard) or earlier. If you encounter this problem, your choices are:
   • Upgrade your system to a more recent version of MacOS (if possible);
   • Build glmmadmb from its TPL file on your machine. This will be a bit tricky if you are not reasonably experienced
     • Download the full AD Model Builder source code from the AD Model Builder download page and follow the directions for building AD Model Builder from source; you may need to install Xcode, and you may need to ask for help at users@admb-project.org. (Googling "admb macos 10.5" will be helpful as well, although it's possible that you will need the most recent version of the ADMB source code to compile glmmadmb.tpl properly ...)
     • find the glmmadmb.tpl file in the glmmADMB package directories and use ADMB to compile it to a binary
     • copy the resulting binary to the bin/macos32 or bin/macos64 directory as appropriate.
   • Contact the maintainers to appeal for help and find out if there any new developments in support for MacOS versions less than 10.6.
   • A similar process may work for other unsupported operating systems such as Solaris, but in that case it's also probably a good idea to contact the maintainers.

Additional documentation

• We recommend the R mixed models list at r-sig-mixed-models@r-project.org for glmmADMB questions, although if you feel that your question is more AD Model Builder-oriented than R-oriented you may also want to try the AD Model Builder user's list.
• Current (fairly minimal) documentation/example for ADMB: HTML, PDF: this is also accessible from within R (once glmmADMB is installed) via vignette("glmmADMB",package="glmmADMB")
• The GLMM FAQ page gives general advice about GLMMs, although its content is slightly more oriented toward the lme4 package.

Note on new versions

New versions of glmmADMB (>0.6.4) have the following major changes:

• new formula format, similar to that of the lme4 package, where random and fixed effects are specified as part of a single formula (random can also be specified separately, as in lme)
• multiple grouping variables (random effects) are allowed
• wider range of distributions and link functions supported (e.g. binomial with N> 1)