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:

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visit the following webpages for more information about the glmmADMB package (please note the latter is somewhat out of date, although it may still contain useful information):

Installation

Your best bet is
install.packages("R2admb")
install.packages("glmmADMB", 
    repos=c("http://glmmadmb.r-forge.r-project.org/repos",
            getOption("repos")),
    type="source")

If you have trouble with the binary provided with your version of glmmADMB, here are the instructions for replacing it with a newer/different version:
  1. look at the output of glmmADMB:::get_bin_loc() to determine where R will look for the compiled code for glmmADMB.
  2. Go to the Buildbot page and retrieve a binary that is compatible with your OS. In general, the file name format is something like glmmadmb-r[version]-[OS]-[compiler]-[nbit]bit.(bin|exe), although the file names do change from time to time. In general you want to look for the highest numbered version compatible with your system (go to the bottom of the list and scroll up, except that the Windows versions are named differently and ended up at the top of the list). For example, as of today (7 Oct 2015) I would choose from among the following:
    glmmadmb-mingw64-r2928-windows8-mingw32.exe
    glmmadmb-mingw64-r2928-windows8-mingw64.exe
    glmmadmb-r2924-macos10-xcode7-32bit.bin
    glmmadmb-r2924-macos10-xcode7-64bit.bin
    glmmadmb-r2928-ubuntu14-64bit.bin
    glmmadmb-r2928-fedora22-gcc5.1-32bit.bin
    glmmadmb-r2928-fedora22-gcc5.1-64bit.bin
    
    (it looks like you may be stuck if you want to run on 32-bit Ubuntu). Once you've found the binary you want, copy it to the location you determined in step #1 (you'll need to rename it to glmmadmb or glmmadmb.exe to match what was there before); you might want to make a backup of the old version).
  3. Try your code again and see if that helped.
  4. If you can't find an appropriate binary on the system, you may have to buildthe glmmadmb binary from its TPL (system.file("tpl","glmmadmb.tpl",package="glmmADMB")) on your system (or find someone with a compatible system who can do it for you) and copy it to the appropriate location.

The binaries included in the glmmADMB will not run on MacOS 10.5 (Leopard) or earlier, and may have trouble with very old versions of Linux as well. If you encounter this problem, your choices are:

Additional documentation

Newer versions

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

The new release is somewhat slower (for the time being) than older (pre-0.5.2) versions: if you have a desperate need for a copy of an old version, you can download a source version and follow alternative #3 from the installation instructions above.