glmmTMB

glmmTMB is an R package for fitting generalized linear mixed models (GLMMs) and extensions, built on Template Model Builder, which is in turn built on CppAD and Eigen. It is intended to handle a wide range of statistical distributions (Gaussian, Poisson, binomial, negative binomial, Beta ...) as well as model extensions such as zero-inflation, heteroscedasticity, and autocorrelation. Fixed and random effects models can be specified for the conditional and zero-inflated components of the model, as well as fixed effects models for the dispersion parameter.

Where to ask questions

r-sig-mixed-models@r-project.org for general questions about glmmTMB usage and mixed models
https://github.com/glmmTMB/glmmTMB/issues for bug, infelicity, and wishlist reporting
https://groups.google.com/forum/#!forum/tmb-users for TMB-specific questions
maintainer e-mail only for urgent/private communications

Installation

From CRAN

glmmTMB is on CRAN, so you can install the latest release version in the usual way, i.e. install.packages("glmmTMB") .

Handling TMB/Matrix/glmmTMB mismatches

When loading glmmTMB you may encounter this message:

Package version inconsistency detected.
TMB was built with Matrix version [xxxx]
Current Matrix version is [yyyy]
Please re-install 'TMB' from source or restore original 'Matrix' package

This may happen because you have installed a new version of glmmTMB from CRAN but haven't updated the Matrix package to its newest version. If this is the case, just use update.packages() (to update all of your packages) or install.packages("Matrix") (to install just the latest version of Matrix from CRAN).

Alternately (slightly more problematically), this may happen because you've updated the Matrix package to a newer version that was published on CRAN more recently than the latest CRAN version of TMB. Installing a new binary version of TMB from CRAN (i.e., via update.packages() or install.packages("TMB") on Windows or MacOS) probably won't help, because the binary package on CRAN will have been built with the older version.

To re-install TMB from source, or to restore an older version of Matrix, you will need to have developer tools (compilers etc.) installed; these are not R packages, but additional packages and libraries for your operating system. You can try devtools::dr_devtools() to see if you have them already; if not, see the RStudio devtools docs for links to download and install them.

At this point, if you're lucky, install.packages("TMB",type="source") will take care of everything.

If you're unlucky (e.g. you're using MacOS and originally installed R from a binary package), you may have some more work to do.

if you get errors about library not found for -lgfortran or library not found for -lquadmath you need to follow these instructions to update your Fortran compilers.
if you get errors about unsupported option '-fopenmp'you need to turn off OpenMP compilation by adding the line SHLIB_OPENMP_CFLAGS= to your ~/.R/Makevars file. If you've already done step #1 this file will already exist; use a text editor to add the line above. Otherwise, you need to create it.

After updating your compilers (if necessary) and turning off OpenMP compilation, re-try the installation from source.

If you opt to restore an older version of Matrix, try devtools::install_version("Matrix","[xxxx]"), where [xxxx] is the version of Matrix shown in the original error message. This will also require installation from source.

If all else fails you can ask a maintainer to provide a binary version of the TMB package that works for your OS and Matrix version.

From Github (source)

You can install the most recent development version of glmmTMB via

devtools::install_github("glmmTMB/glmmTMB/glmmTMB")