Generalised Linear Mixed Model Specification, Analysis, Fitting, and Optimal Design in R with the glmmr Packages

We describe the R package glmmrBase and an extension glmmrOptim. glmmrBase provides a flexible approach to specifying and analysing generalised linear mixed models. We use an object-orientated class system within R to provide methods for a wide range of covariance and mean functions relevant to multiple applications including cluster randomised trials, cohort studies, spatial and spatio-temporal modelling, and split-plot designs. The class generates relevant matrices and statistics and a wide range of methods including full likelihood estimation of generalised linear mixed models using Markov Chain Monte Carlo Maximum Likelihood, Laplace approximation, power calculation, and access to relevant calculations. The class also includes Hamiltonian Monte Carlo simulation of random effects, sparse matrix methods, and other functionality to support efficient estimation. The glmmrOptim package implements a set of algorithms to identify c-optimal experimental designs where observations are correlated and can be specified using a generalised linear mixed model. Several examples and comparisons to existing packages are provided to illustrate use of the packages.