A Comparison of $\texttt{R}$ Packages for Estimating Generalized Linear Mixed Models

Abstract

Generalized linear mixed models (GLMMs) are widely used for analyzing correlated data, such as longitudinal and multilevel data. With over 15 $\texttt{R}$ packages available on $\texttt{CRAN}$ for fitting GLMMs, practitioners face a difficult choice regarding which package yields accurate estimates, converges reliably, and offers reasonable computational speed. Existing comparisons are either limited to methods within a single package or focus on narrow criteria such as speed alone. To address this gap, we systematically compared seven representative $\texttt{R}$ packages -- $\texttt{lme4}$, $\texttt{GLMMadaptive}$, $\texttt{glmmTMB}$, $\texttt{MASS}$, $\texttt{hglm}$, $\texttt{brms}$, and $\texttt{rstanarm}$ -- that implement different estimation frameworks. By using Monte Carlo simulations across 24 scenarios, we evaluated each package in terms of convergence ratios, computational time, estimation accuracy, and hypothesis testing performance. Our results showed that $\texttt{lme4_AGQ}$ and $\texttt{GLMMadaptive}$ yield the highest accuracy and convergence ratios, although $\texttt{GLMMadaptive}$ becomes slower under complex random-effect structures. $\texttt{lme4_LA}$ and $\texttt{glmmTMB}$ are computationally fast but exhibit lower convergence ratios and larger bias, especially for variance components. $\texttt{MASS}$ and $\texttt{hglm}$ are also fast, but $\texttt{MASS}$ yields liberal univariate tests and $\texttt{hglm}$ lacks support for correlated random effects and multivariate testing. Between two Bayesian packages, $\texttt{rstanarm}$ converges reliably and produces valid univariate tests, whereas $\texttt{brms}$ is extremely slow, limiting its practical utility. Based on these findings, we provide practical recommendations for choosing GLMM tool in applied research.