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glmmTMB (version 1.1.13)

Generalized Linear Mixed Models using Template Model Builder

Description

Fit linear and generalized linear mixed models with various extensions, including zero-inflation. The models are fitted using maximum likelihood estimation via 'TMB' (Template Model Builder). Random effects are assumed to be Gaussian on the scale of the linear predictor and are integrated out using the Laplace approximation. Gradients are calculated using automatic differentiation.

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Install

install.packages('glmmTMB')

Monthly Downloads

49,879

Version

1.1.13

License

AGPL-3

Issues

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Repository

https://github.com/glmmTMB/glmmTMB

Maintainer

Mollie Brooks

Last Published

October 9th, 2025

Functions in glmmTMB (1.1.13)

.collectDuplicates

collapse duplicated observations

Extract or Get Generalize Components from a Fitted Mixed Effects Model

Simple Cluster Based Meat Matrix Estimator

map.theta.propto

Set map values for theta to be fixed (NA) for propto

Extract Empirical Estimating Functions

Get Grouping Variable

Calculate random effect structure Calculates number of random effects, number of parameters, block size and number of blocks. Mostly for internal use.

formula.glmmTMB

Extract the formula of a glmmTMB object

Extract info from formulas, reTrms, etc., format for TMB

use of priors in glmmTMB

helper function to modify simulation settings for random effects

Sandwich Estimator based on Bread and Meat Matrices

Family functions for glmmTMB

Create X and random effect terms from formula

Methods for extracting developer-level information from glmmTMB models

transform correlation parameters to and from glmmTMB parameterization

retrieve current value of TMB autopar setting

print.VarCorr.glmmTMB

Printing The Variance and Correlation Parameters of a glmmTMB

predict.glmmTMB

Spider data from CANOCO, long format

Simulate from covariate/metadata in the absence of a real data set (EXPERIMENTAL)

summary.glmmTMB

summary for glmmTMB fits

getCapabilities

List model options that glmmTMB knows about

Factor with numeric interpretable levels.

getGroups.glmmTMB

Extract Grouping Factors from an Object

Change starting parameters, either by residual method or by user input (start)

Fit Models with TMB

Control parameters for glmmTMB optimization

profile.glmmTMB

Compute likelihood profiles for a fitted model

conditionally update glmmTMB object fitted with an old TMB version

weights.glmmTMB

Extract weights from a glmmTMB object

Check OpenMP status

Calculate Variance-Covariance Matrix for a Fitted glmmTMB model

Reinstalling binary dependencies

residuals.glmmTMB

Compute residuals for a glmmTMB object

Objects exported from other packages

Extract Random Effects

simulate.glmmTMB

Simulate from a glmmTMB fitted model

Extract residual standard deviation or dispersion parameter

Cluster Robust Variance-Covariance Matrix Estimator

diagnose model problems

Get theta parameterisation of a covariance structure

Adjust a model matrix When not rank deficient, do nothing. When rank deficient matrix, drop columns.

confint.glmmTMB

Calculate confidence intervals

compute denominator degrees-of-freedom approximations

support methods for parametric bootstrapping

Bread Matrix for Sandwich Estimator

Optimize TMB models and package results, modularly

dtruncated_nbinom2

truncated distributions

Retrieve family-specific parameters

Downstream methods

Repeated counts of salamanders in streams

Begging by Owl Nestlings

Seizure Counts for Epileptics - Extended

VarCorr.glmmTMB

Extract variance and correlation components

Check for identifiability of fixed effects matrices X, Xzi, Xdisp. When rank_check='adjust', drop columns in X and remove associated parameters.

Extract fixed-effects estimates

format columns corresponding to std. dev. and/or variance

Format the 'VarCorr' Matrix of Random Effects