Package: glmmTMB 1.1.15

Mollie Brooks

glmmTMB: Generalized Linear Mixed Models using Template Model Builder

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.

Authors:Mollie Brooks [aut, cre], Ben Bolker [aut], Kasper Kristensen [aut], Martin Maechler [aut], Arni Magnusson [aut], Maeve McGillycuddy [ctb], Hans Skaug [aut], Anders Nielsen [aut], Casper Berg [aut], Koen van Bentham [aut], Nafis Sadat [ctb], Daniel Lüdecke [ctb], Russ Lenth [ctb], Joseph O'Brien [ctb], Charles J. Geyer [ctb], Mikael Jagan [ctb], Brenton Wiernik [ctb], Daniel B. Stouffer [ctb], Michael Agronah [ctb], Hatice Tül Kübra Akdur [ctb], Daniel Sabanés Bové [ctb], Nikolas Krieger [ctb], Coralie Williams [ctb]

glmmTMB_1.1.15.tar.gz
glmmTMB_1.1.15.zip(r-4.7)glmmTMB_1.1.15.zip(r-4.6)glmmTMB_1.1.15.zip(r-4.5)
glmmTMB_1.1.15.tgz(r-4.6-x86_64)glmmTMB_1.1.15.tgz(r-4.6-arm64)glmmTMB_1.1.15.tgz(r-4.5-x86_64)glmmTMB_1.1.15.tgz(r-4.5-arm64)
glmmTMB_1.1.15.tar.gz(r-4.7-arm64)glmmTMB_1.1.15.tar.gz(r-4.7-x86_64)glmmTMB_1.1.15.tar.gz(r-4.6-arm64)glmmTMB_1.1.15.tar.gz(r-4.6-x86_64)
glmmTMB_1.1.15.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
glmmTMB/json (API)

# Install 'glmmTMB' in R:
install.packages('glmmTMB', repos = c('https://staffanbetner.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/glmmtmb/glmmtmb/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • epil2 - Seizure Counts for Epileptics - Extended
  • Owls - Begging by Owl Nestlings
  • Salamanders - Repeated counts of salamanders in streams
  • spider_long - Spider data from CANOCO, long format

On CRAN:

Conda:

cppopenmp

17.72 score 369 stars 39 packages 7.9k scripts 53k downloads 373 mentions 59 exports 63 dependencies

Last updated from:eb5fba5040. Checks:13 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK344
linux-devel-x86_64OK369
source / vignettesOK502
linux-release-arm64OK336
linux-release-x86_64OK363
macos-release-arm64OK245
macos-release-x86_64OK416
macos-oldrel-arm64OK303
macos-oldrel-x86_64OK669
windows-develOK250
windows-releaseOK389
windows-oldrelOK394
wasm-releaseOK233

Exports:bellbeta_familybetabinomialbreadcompoisdbelldgenpoisdiagnosedof_KRdof_sattdtruncated_nbinom1dtruncated_nbinom2dtruncated_poissonestfunfamily_paramsfinalizeTMBfitTMBfixefgenpoisget_corgetCapabilitiesgetGroupsgetGrpVargetMEgetReStrucglmmTMBglmmTMBControlgt_loadlognormalmeatHCnbinom1nbinom12nbinom2numFactoromp_checkordbetaparseNumLevelspbellpgenpoisput_corranefrefitrgenpoissandwichset_simcodessigmasimulate_newskewnormalt_familytruncated_compoistruncated_genpoistruncated_nbinom1truncated_nbinom2truncated_poissontweedieup2dateVarCorrvcovHCziGamma

Dependencies:backportsbootbroomclicolorspacecowplotcpp11DerivdoBydplyrfarverforecastfracdiffgenericsggplot2gluegtableisobandlabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixmgcvmicrobenchmarkminqamodelrnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpurrrR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangS7sandwichscalesstringistringrtibbletidyrtidyselecttimeDateTMBurcautf8vctrsviridisLitewithrzoo

Priors in glmmTMB
Motivation | Load packages | Culcita example: near-complete separation | Gopher tortoise example: mitigate singular fit | Zero-inflation | TO DO/FIX ME | Development issues | References
Rendered frompriors.rmdusingknitr::rmarkdown

Last update: 2026-06-01
Started: 2024-03-17

basic examples of glmmTMB usage
Introduction/quick start | Preliminaries: packages and data | Sample timings
Rendered fromglmmTMB.Rnwusingknitr::knitr

Last update: 2026-01-14
Started: 2015-12-01

Covariance structures with glmmTMB
Overview | The AR(1) covariance structure | Demonstration on simulated data | Increasing the sample size | The unstructured covariance | The Toeplitz structure | Compound symmetry | Anova tables | Adding coordinate information | Ornstein–Uhlenbeck | Spatial correlations | Matérn | Gaussian | Exponential | A spatial covariance example | Mappings | Unstructured | Generalized latent variable model | Reduced-rank | Proportional | Equal | Construction of structured covariance matrices | References
Rendered fromcovstruct.rmdusingknitr::rmarkdown

Last update: 2026-01-08
Started: 2016-12-02

Model evaluation
model checking and diagnostics | Inference | Extracting coefficients, coefficient plots and tables | influence measures | Robust sandwich standard errors | to do
Rendered frommodel_evaluation.Rnwusingknitr::knitr

Last update: 2025-08-14
Started: 2019-06-18

Troubleshooting with glmmTMB
Warnings | Model convergence problem; non-positive-definite Hessian matrix; NA values for likelihood/AIC/etc. | Example 1. | Example 2. | Example 3. | Model convergence problem: eigenvalue problems | NA/NaN function evaluation | false convergence | Errors | NA/NaN gradient evaluation | gradient length
Rendered fromtroubleshooting.rmdusingknitr::rmarkdown

Last update: 2025-07-07
Started: 2017-02-16

Post-hoc MCMC with glmmTMB
Overview | Setup | Salamander example | Metropolis-Hastings (DIY) | tmbstan | Sleep study example
Rendered frommcmc.rmdusingknitr::rmarkdown

Last update: 2025-04-02
Started: 2016-10-19

Simulate from a fitted glmmTMB model or a formula
Simulating from a fitted model | Simulating from scratch (de novo) | example 1: linear regression | example 2: random effects (including correlations) | example 3: AR1 model | FIXME/TO DO
Rendered fromsim.rmdusingknitr::rmarkdown

Last update: 2024-06-20
Started: 2016-11-22

Hacking glmmTMB
Adding a family | C++ | modify glmmTMB.cpp | R code | modifying family.R | modifying glmmTMB.R | updating NAMESPACE | updating enum.R | Finishing up | Reinstall | Test | Additional distributional parameters | Adding a covariance structure | C++ code | Structure of a glmmTMB object
Rendered fromhacking.rmdusingknitr::rmarkdown

Last update: 2023-07-19
Started: 2022-10-24

Parallel optimization using glmmTMB
Notes on OpenMP support | System information
Rendered fromparallel.rmdusingknitr::rmarkdown

Last update: 2022-10-24
Started: 2019-06-18

Miscellaneous examples
Beta dispersion model
Rendered frommiscEx.rmdusingknitr::rmarkdown

Last update: 2021-01-03
Started: 2017-05-03

Readme and manuals

Help Manual

Help pageTopics
Downstream methodsAnova.glmmTMB downstream_methods Effect.glmmTMB emmeans.glmmTMB
Get theta parameterisation of a covariance structureas.theta.vcov
Bread Matrix for Sandwich Estimatorbread bread.glmmTMB
Calculate confidence intervalsconfint.glmmTMB
The Bell Distributiondbell pbell
The Generalized Poisson Distributiondgenpois pgenpois rgenpois
diagnose model problemsdiagnose
compute denominator degrees-of-freedom approximationsdof_KR dof_satt
truncated distributionsdtruncated_nbinom1 dtruncated_nbinom2 dtruncated_poisson
Seizure Counts for Epileptics - Extendedepil2
Extract Empirical Estimating Functionsestfun estfun.glmmTMB
Retrieve family-specific parametersfamily_params
Optimize TMB models and package results, modularlyfinalizeTMB fitTMB
Extract fixed-effects estimatesfixef fixef.glmmTMB
Extract the formula of a glmmTMB objectformula.glmmTMB
retrieve current value of TMB autopar settingget_autopar
transform correlation parameters to and from glmmTMB parameterizationget_cor put_cor
List model options that glmmTMB knows aboutgetCapabilities
Extract Grouping Factors from an ObjectgetGroups getGroups.glmmTMB
Extract or Get Generalize Components from a Fitted Mixed Effects ModelgetME getME.glmmTMB
Calculate random effect structure Calculates number of random effects, number of parameters, block size and number of blocks. Mostly for internal use.getReStruc
Create X and random effect terms from formulagetXReTrms
Fit Models with TMBglmmTMB
Control parameters for glmmTMB optimizationglmmTMBControl
support methods for parametric bootstrappingisLMM.glmmTMB refit.glmmTMB
Set map values for theta to be fixed (NA) for proptomap.theta.propto
Simple Cluster Based Meat Matrix EstimatormeatHC meatHC.default meatHC.glmmTMB
Family functions for glmmTMBbell betabinomial beta_family compois family_glmmTMB genpois lognormal nbinom1 nbinom12 nbinom2 ordbeta skewnormal truncated_compois truncated_genpois truncated_nbinom1 truncated_nbinom2 truncated_poisson tweedie t_family ziGamma
Factor with numeric interpretable levels.numFactor parseNumLevels
Check OpenMP statusomp_check openmp
Begging by Owl NestlingsOwlModel OwlModel_nb1_bs OwlModel_nb1_bs_mcmc Owls
predictionpredict.glmmTMB
Printing The Variance and Correlation Parameters of a 'glmmTMB'print.VarCorr.glmmTMB
use of priors in glmmTMBpriors
Compute likelihood profiles for a fitted modelconfint.profile.glmmTMB profile.glmmTMB
Extract Random Effectsas.data.frame.ranef.glmmTMB coef.glmmTMB ranef ranef.glmmTMB
Reinstalling binary dependenciesreinstalling
Compute residuals for a glmmTMB objectdeviance.glmmTMB residuals.glmmTMB
Repeated counts of salamanders in streamsSalamanders
Sandwich Estimator based on Bread and Meat Matricessandwich sandwich.default sandwich.glmmTMB
helper function to modify simulation settings for random effectsset_simcodes
Extract residual standard deviation or dispersion parametersigma sigma.glmmTMB
Simulate from covariate/metadata in the absence of a real data set (EXPERIMENTAL)simulate_new
Simulate from a glmmTMB fitted modelsimulate.glmmTMB
Spider data from CANOCO, long formatspider_long
summary for glmmTMB fitssummary.glmmTMB
Methods for extracting developer-level information from 'glmmTMB' modelsmodel.matrix.glmmTMB terms.glmmTMB
conditionally update glmmTMB object fitted with an old TMB versiongt_load up2date
Calculate Variance-Covariance Matrix for a Fitted glmmTMB modelvcov.glmmTMB
Cluster Robust Variance-Covariance Matrix EstimatorvcovHC vcovHC.glmmTMB
Extract weights from a glmmTMB objectweights.glmmTMB