Package: glmmTMB 1.1.10.9000

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]

glmmTMB_1.1.10.9000.tar.gz
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glmmTMB.pdf |glmmTMB.html✨
glmmTMB/json (API)
NEWS

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

Peer review:

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

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

On CRAN:

16.78 score 294 stars 25 packages 3.7k scripts 24k downloads 373 mentions 46 exports 16 dependencies

Last updated 9 days agofrom:3327163008. Checks:OK: 9. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 13 2024
R-4.5-win-x86_64OKNov 13 2024
R-4.5-linux-x86_64OKNov 13 2024
R-4.4-win-x86_64OKNov 13 2024
R-4.4-mac-x86_64OKNov 13 2024
R-4.4-mac-aarch64OKNov 13 2024
R-4.3-win-x86_64OKNov 13 2024
R-4.3-mac-x86_64OKNov 13 2024
R-4.3-mac-aarch64OKNov 13 2024

Exports:bellbeta_familybetabinomialcompoisdiagnosedtruncated_nbinom1dtruncated_nbinom2dtruncated_poissonfamily_paramsfinalizeTMBfitTMBfixefgenpoisget_corgetCapabilitiesgetGrpVargetMEgetReStrucglmmTMBglmmTMBControlgt_loadlognormalnbinom1nbinom12nbinom2numFactoromp_checkordbetaparseNumLevelsput_corranefrefitset_simcodessigmasimulate_newskewnormalt_familytruncated_compoistruncated_genpoistruncated_nbinom1truncated_nbinom2truncated_poissontweedieup2dateVarCorrziGamma

Dependencies:bootlatticelme4MASSMatrixmgcvminqanlmenloptrnumDerivrbibutilsRcppRcppEigenRdpackreformulasTMB

basic examples of glmmTMB usage

Rendered fromglmmTMB.Rnwusingknitr::knitron Nov 13 2024.

Last update: 2023-03-15
Started: 2015-12-01

Covariance structures with glmmTMB

Kasper Kristensen and Maeve McGillycuddy

Rendered fromcovstruct.rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2024-11-05
Started: 2016-12-02

Hacking glmmTMB

Rendered fromhacking.rmdusingknitr::rmarkdownon Nov 13 2024.

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

Miscellaneous examples

Rendered frommiscEx.rmdusingknitr::rmarkdownon Nov 13 2024.

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

Model evaluation

Rendered frommodel_evaluation.Rnwusingknitr::knitron Nov 13 2024.

Last update: 2023-04-25
Started: 2019-06-18

Parallel optimization using glmmTMB

Nafis Sadat

Rendered fromparallel.rmdusingknitr::rmarkdownon Nov 13 2024.

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

Post-hoc MCMC with glmmTMB

Ben Bolker

Rendered frommcmc.rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2024-03-17
Started: 2016-10-19

Priors in glmmTMB

Ben Bolker

Rendered frompriors.rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2024-04-05
Started: 2024-03-17

Simulate from a fitted glmmTMB model or a formula

Mollie Brooks and Ben Bolker

Rendered fromsim.rmdusingknitr::rmarkdownon Nov 13 2024.

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

Troubleshooting with glmmTMB

Rendered fromtroubleshooting.rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2021-09-09
Started: 2017-02-16

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
Calculate confidence intervalsconfint.glmmTMB
diagnose model problemsdiagnose
truncated distributionsdtruncated_nbinom1 dtruncated_nbinom2 dtruncated_poisson
Seizure Counts for Epileptics - Extendedepil2
Retrieve family-specific parametersfamily_params
Optimize TMB models and package results, modularlyfinalizeTMB fitTMB
Extract fixed-effects estimatesfixef fixef.glmmTMB
Format the 'VarCorr' Matrix of Random EffectsformatVC
Extract the formula of a glmmTMB objectformula.glmmTMB
translate vector of correlation parameters to correlation valuesget_cor put_cor
List model options that glmmTMB knows aboutgetCapabilities
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
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
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
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
Extract weights from a glmmTMB objectweights.glmmTMB