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glmmTMB (version 1.1.11)

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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Version

Install

install.packages('glmmTMB')

Monthly Downloads

26,488

Version

1.1.11

License

AGPL-3

Issues

200

Pull Requests

5

Stars

315

Forks

63

Maintainer

Mollie Brooks

Last Published

April 2nd, 2025

Functions in glmmTMB (1.1.11)

getCapabilities

List model options that glmmTMB knows about
getGrpVar

Get Grouping Variable
fitTMB

Optimize TMB models and package results, modularly
Anova.glmmTMB

Downstream methods
dtruncated_nbinom2

truncated distributions
glmmTMBControl

Control parameters for glmmTMB optimization
terms.glmmTMB

Methods for extracting developer-level information from glmmTMB models
formatVC

Format the 'VarCorr' Matrix of Random Effects
up2date

conditionally update glmmTMB object fitted with an old TMB version
map.theta.propto

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

Extract fixed-effects estimates
family_params

Retrieve family-specific parameters
epil2

Seizure Counts for Epileptics - Extended
get_cor

transform correlation parameters to and from glmmTMB parameterization
glmmTMB

Fit Models with TMB
numFactor

Factor with numeric interpretable levels.
priors

use of priors in glmmTMB
reexports

Objects exported from other packages
ranef.glmmTMB

Extract Random Effects
getXReTrms

Create X and random effect terms from formula
get_autopar

retrieve current value of TMB autopar setting
simulate.glmmTMB

Simulate from a glmmTMB fitted model
profile.glmmTMB

Compute likelihood profiles for a fitted model
print.VarCorr.glmmTMB

Printing The Variance and Correlation Parameters of a glmmTMB
predict.glmmTMB

prediction
spider_long

Spider data from CANOCO, long format
reinstalling

Reinstalling binary dependencies
residuals.glmmTMB

Compute residuals for a glmmTMB object
simulate_new

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

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

Extract the formula of a glmmTMB object
mkTMBStruc

Extract info from formulas, reTrms, etc., format for TMB
nbinom2

Family functions for glmmTMB
getME.glmmTMB

Extract or Get Generalize Components from a Fitted Mixed Effects Model
set_simcodes

helper function to modify simulation settings for random effects
sigma.glmmTMB

Extract residual standard deviation or dispersion parameter
omp_check

Check OpenMP status
vcov.glmmTMB

Calculate Variance-Covariance Matrix for a Fitted glmmTMB model
weights.glmmTMB

Extract weights from a glmmTMB object
getReStruc

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

Begging by Owl Nestlings
isLMM.glmmTMB

support methods for parametric bootstrapping
as.theta.vcov

Get theta parameterisation of a covariance structure
diagnose

diagnose model problems
confint.glmmTMB

Calculate confidence intervals
VarCorr.glmmTMB

Extract variance and correlation components
.adjustX

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

Repeated counts of salamanders in streams
.collectDuplicates

collapse duplicated observations
.checkRankX

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