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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.

Functions (39)

Owls

Begging by Owl Nestlings

Salamanders

Repeated counts of salamanders in streams

VarCorr.glmmTMB

Extract variance and correlation components

bootmer_methods

support methods for parametric bootstrapping

confint.glmmTMB

Calculate confidence intervals

dot-collectDuplicates

collapse duplicated observations

downstream_methods

Downstream methods

epil2

Seizure Counts for Epileptics - Extended

expandAllGrpVar

expand interactions/combinations of grouping variables

fbx

(f)ind (b)ars e(x)tended: recursive

findReTrmClasses

list of specials – taken from enum.R

fitTMB

Optimize a TMB model and package results

fixef

Extract fixed-effects estimates

formFuns

test formula: does it contain a particular element?

formatVC

Format the 'VarCorr' Matrix of Random Effects

formula.glmmTMB

Extract the formula of a glmmTMB object

getCapabilities

List model options that glmmTMB knows about

getGrpVar

Get Grouping Variable

getME.glmmTMB

Extract or Get Generalize Components from a Fitted Mixed Effects Model

getReStruc

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

getXReTrms

Create X and random effect terms from formula

get_cor

translate vector of correlation parameters to correlation values

glmmTMB

Fit Models with TMB

glmmTMBControl

Control parameters for glmmTMB optimization

glmmTMB_methods

Methods for extracting developer-level information from glmmTMB models

mkTMBStruc

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

nbinom2

Family functions for glmmTMB

numFactor

Factor with numeric interpretable levels.

predict.glmmTMB

prediction

print.VarCorr.glmmTMB

Printing The Variance and Correlation Parameters of a glmmTMB

profile.glmmTMB

Compute likelihood profiles for a fitted model

ranef.glmmTMB

Extract Random Effects

reexports

Objects exported from other packages

residuals.glmmTMB

Compute residuals for a glmmTMB object

sigma.glmmTMB

Extract residual standard deviation or dispersion parameter

simulate.glmmTMB

Simulate from a glmmTMB fitted model

splitForm

Combine right-hand sides of an arbitrary number of formulas

vcov.glmmTMB

Calculate Variance-Covariance Matrix for a Fitted glmmTMB model

weights.glmmTMB

Extract weights from a glmmTMB object

glmmTMB

Generalized Linear Mixed Models using Template Model Builder

v1.0.2.1

AGPL-3

Authors

Arni Magnusson [aut] (<https://orcid.org/0000-0003-2769-6741>), Hans Skaug [aut], Anders Nielsen [aut] (<https://orcid.org/0000-0001-9683-9262>), Casper Berg [aut] (<https://orcid.org/0000-0002-3812-5269>), Kasper Kristensen [aut], Martin Maechler [aut] (<https://orcid.org/0000-0002-8685-9910>), Koen van Bentham [aut], Ben Bolker [aut] (<https://orcid.org/0000-0002-2127-0443>), Nafis Sadat [ctb] (<https://orcid.org/0000-0001-5715-616X>), Daniel Lüdecke [ctb] (<https://orcid.org/0000-0002-8895-3206>), Russ Lenth [ctb], Joseph O'Brien [ctb] (<https://orcid.org/0000-0001-9851-5077>), Mollie Brooks [aut, cre] (<https://orcid.org/0000-0001-6963-8326>)

Initial release

glmmTMB

Functions (39)

glmmTMB

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