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glmmTMB (version 1.1.2.2)

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

24,954

Version

1.1.2.2

License

AGPL-3

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Repository

https://github.com/glmmTMB/glmmTMB

Maintainer

Last Published

September 1st, 2021

Functions in glmmTMB (1.1.2.2)

VarCorr.glmmTMB

Extract variance and correlation components

confint.glmmTMB

Calculate confidence intervals

support methods for parametric bootstrapping

diagnose model problems

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

Seizure Counts for Epileptics - Extended

Repeated counts of salamanders in streams

expandAllGrpVar

expand interactions/combinations of grouping variables

.collectDuplicates

collapse duplicated observations

Begging by Owl Nestlings

Optimize a TMB model and package results

translate vector of correlation parameters to correlation values

findReTrmClasses

list of specials -- taken from enum.R

Fit Models with TMB

Family functions for glmmTMB

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

formula.glmmTMB

Extract the formula of a glmmTMB object

getCapabilities

List model options that glmmTMB knows about

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

Combine right-hand sides of an arbitrary number of formulas

Extract fixed-effects estimates

Control parameters for glmmTMB optimization

Downstream methods

Methods for extracting developer-level information from glmmTMB models

test formula: does it contain a particular element?

profile.glmmTMB

Compute likelihood profiles for a fitted model

Extract or Get Generalize Components from a Fitted Mixed Effects Model

Get Grouping Variable

predict.glmmTMB

print.VarCorr.glmmTMB

Printing The Variance and Correlation Parameters of a glmmTMB

Create X and random effect terms from formula

Format the 'VarCorr' Matrix of Random Effects

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

Calculate Variance-Covariance Matrix for a Fitted glmmTMB model

Extract Random Effects

weights.glmmTMB

Extract weights from a glmmTMB object

Check OpenMP status

Factor with numeric interpretable levels.

Extract residual standard deviation or dispersion parameter

Objects exported from other packages

residuals.glmmTMB

Compute residuals for a glmmTMB object

simulate.glmmTMB

Simulate from a glmmTMB fitted model