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glmmTMB (version 1.0.2.1)

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

1.0.2.1

License

AGPL-3

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Repository

https://github.com/glmmTMB/glmmTMB

Maintainer

Last Published

July 2nd, 2020

Functions in glmmTMB (1.0.2.1)

Seizure Counts for Epileptics - Extended

confint.glmmTMB

Calculate confidence intervals

Downstream methods

support methods for parametric bootstrapping

Repeated counts of salamanders in streams

.collectDuplicates

collapse duplicated observations

Begging by Owl Nestlings

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

VarCorr.glmmTMB

Extract variance and correlation components

expandAllGrpVar

expand interactions/combinations of grouping variables

findReTrmClasses

list of specials -- taken from enum.R

Optimize a TMB model and package results

Format the 'VarCorr' Matrix of Random Effects

translate vector of correlation parameters to correlation values

Create X and random effect terms from formula

formula.glmmTMB

Extract the formula of a glmmTMB object

weights.glmmTMB

Extract weights from a glmmTMB object

Family functions for glmmTMB

Factor with numeric interpretable levels.

Methods for extracting developer-level information from glmmTMB models

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

getCapabilities

List model options that glmmTMB knows about

Combine right-hand sides of an arbitrary number of formulas

Calculate Variance-Covariance Matrix for a Fitted glmmTMB model

Extract Random Effects

profile.glmmTMB

Compute likelihood profiles for a fitted model

Get Grouping Variable

print.VarCorr.glmmTMB

Printing The Variance and Correlation Parameters of a glmmTMB

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

simulate.glmmTMB

Simulate from a glmmTMB fitted model

Extract or Get Generalize Components from a Fitted Mixed Effects Model

Extract residual standard deviation or dispersion parameter

predict.glmmTMB

Extract fixed-effects estimates

Fit Models with TMB

Control parameters for glmmTMB optimization

test formula: does it contain a particular element?

residuals.glmmTMB

Compute residuals for a glmmTMB object

Objects exported from other packages