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glmmTMB (version 0.2.0)

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

25,060

Version

0.2.0

License

AGPL-3

Maintainer

Mollie Brooks

Last Published

December 11th, 2017

Functions in glmmTMB (0.2.0)

VarCorr.glmmTMB

Extract variance and correlation components
expandAllGrpVar

expand interactions/combinations of grouping variables
confint.glmmTMB

Calculate confidence intervals
findReTrmClasses

list of specials -- taken from enum.R
Owls

Begging by Owl Nestlings
fixef

Extract fixed-effects estimates
formatVC

Format the 'VarCorr' Matrix of Random Effects
Salamanders

Repeated counts of salamanders in streams
getCapabilities

List model options that glmmTMB knows about
getME.glmmTMB

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

Get Grouping Variable
getXReTrms

Create X and random effect terms from formula
getReStruc

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

Fit models with TMB
glmmTMBControl

Control parameters for glmmTMB optimization
predict.glmmTMB

prediction
print.VarCorr.glmmTMB

Printing The Variance and Correlation Parameters of a glmmTMB
mkTMBStruc

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

Extract Random Effects
nbinom2

Family functions for glmmTMB
residuals.glmmTMB

Compute residuals for a glmmTMB object
numFactor

Factor with numeric interpretable levels.
fbx

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

Combine right-hand sides of an arbitrary number of formulas
vcov.glmmTMB

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

Extract residual standard deviation or dispersion parameter
simulate.glmmTMB

Simulate from a glmmTMB fitted model
epil2

Seizure Counts for Epileptics - Extended