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glmmTMB (version 0.2.2.0)

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

35,703

Version

0.2.2.0

License

AGPL-3

Maintainer

Mollie Brooks

Last Published

July 3rd, 2018

Functions in glmmTMB (0.2.2.0)

glmmTMBControl

Control parameters for glmmTMB optimization
ranef.glmmTMB

Extract Random Effects
profile.glmmTMB

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

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

Simulate from a glmmTMB fitted model
addForm

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

Extract residual standard deviation or dispersion parameter
numFactor

Factor with numeric interpretable levels.
predict.glmmTMB

prediction
tmbroot

Compute likelihood profile confidence intervals of a TMB object by root-finding (generalized from TMB::tmbprofile)
vcov.glmmTMB

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

Compute residuals for a glmmTMB object
formatVC

Format the 'VarCorr' Matrix of Random Effects
getGrpVar

Get Grouping Variable
mkTMBStruc

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

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

Create X and random effect terms from formula
getCapabilities

List model options that glmmTMB knows about
glmmTMB

Fit models with TMB
getReStruc

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

list of specials -- taken from enum.R
inForm

test formula: does it contain a particular element?
fbx

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

Extract fixed-effects estimates
Salamanders

Repeated counts of salamanders in streams
epil2

Seizure Counts for Epileptics - Extended
Owls

Begging by Owl Nestlings
VarCorr.glmmTMB

Extract variance and correlation components
confint.glmmTMB

Calculate confidence intervals
expandAllGrpVar

expand interactions/combinations of grouping variables
nbinom2

Family functions for glmmTMB