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glmmTMB (version 1.1.4)

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

64,079

Version

1.1.4

License

AGPL-3

Issues

219

Pull Requests

10

Stars

359

Forks

73

Maintainer

Mollie Brooks

Last Published

July 12th, 2022

Functions in glmmTMB (1.1.4)

diagnose

diagnose model problems
VarCorr.glmmTMB

Extract variance and correlation components
checkDepPackageVersion

Check for version mismatch in dependent binary packages
RHSForm

extract right-hand side of a formula
Anova.glmmTMB

Downstream methods
fixef

Extract fixed-effects estimates
fitTMB

Optimize a TMB model and package results
formatVC

Format the 'VarCorr' Matrix of Random Effects
omp_check

Check OpenMP status
expandDoubleVert

expand double-bar RE notation by splitting
up2date

conditionally update glmmTMB object fitted with an old TMB version
mkTMBStruc

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

Create X and random effect terms from formula
getReStruc

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

Extract Random Effects
reexports

Objects exported from other packages
profile.glmmTMB

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

Printing The Variance and Correlation Parameters of a glmmTMB
expandGrpVar

apply
findReTrmClasses

list of specials -- taken from enum.R
predict.glmmTMB

prediction
splitForm

Split formula containing special random effect terms
startParams

Change starting parameters, either by residual method or by user input (start)
dtruncated_nbinom2

truncated distributions
glmmTMBControl

Control parameters for glmmTMB optimization
terms.glmmTMB

Methods for extracting developer-level information from glmmTMB models
epil2

Seizure Counts for Epileptics - Extended
get_cor

translate vector of correlation parameters to correlation values
glmmTMB

Fit Models with TMB
vcov.glmmTMB

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

Extract weights from a glmmTMB object
residuals.glmmTMB

Compute residuals for a glmmTMB object
reinstalling

Reinstalling binary dependencies
getCapabilities

List model options that glmmTMB knows about
formula.glmmTMB

Extract the formula of a glmmTMB object
getGrpVar

Get Grouping Variable
getME.glmmTMB

Extract or Get Generalize Components from a Fitted Mixed Effects Model
nbinom2

Family functions for glmmTMB
numFactor

Factor with numeric interpretable levels.
simulate.glmmTMB

Simulate from a glmmTMB fitted model
sigma.glmmTMB

Extract residual standard deviation or dispersion parameter
Salamanders

Repeated counts of salamanders in streams
isLMM.glmmTMB

support methods for parametric bootstrapping
confint.glmmTMB

Calculate confidence intervals
.collectDuplicates

collapse duplicated observations
Owls

Begging by Owl Nestlings