Learn R Programming
⚠️There's a newer version (1.1.11) of this package.Take me there.

glmmTMB (version 1.1.5)

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.

Copy Link

Version

Install

install.packages('glmmTMB')

Monthly Downloads

23,421

Version

1.1.5

License

AGPL-3

Issues

208

Pull Requests

8

Stars

328

Forks

65

Maintainer

Mollie Brooks

Last Published

November 16th, 2022

Functions in glmmTMB (1.1.5)

findReTrmClasses

list of specials -- taken from enum.R
formatVC

Format the 'VarCorr' Matrix of Random Effects
expandGrpVar

apply
fitTMB

Optimize a TMB model and package results
epil2

Seizure Counts for Epileptics - Extended
family_params

Retrieve family-specific parameters
dtruncated_nbinom2

truncated distributions
Anova.glmmTMB

Downstream methods
.collectDuplicates

collapse duplicated observations
fixef

Extract fixed-effects estimates
getReStruc

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

Fit Models with TMB
getXReTrms

Create X and random effect terms from formula
get_cor

translate vector of correlation parameters to correlation values
getCapabilities

List model options that glmmTMB knows about
expandDoubleVert

expand double-bar RE notation by splitting
getME.glmmTMB

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

Control parameters for glmmTMB optimization
formula.glmmTMB

Extract the formula of a glmmTMB object
getGrpVar

Get Grouping Variable
terms.glmmTMB

Methods for extracting developer-level information from glmmTMB models
up2date

conditionally update glmmTMB object fitted with an old TMB version
predict.glmmTMB

prediction
print.VarCorr.glmmTMB

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

Extract Random Effects
profile.glmmTMB

Compute likelihood profiles for a fitted model
numFactor

Factor with numeric interpretable levels.
omp_check

Check OpenMP status
nbinom2

Family functions for glmmTMB
mkTMBStruc

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

Objects exported from other packages
simulate.glmmTMB

Simulate from a glmmTMB fitted model
residuals.glmmTMB

Compute residuals for a glmmTMB object
sigma.glmmTMB

Extract residual standard deviation or dispersion parameter
reinstalling

Reinstalling binary dependencies
vcov.glmmTMB

Calculate Variance-Covariance Matrix for a Fitted glmmTMB model
startParams

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

Extract weights from a glmmTMB object
splitForm

Split formula containing special random effect terms
Salamanders

Repeated counts of salamanders in streams
confint.glmmTMB

Calculate confidence intervals
diagnose

diagnose model problems
RHSForm

extract right-hand side of a formula
checkDepPackageVersion

Check for version mismatch in dependent binary packages
isLMM.glmmTMB

support methods for parametric bootstrapping
VarCorr.glmmTMB

Extract variance and correlation components
Owls

Begging by Owl Nestlings
.adjustX

Adjust a model matrix When not rank deficient, do nothing. When rank deficient matrix, drop columns.
.checkRankX

Check for identifiability of fixed effects matrices X, Xzi, Xd. When rank_check='adjust', drop columns in X and remove associated parameters.