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

glmmTMB (version 1.1.6)

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

25,115

Version

1.1.6

License

AGPL-3

Issues

208

Pull Requests

7

Stars

330

Forks

66

Maintainer

Mollie Brooks

Last Published

March 19th, 2023

Functions in glmmTMB (1.1.6)

findReTrmClasses

list of specials -- taken from enum.R
formatVC

Format the 'VarCorr' Matrix of Random Effects
fitTMB

Optimize a TMB model and package results
fixef

Extract fixed-effects estimates
getCapabilities

List model options that glmmTMB knows about
Anova.glmmTMB

Downstream methods
glmmTMBControl

Control parameters for glmmTMB optimization
glmmTMB

Fit Models with TMB
formula.glmmTMB

Extract the formula of a glmmTMB object
expandDoubleVert

expand double-bar RE notation by splitting
getGrpVar

Get Grouping Variable
getReStruc

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

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

Extract info from formulas, reTrms, etc., format for TMB
nbinom2

Family functions for glmmTMB
predict.glmmTMB

prediction
print.VarCorr.glmmTMB

Printing The Variance and Correlation Parameters of a glmmTMB
up2date

conditionally update glmmTMB object fitted with an old TMB version
expandGrpVar

apply
family_params

Retrieve family-specific parameters
residuals.glmmTMB

Compute residuals for a glmmTMB object
sigma.glmmTMB

Extract residual standard deviation or dispersion parameter
reinstalling

Reinstalling binary dependencies
terms.glmmTMB

Methods for extracting developer-level information from glmmTMB models
getXReTrms

Create X and random effect terms from formula
get_cor

translate vector of correlation parameters to correlation values
splitForm

Split formula containing special random effect terms
numFactor

Factor with numeric interpretable levels.
simulate_new

Simulate from covariate/metadata in the absence of a real data set (EXPERIMENTAL)
startParams

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

Extract Random Effects
omp_check

Check OpenMP status
simulate.glmmTMB

Simulate from a glmmTMB fitted model
weights.glmmTMB

Extract weights from a glmmTMB object
profile.glmmTMB

Compute likelihood profiles for a fitted model
reexports

Objects exported from other packages
vcov.glmmTMB

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

Extract variance and correlation components
confint.glmmTMB

Calculate confidence intervals
diagnose

diagnose model problems
RHSForm

extract right-hand side of a formula
isLMM.glmmTMB

support methods for parametric bootstrapping
checkDepPackageVersion

Check for version mismatch in dependent binary packages
dtruncated_nbinom2

truncated distributions
Salamanders

Repeated counts of salamanders in streams
.adjustX

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

Begging by Owl Nestlings
.checkRankX

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

collapse duplicated observations
epil2

Seizure Counts for Epileptics - Extended