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glmmTMB (version 1.1.8)

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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Install

install.packages('glmmTMB')

Monthly Downloads

55,474

Version

1.1.8

License

AGPL-3

Issues

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Repository

https://github.com/glmmTMB/glmmTMB

Maintainer

Mollie Brooks

Last Published

October 7th, 2023

Functions in glmmTMB (1.1.8)

Optimize TMB models and package results, modularly

Downstream methods

Create X and random effect terms from formula

formula.glmmTMB

Extract the formula of a glmmTMB object

expandDoubleVert

expand double-bar RE notation by splitting

getCapabilities

List model options that glmmTMB knows about

Extract or Get Generalize Components from a Fitted Mixed Effects Model

Get Grouping Variable

Fit Models with TMB

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

translate vector of correlation parameters to correlation values

Control parameters for glmmTMB optimization

Check OpenMP status

profile.glmmTMB

Compute likelihood profiles for a fitted model

Factor with numeric interpretable levels.

conditionally update glmmTMB object fitted with an old TMB version

Family functions for glmmTMB

Methods for extracting developer-level information from glmmTMB models

Extract Random Effects

print.VarCorr.glmmTMB

Printing The Variance and Correlation Parameters of a glmmTMB

predict.glmmTMB

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

simulate.glmmTMB

Simulate from a glmmTMB fitted model

Calculate Variance-Covariance Matrix for a Fitted glmmTMB model

Objects exported from other packages

Split formula containing special random effect terms

residuals.glmmTMB

Compute residuals for a glmmTMB object

Extract residual standard deviation or dispersion parameter

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

Substitute safe chars (+) for specials (for use in model.frame) (Generalized from lme4's subbars function.)

weights.glmmTMB

Extract weights from a glmmTMB object

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

Reinstalling binary dependencies

diagnose model problems

confint.glmmTMB

Calculate confidence intervals

VarCorr.glmmTMB

Extract variance and correlation components

checkDepPackageVersion

Check for version mismatch in dependent binary packages

extract right-hand side of a formula

support methods for parametric bootstrapping

Repeated counts of salamanders in streams

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

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

Begging by Owl Nestlings

dtruncated_nbinom2

truncated distributions

.collectDuplicates

collapse duplicated observations

Extract fixed-effects estimates

Seizure Counts for Epileptics - Extended

findReTrmClasses

list of specials -- taken from enum.R

Retrieve family-specific parameters

Format the 'VarCorr' Matrix of Random Effects