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glmmTMB (version 1.1.7)

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

24,954

Version

1.1.7

License

AGPL-3

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Repository

https://github.com/glmmTMB/glmmTMB

Maintainer

Last Published

April 5th, 2023

Functions in glmmTMB (1.1.7)

Repeated counts of salamanders in streams

confint.glmmTMB

Calculate confidence intervals

VarCorr.glmmTMB

Extract variance and correlation components

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

diagnose model problems

.collectDuplicates

collapse duplicated observations

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

dtruncated_nbinom2

truncated distributions

Extract or Get Generalize Components from a Fitted Mixed Effects Model

Extract fixed-effects estimates

Downstream methods

support methods for parametric bootstrapping

checkDepPackageVersion

Check for version mismatch in dependent binary packages

Begging by Owl Nestlings

findReTrmClasses

list of specials -- taken from enum.R

Format the 'VarCorr' Matrix of Random Effects

Create X and random effect terms from formula

Optimize a TMB model and package results

Seizure Counts for Epileptics - Extended

Retrieve family-specific parameters

profile.glmmTMB

Compute likelihood profiles for a fitted model

translate vector of correlation parameters to correlation values

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

Fit Models with TMB

Control parameters for glmmTMB optimization

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

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

Family functions for glmmTMB

Calculate Variance-Covariance Matrix for a Fitted glmmTMB model

Factor with numeric interpretable levels.

weights.glmmTMB

Extract weights from a glmmTMB object

getCapabilities

List model options that glmmTMB knows about

extract right-hand side of a formula

residuals.glmmTMB

Compute residuals for a glmmTMB object

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

predict.glmmTMB

expandDoubleVert

expand double-bar RE notation by splitting

Check OpenMP status

Split formula containing special random effect terms

print.VarCorr.glmmTMB

Printing The Variance and Correlation Parameters of a glmmTMB

Reinstalling binary dependencies

formula.glmmTMB

Extract the formula of a glmmTMB object

conditionally update glmmTMB object fitted with an old TMB version

Extract Random Effects

Get Grouping Variable

Methods for extracting developer-level information from glmmTMB models

simulate.glmmTMB

Simulate from a glmmTMB fitted model

Objects exported from other packages

Extract residual standard deviation or dispersion parameter