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glmmTMB (version 1.1.9)

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

1.1.9

License

AGPL-3

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Repository

https://github.com/glmmTMB/glmmTMB

Maintainer

Last Published

March 20th, 2024

Functions in glmmTMB (1.1.9)

.collectDuplicates

collapse duplicated observations

VarCorr.glmmTMB

Extract variance and correlation components

findReTrmClasses

list of specials -- taken from enum.R

Optimize TMB models and package results, modularly

translate vector of correlation parameters to correlation values

expandDoubleVert

expand double-bar RE notation by splitting

Create X and random effect terms from formula

Get Grouping Variable

Downstream methods

getCapabilities

List model options that glmmTMB knows about

formula.glmmTMB

Extract the formula of a glmmTMB object

predict.glmmTMB

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

Extract or Get Generalize Components from a Fitted Mixed Effects Model

Methods for extracting developer-level information from glmmTMB models

Family functions for glmmTMB

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

print.VarCorr.glmmTMB

Printing The Variance and Correlation Parameters of a glmmTMB

Extract fixed-effects estimates

Extract Random Effects

Check OpenMP status

Factor with numeric interpretable levels.

Objects exported from other packages

Calculate Variance-Covariance Matrix for a Fitted glmmTMB model

Reinstalling binary dependencies

residuals.glmmTMB

Compute residuals for a glmmTMB object

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

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

Control parameters for glmmTMB optimization

Format the 'VarCorr' Matrix of Random Effects

use of priors in glmmTMB

Fit Models with TMB

Split formula containing special random effect terms

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

profile.glmmTMB

Compute likelihood profiles for a fitted model

weights.glmmTMB

Extract weights from a glmmTMB object

conditionally update glmmTMB object fitted with an old TMB version

Extract residual standard deviation or dispersion parameter

simulate.glmmTMB

Simulate from a glmmTMB fitted model

Repeated counts of salamanders in streams

support methods for parametric bootstrapping

extract right-hand side of a formula

confint.glmmTMB

Calculate confidence intervals

checkDepPackageVersion

Check for version mismatch in dependent binary packages

Retrieve family-specific parameters

diagnose model problems

dtruncated_nbinom2

truncated distributions

Begging by Owl Nestlings

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.

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