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glmmTMB (version 1.1.10)

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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Version

Install

install.packages('glmmTMB')

Monthly Downloads

24,954

Version

1.1.10

License

AGPL-3

Issues

185

Pull Requests

5

Stars

292

Forks

60

Maintainer

Mollie Brooks

Last Published

September 26th, 2024

Functions in glmmTMB (1.1.10)

Salamanders

Repeated counts of salamanders in streams
epil2

Seizure Counts for Epileptics - Extended
getXReTrms

Create X and random effect terms from formula
omp_check

Check OpenMP status
nbinom2

Family functions for glmmTMB
mkTMBStruc

Extract info from formulas, reTrms, etc., format for TMB
map.theta.propto

Set map values for theta to be fixed (NA) for propto
family_params

Retrieve family-specific parameters
get_cor

translate vector of correlation parameters to correlation values
predict.glmmTMB

prediction
formatVC

Format the 'VarCorr' Matrix of Random Effects
sigma.glmmTMB

Extract residual standard deviation or dispersion parameter
numFactor

Factor with numeric interpretable levels.
fitTMB

Optimize TMB models and package results, modularly
fixef

Extract fixed-effects estimates
simulate.glmmTMB

Simulate from a glmmTMB fitted model
getCapabilities

List model options that glmmTMB knows about
getGrpVar

Get Grouping Variable
getME.glmmTMB

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

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

use of priors in glmmTMB
weights.glmmTMB

Extract weights from a glmmTMB object
residuals.glmmTMB

Compute residuals for a glmmTMB object
Anova.glmmTMB

Downstream methods
dtruncated_nbinom2

truncated distributions
set_simcodes

helper function to modify simulation settings for random effects
glmmTMB

Fit Models with TMB
glmmTMBControl

Control parameters for glmmTMB optimization
simulate_new

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

Extract the formula of a glmmTMB object
spider_long

Spider data from CANOCO, long format
terms.glmmTMB

Methods for extracting developer-level information from glmmTMB models
up2date

conditionally update glmmTMB object fitted with an old TMB version
reexports

Objects exported from other packages
reinstalling

Reinstalling binary dependencies
startParams

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

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

collapse duplicated observations
as.theta.vcov

Get theta parameterisation of a covariance structure
confint.glmmTMB

Calculate confidence intervals
isLMM.glmmTMB

support methods for parametric bootstrapping
diagnose

diagnose model problems
.checkRankX

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

Extract variance and correlation components
.adjustX

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

Begging by Owl Nestlings