# Generalized Linear Mixed Models using Template Model Builder

## Documentation for package ‘glmmTMB’ version 1.1.13

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G I L M N O P R S T U V W Z

## -- A --

Anova.glmmTMB | Downstream methods
as.data.frame.ranef.glmmTMB | Extract Random Effects
as.theta.vcov | Get theta parameterisation of a covariance structure

## -- B --

bell | Family functions for glmmTMB
betabinomial | Family functions for glmmTMB
beta_family | Family functions for glmmTMB
bread | Bread Matrix for Sandwich Estimator
bread.glmmTMB | Bread Matrix for Sandwich Estimator

## -- C --

coef.glmmTMB | Extract Random Effects
compois | Family functions for glmmTMB
confint.glmmTMB | Calculate confidence intervals
confint.profile.glmmTMB | Compute likelihood profiles for a fitted model

## -- D --

deviance.glmmTMB | Compute residuals for a glmmTMB object
diagnose | diagnose model problems
dof_KR | compute denominator degrees-of-freedom approximations
dof_satt | compute denominator degrees-of-freedom approximations
downstream_methods | Downstream methods
dtruncated_nbinom1 | truncated distributions
dtruncated_nbinom2 | truncated distributions
dtruncated_poisson | truncated distributions

## -- E --

Effect.glmmTMB | Downstream methods
emmeans.glmmTMB | Downstream methods
epil2 | Seizure Counts for Epileptics - Extended
estfun | Extract Empirical Estimating Functions
estfun.glmmTMB | Extract Empirical Estimating Functions

## -- F --

family_glmmTMB | Family functions for glmmTMB
family_params | Retrieve family-specific parameters
finalizeTMB | Optimize TMB models and package results, modularly
fitTMB | Optimize TMB models and package results, modularly
fixef | Extract fixed-effects estimates
fixef.glmmTMB | Extract fixed-effects estimates
formatVC | Format the 'VarCorr' Matrix of Random Effects
format_corr | format columns corresponding to std. dev. and/or variance
format_sdvar | format columns corresponding to std. dev. and/or variance
formula.glmmTMB | Extract the formula of a glmmTMB object

## -- G --

genpois | Family functions for glmmTMB
getCapabilities | List model options that glmmTMB knows about
getGroups | Extract Grouping Factors from an Object
getGroups.glmmTMB | Extract Grouping Factors from an Object
getME | Extract or Get Generalize Components from a Fitted Mixed Effects Model
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.
getXReTrms | Create X and random effect terms from formula
get_autopar | retrieve current value of TMB autopar setting
get_cor | transform correlation parameters to and from glmmTMB parameterization
get_sd | format columns corresponding to std. dev. and/or variance
glmmTMB | Fit Models with TMB
glmmTMBControl | Control parameters for glmmTMB optimization
gt_load | conditionally update glmmTMB object fitted with an old TMB version

## -- I --

isLMM.glmmTMB | support methods for parametric bootstrapping

## -- L --

lognormal | Family functions for glmmTMB

## -- M --

map.theta.propto | Set map values for theta to be fixed (NA) for propto
meatHC | Simple Cluster Based Meat Matrix Estimator
meatHC.default | Simple Cluster Based Meat Matrix Estimator
meatHC.glmmTMB | Simple Cluster Based Meat Matrix Estimator
model.matrix.glmmTMB | Methods for extracting developer-level information from 'glmmTMB' models

## -- N --

nbinom1 | Family functions for glmmTMB
nbinom12 | Family functions for glmmTMB
nbinom2 | Family functions for glmmTMB
numFactor | Factor with numeric interpretable levels.

## -- O --

omp_check | Check OpenMP status
openmp | Check OpenMP status
ordbeta | Family functions for glmmTMB
OwlModel | Begging by Owl Nestlings
OwlModel_nb1_bs | Begging by Owl Nestlings
OwlModel_nb1_bs_mcmc | Begging by Owl Nestlings
Owls | Begging by Owl Nestlings

## -- P --

parseNumLevels | Factor with numeric interpretable levels.
predict.glmmTMB | prediction
print.VarCorr.glmmTMB | Printing The Variance and Correlation Parameters of a 'glmmTMB'
priors | use of priors in glmmTMB
profile.glmmTMB | Compute likelihood profiles for a fitted model
put_cor | transform correlation parameters to and from glmmTMB parameterization

## -- R --

ranef | Extract Random Effects
ranef.glmmTMB | Extract Random Effects
refit.glmmTMB | support methods for parametric bootstrapping
reinstalling | Reinstalling binary dependencies
residuals.glmmTMB | Compute residuals for a glmmTMB object

## -- S --

Salamanders | Repeated counts of salamanders in streams
sandwich | Sandwich Estimator based on Bread and Meat Matrices
sandwich.default | Sandwich Estimator based on Bread and Meat Matrices
sandwich.glmmTMB | Sandwich Estimator based on Bread and Meat Matrices
set_simcodes | helper function to modify simulation settings for random effects
sigma | Extract residual standard deviation or dispersion parameter
sigma.glmmTMB | Extract residual standard deviation or dispersion parameter
simulate.glmmTMB | Simulate from a glmmTMB fitted model
simulate_new | Simulate from covariate/metadata in the absence of a real data set (EXPERIMENTAL)
skewnormal | Family functions for glmmTMB
spider_long | Spider data from CANOCO, long format
summary.glmmTMB | summary for glmmTMB fits

## -- T --

terms.glmmTMB | Methods for extracting developer-level information from 'glmmTMB' models
truncated_compois | Family functions for glmmTMB
truncated_genpois | Family functions for glmmTMB
truncated_nbinom1 | Family functions for glmmTMB
truncated_nbinom2 | Family functions for glmmTMB
truncated_poisson | Family functions for glmmTMB
tweedie | Family functions for glmmTMB
t_family | Family functions for glmmTMB

## -- U --

up2date | conditionally update glmmTMB object fitted with an old TMB version

## -- V --

vcov.glmmTMB | Calculate Variance-Covariance Matrix for a Fitted glmmTMB model
vcovHC | Cluster Robust Variance-Covariance Matrix Estimator
vcovHC.glmmTMB | Cluster Robust Variance-Covariance Matrix Estimator

## -- W --

weights.glmmTMB | Extract weights from a glmmTMB object

## -- Z --

ziGamma | Family functions for glmmTMB