Package index • glmmTMB

All functions

Owls: Begging by Owl Nestlings
Salamanders: Repeated counts of salamanders in streams
as.theta.vcov(): Get theta parameterisation of a covariance structure
isLMM(<glmmTMB>) refit(<glmmTMB>): support methods for parametric bootstrapping
bread(<glmmTMB>): Bread Matrix for Sandwich Estimator
confint(<glmmTMB>): Calculate confidence intervals
diagnose(): diagnose model problems
dof_KR() dof_satt(): compute denominator degrees-of-freedom approximations
Anova.glmmTMB() Effect.glmmTMB(): Downstream methods
dtruncated_nbinom2() dtruncated_poisson() dtruncated_nbinom1(): truncated distributions
epil2: Seizure Counts for Epileptics - Extended
estfun(<glmmTMB>): Extract Empirical Estimating Functions
family_params(): Retrieve family-specific parameters
fitTMB() finalizeTMB(): Optimize TMB models and package results, modularly
fixef(<glmmTMB>): Extract fixed-effects estimates
formula(<glmmTMB>): Extract the formula of a glmmTMB object
getCapabilities(): List model options that glmmTMB knows about
getGroups(<glmmTMB>): Extract Grouping Factors from an Object
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() put_cor(): transform correlation parameters to and from glmmTMB parameterization
glmmTMB(): Fit Models with TMB
glmmTMBControl(): Control parameters for glmmTMB optimization
terms(<glmmTMB>) model.matrix(<glmmTMB>): Methods for extracting developer-level information from glmmTMB models
up2date() gt_load(): conditionally update glmmTMB object fitted with an old TMB version
map.theta.propto(): Set map values for theta to be fixed (NA) for propto
meatHC(): Simple Cluster Based Meat Matrix Estimator
nbinom2() nbinom1() nbinom12() compois() truncated_compois() genpois() truncated_genpois() truncated_poisson() truncated_nbinom2() truncated_nbinom1() beta_family() betabinomial() tweedie() skewnormal() lognormal() ziGamma() t_family() ordbeta() bell(): Family functions for glmmTMB
numFactor() parseNumLevels(): Factor with numeric interpretable levels.
omp_check(): Check OpenMP status
predict(<glmmTMB>): prediction
print(<VarCorr.glmmTMB>): Printing The Variance and Correlation Parameters of a glmmTMB
priors: use of priors in glmmTMB
profile(<glmmTMB>) confint(<profile.glmmTMB>): Compute likelihood profiles for a fitted model
ranef(<glmmTMB>) as.data.frame(<ranef.glmmTMB>) coef(<glmmTMB>): Extract Random Effects
reinstalling: Reinstalling binary dependencies
residuals(<glmmTMB>) deviance(<glmmTMB>): Compute residuals for a glmmTMB object
sandwich(): Sandwich Estimator based on Bread and Meat Matrices
set_simcodes(): helper function to modify simulation settings for random effects
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)
spider_long: Spider data from CANOCO, long format
summary(<glmmTMB>): summary for glmmTMB fits
vcov(<glmmTMB>): Calculate Variance-Covariance Matrix for a Fitted glmmTMB model
vcovHC(<glmmTMB>): Cluster Robust Variance-Covariance Matrix Estimator
weights(<glmmTMB>): Extract weights from a glmmTMB object