insight (version 1.0.0)

get_parameters.glmmTMB: Get model parameters from mixed models

Description

Returns the coefficients from a model.

Usage

# S3 method for glmmTMB
get_parameters(x, effects = "fixed", component = "all", ...)

Value

If effects = "fixed", a data frame with two columns: the parameter names and the related point estimates. If effects = "random", a list of data frames with the random effects (as returned by ranef()), unless the random effects have the same simplified structure as fixed effects (e.g. for models from MCMCglmm).

Arguments

x

A fitted model.

effects

Should variables for fixed effects ("fixed"), random effects ("random") or both ("all") be returned? Only applies to mixed models. May be abbreviated.

component

Which type of parameters to return, such as parameters for the conditional model, the zero-inflated part of the model, the dispersion term, the instrumental variables or marginal effects be returned? Applies to models with zero-inflated and/or dispersion formula, or to models with instrumental variables (so called fixed-effects regressions), or models with marginal effects (from mfx). See details in section Model Components .May be abbreviated. Note that the conditional component also refers to the count or mean component - names may differ, depending on the modeling package. There are three convenient shortcuts (not applicable to all model classes):

• component = "all" returns all possible parameters.

• If component = "location", location parameters such as conditional, zero_inflated, smooth_terms, or instruments are returned (everything that are fixed or random effects - depending on the effects argument - but no auxiliary parameters).

• For component = "distributional" (or "auxiliary"), components like sigma, dispersion, beta or precision (and other auxiliary parameters) are returned.

...

Currently not used.

Model components

Possible values for the component argument depend on the model class. Following are valid options:

• "all": returns all model components, applies to all models, but will only have an effect for models with more than just the conditional model component.

• "conditional": only returns the conditional component, i.e. "fixed effects" terms from the model. Will only have an effect for models with more than just the conditional model component.

• "smooth_terms": returns smooth terms, only applies to GAMs (or similar models that may contain smooth terms).

• "zero_inflated" (or "zi"): returns the zero-inflation component.

• "dispersion": returns the dispersion model component. This is common for models with zero-inflation or that can model the dispersion parameter.

• "instruments": for instrumental-variable or some fixed effects regression, returns the instruments.

• "nonlinear": for non-linear models (like models of class nlmerMod or nls), returns staring estimates for the nonlinear parameters.

• "correlation": for models with correlation-component, like gls, the variables used to describe the correlation structure are returned.

• "location": returns location parameters such as conditional, zero_inflated, smooth_terms, or instruments (everything that are fixed or random effects - depending on the effects argument - but no auxiliary parameters).

• "distributional" (or "auxiliary"): components like sigma, dispersion, beta or precision (and other auxiliary parameters) are returned.

Special models

Some model classes also allow rather uncommon options. These are:

• mhurdle: "infrequent_purchase", "ip", and "auxiliary"

• BGGM: "correlation" and "intercept"

• BFBayesFactor, glmx: "extra"

• averaging:"conditional" and "full"

• mjoint: "survival"

• mfx: "precision", "marginal"

• betareg, DirichletRegModel: "precision"

• mvord: "thresholds" and "correlation"

• clm2: "scale"

• selection: "selection", "outcome", and "auxiliary"

For models of class brmsfit (package brms), even more options are possible for the component argument, which are not all documented in detail here.

Details

In most cases when models either return different "effects" (fixed, random) or "components" (conditional, zero-inflated, ...), the arguments effects and component can be used. See details in the section Model Components.

Examples

if (FALSE) { # requireNamespace("glmmTMB", quietly = TRUE)
data(Salamanders, package = "glmmTMB")
m <- glmmTMB::glmmTMB(
  count ~ mined + (1 | site),
  ziformula = ~mined,
  family = poisson(),
  data = Salamanders
)
get_parameters(m)
}