HibModelBRMS — HibModelBRMS • hibiiscus

This is the template object for an R6 brms model class. It contains functions for summarising and visualising the model results.

Details

Template object for brms model

Public fields

dataset_name: (character)
Identifies the dataset used.
last_update: (character)
Identifies the most recent update to the object (YYYY-MM-DD).
data: (data.frame)
The data used in model fitting.
model: (brmsfit)
The brms model object.
extra_args: (list())
Identifies addition arguments supplied during model fitting (found in '...' when calling hib_fit_brms).
fixedef_coefficients: (data.frame)
The fixed effects coefficients.
metrics: (list)
List containing model performance metrics.
processing_flags: (list())
Identifies the processing steps used for the HibDatabase object that was used for model fitting.
site_locations: (data.frame)
Contains columns for "SSBS", "Longitude" ,"Latitude"

Methods

`HibModelBRMS$new()`

Creates a new instance of this R6 class. Note, this object is constructed via the hib_fit_brms function found within this package.

Usage

HibModelBRMS$new(
  db_obj,
  mod_df,
  brms_obj,
  fixef_df,
  metr_ls,
  n_spp,
  n_taxa,
  n_sites,
  extra_args
)

Arguments

db_obj

(HibDatabase, or list)
The HibDatabase object/s used to fit the model.

mod_df

(data.frame)
The data.frame of the data used in model fitting.

brms_obj

(brmsfit)
The brms model object.

fixef_df

(data.frame)
The fixed effects from the fitted model.

metr_ls

(list)
The list of model performance metrics.

n_spp

(integer or list)
Number of species contributing to the fitted model.

n_taxa

(integer or list)
Number of orignal taxa names contributing to the fitted model.

n_sites

(integer or list)
Number of sites contributing to the fitted model.

extra_args

(list)
Additional arguments specified during model fitting.

@return (HibModelBRMS)

`HibModelBRMS$print()`

Base printout function presents core information about the object.

Usage

HibModelBRMS$print()

Returns

(NULL).

`HibModelBRMS$plot()`

Function to generate figures summarising the model.

Usage

HibModelBRMS$plot(type = "fixed-effects")

Arguments

type: (character()) Options are: "fixed-effects", "random-effects", "map-sites".

Returns

(ggplot).

`HibModelBRMS$check_model()`

Function to assess the model using the performance package.

Usage

HibModelBRMS$check_model()

Returns

(NULL).

`HibModelBRMS$clone()`

The objects of this class are cloneable with this method.

Usage

HibModelBRMS$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.