HibModelINLA

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

Details

Template object for INLA 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

(inla)
The INLA::inla model object.

processing_flags

(list())
Identifies the processing steps used for the HibDatabase object that was used for model fitting.

fixedef_coefficients

(data.frame)
The fixed effects coefficients.

user_formula

(formula or list)
The model formula supplied by the user (includes the fixed effects and non-spatial random effects).

inla_fitted_formula

(formula)
The fitted model formula (includes all effects).

inla_incl_spatial_term

(logical)
TRUE or FALSE, does the model include a spatial term.

inla_stack

(inla.data.stack)
The data.stack used in model fitting, an INLA object.

inla_mesh

(inla.mesh or NULL)
If used, the mesh used in model fitting.

inla_mesh_settings

(list)
A list of specifications for generating the mesh, if used in modelling.

inla_mesh_source

(character or NULL)
A description of the mesh source - if not null, can be either "user_provided" or "mesh_settings".

site_locations

(data.frame)
Contains columns for "SSBS", "Longitude" ,"Latitude".

Methods

Public methods

• HibModelINLA$new()

• HibModelINLA$print()

• HibModelINLA$plot()

• HibModelINLA$clone()

---

HibModelINLA$new()

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

Usage

HibModelINLA$new(
  db_obj,
  mod_df,
  inla_obj,
  fixef_df,
  user_formula,
  inla_fitted_formula,
  inla_incl_spatial_term,
  inla_stack,
  inla_mesh,
  inla_mesh_settings,
  inla_mesh_source,
  n_spp,
  n_taxa,
  n_sites
)

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.

inla_obj

(inla)
The inla model object.

fixef_df

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

user_formula

(formula or list)
The model formula supplied by the user.

inla_fitted_formula

(formula)
The fitted model formula.

inla_incl_spatial_term

(logical)
TRUE or FALSE, does the model include a spatial term.

inla_stack

(inla.data.stack)
The data.stack used in model fitting, an INLA object.

inla_mesh

(inla.mesh or NULL)
If used, the mesh used in model fitting.

inla_mesh_settings

(list)
A list of specifications for generating the mesh.

inla_mesh_source

(character or NULL)
A description of the mesh source.

n_spp

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

n_taxa

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

n_sites

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

@return (HibModelINLA)

metr_ls

(list)
The list of model performance metrics.

---

HibModelINLA$print()

Base printout function presents core information about the object.

Usage

HibModelINLA$print()

Returns

(NULL).

---

HibModelINLA$plot()

Function to generate figures summarising the model.

Usage

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

Arguments

type

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

Returns

(ggplot).

---

HibModelINLA$clone()

The objects of this class are cloneable with this method.

Usage

HibModelINLA$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.