HibModelLME4 — HibModelLME4 • hibiiscus

This is the template object for an R6 lme4 model class. It contains functions for summarising and visualising the model results.

Details

Template object for lme4 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: (merMod)
The lme4 model object.
fixedef_coefficients: (data.frame)
The fixed effects coefficients.
ci_type: (character, or NA)
Identifies the types of confidence intervals calculated.
metrics: (numeric)
Named vector 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

`HibModelLME4$new()`

Creates a new instance of this R6 class. Note, this object is constructed via the hib_fit_lme4 function found within this package.

Usage

HibModelLME4$new(
  db_obj,
  mod_df,
  lme4_obj,
  fixef_df,
  ci_type,
  metr_vec,
  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.

lme4_obj

(merMod)
The lme4 model object.

fixef_df

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

ci_type

(character, or NA)
The type of confidence intervals calculated.

metr_vec

(numeric)
The named vector 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.

@return (HibModelLME4)

`HibModelLME4$print()`

Base printout function presents core information about the object.

Usage

HibModelLME4$print()

Returns

(NULL).

`HibModelLME4$plot()`

Function to generate figures summarising the model.

Usage

HibModelLME4$plot(type = "fixed-effects")

Arguments

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

Returns

(ggplot).

`HibModelLME4$check_model()`

Function to assess the model using the performance package.

Usage

HibModelLME4$check_model()

Returns

(NULL).

`HibModelLME4$clone()`

The objects of this class are cloneable with this method.

Usage

HibModelLME4$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.