BiodiversityDataset prototype description

Public fields

name: The default name of this dataset as character.
id: A character with the unique id for this dataset.
equation: A formula object containing the equation of how this dataset is modelled.
family: The family used for this dataset as character.
link: The link function used for this data as character.
type: A character with the type as character.
weight: A numeric containing custom weights per observation for this dataset.
field_occurrence: A character with the name of the column name containing observations.
data: Contains the observational data in sf format.
use_intercept: A logical flag on whether intercepts are included for this dataset.
pseudoabsence_settings: Optionally provided pseudoabsence settings.

Methods

Public methods

BiodiversityDataset$new()
BiodiversityDataset$print()
BiodiversityDataset$set_equation()
BiodiversityDataset$get_equation()
BiodiversityDataset$show_equation()
BiodiversityDataset$get_id()
BiodiversityDataset$get_type()
BiodiversityDataset$get_column_occ()
BiodiversityDataset$get_family()
BiodiversityDataset$get_link()
BiodiversityDataset$get_data()
BiodiversityDataset$get_weight()
BiodiversityDataset$show()
BiodiversityDataset$get_observations()
BiodiversityDataset$mask()
BiodiversityDataset$clone()

`BiodiversityDataset$new()`

Initializes the object and creates an empty list

Usage

BiodiversityDataset$new(
  name,
  id,
  equation,
  family,
  link,
  type,
  weight,
  field_occurrence,
  data,
  use_intercept,
  pseudoabsence_settings
)

Arguments

name: The default name of this dataset as character.
id: A character with the unique id for this dataset.
equation: A formula object containing the equation of how this dataset is modelled.
family: The family used for this dataset as character.
link: The link function used for this data as character.
type: A character with the type as character.
weight: A numeric containing custom weights per observation for this dataset.
field_occurrence: A character with the name of the column name containing observations.
data: Contains the observational data in sf format.
use_intercept: A logical flag on whether intercepts are included for this dataset.
pseudoabsence_settings: Optionally provided pseudoabsence settings.

Returns

NULL

`BiodiversityDataset$print()`

Print the names and properties of all Biodiversity datasets contained within

Usage

BiodiversityDataset$print()

Returns

A message on screen

`BiodiversityDataset$set_equation()`

Set new equation and writes it into formula

Usage

BiodiversityDataset$set_equation(x)

Arguments

x: A new formula object.

Returns

Invisible

`BiodiversityDataset$get_equation()`

Get equation

Usage

BiodiversityDataset$get_equation()

Returns

A placeholder or formula object.

`BiodiversityDataset$show_equation()`

Function to print the equation

Usage

BiodiversityDataset$show_equation()

Returns

A message on screen.

`BiodiversityDataset$get_id()`

Get Id within the dataset

Usage

BiodiversityDataset$get_id()

Returns

A character with the id.

`BiodiversityDataset$get_type()`

Get type of the dataset.

Usage

BiodiversityDataset$get_type(short = FALSE)

Arguments

short: A logical flag if this should be formatted in shortform.

Returns

A character with the type

`BiodiversityDataset$get_column_occ()`

Get field with occurrence information

Usage

BiodiversityDataset$get_column_occ()

Returns

A character with the occurence field

`BiodiversityDataset$get_family()`

Get family

Usage

BiodiversityDataset$get_family()

Returns

A character with the family for the dataset

`BiodiversityDataset$get_link()`

Get custom link function

Usage

BiodiversityDataset$get_link()

Returns

A character with the family for the dataset

`BiodiversityDataset$get_data()`

Get data from the object

Usage

BiodiversityDataset$get_data()

Returns

A sf object with the data

`BiodiversityDataset$get_weight()`

Get weight

Usage

BiodiversityDataset$get_weight()

Returns

A numeric with the weights within the dataset.

`BiodiversityDataset$show()`

Print input messages

Usage

BiodiversityDataset$show()

Returns

A message on screen.

`BiodiversityDataset$get_observations()`

Collect info statistics about number of observations

Usage

BiodiversityDataset$get_observations()

Returns

A numeric with the number of observations.

`BiodiversityDataset$mask()`

Convenience function to mask all input datasets.

Usage

BiodiversityDataset$mask(mask, inverse = FALSE, ...)

Arguments

mask: A SpatRaster or sf object.
inverse: A logical flag if the inverse should be masked instead.
...: Any other parameters passed on to mask

Returns

Invisible

`BiodiversityDataset$clone()`

The objects of this class are cloneable with this method.

Usage

BiodiversityDataset$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.