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Class for a biodiversity scenario from a trained model

Source: R/class-biodiversityscenario.R
BiodiversityScenario-class.Rd

Base R6 class for any biodiversity scenario objects. Serves as container that supplies data and functions to other R6 classes and functions.

Note

This sets the threshold method internally to 'fixed'.

The latent factor is usually obtained from the fitted model object, unless re-specified and added here to the list.

This requires the "gganimate" package.

This requires a set threshold() to the scenario object.

This requires set threshold prior to projection.

See also

threshold()

add_latent_spatial()

Public fields

modelobject

A name of the model for projection.

modelid

An id of the model used for projection.

limits

A sf object used to constraint the prediction.

predictors

A predictor object for projection.

constraints

Any constraints set for projection.

latentfactors

A list on whether latentfactors are used.

scenarios

The resulting stars objects.

log

A Log object for capturing messages.

Methods

Public methods

BiodiversityScenario$new()

Initializes the object and creates an empty list

Usage

BiodiversityScenario$new()

Returns

NULL

BiodiversityScenario$print()

Print the names and properties of all scenarios.

Usage

BiodiversityScenario$print()

Returns

A message on screen

BiodiversityScenario$verify()

Verify that set Model exist and check self-validity

Usage

BiodiversityScenario$verify()

Returns

Invisible

BiodiversityScenario$show()

Show the name of the Model

Usage

BiodiversityScenario$show()

Returns

Model objectname

BiodiversityScenario$get_projection()

Get projection of the projection.

Usage

BiodiversityScenario$get_projection()

Returns

A sf object with the geographic projection

BiodiversityScenario$get_resolution()

Get resultion of the projection.

Usage

BiodiversityScenario$get_resolution()

Returns

A numeric indication of the resolution.

BiodiversityScenario$get_model()

Get the actual model used for projection

Usage

BiodiversityScenario$get_model(copy = FALSE)

Arguments

copy

A logical flag on whether a deep copy should be created.

Returns

A DistributionModel object.

BiodiversityScenario$get_limits()

Get provided projection limits if set.

Usage

BiodiversityScenario$get_limits()

Returns

A sf object or NULL.

BiodiversityScenario$rm_limits()

Remove current limits.

Usage

BiodiversityScenario$rm_limits()

Returns

Invisible

BiodiversityScenario$get_predictor_names()

Get names of predictors for scenario object.

Usage

BiodiversityScenario$get_predictor_names()

Returns

A character vector with the names.

BiodiversityScenario$get_timeperiod()

Get time period of projection.

Usage

BiodiversityScenario$get_timeperiod(what = "range")

Arguments

what

character on whether full time period or just the range is to be returned.

Returns

A time period from start to end.

BiodiversityScenario$get_constraints()

Get constrains for model

Usage

BiodiversityScenario$get_constraints()

Returns

A list with the constraints within the scenario.

BiodiversityScenario$rm_constraints()

Remove contraints from model

Usage

BiodiversityScenario$rm_constraints()

Returns

Invisible

BiodiversityScenario$get_threshold()

Get thresholds if specified.

Usage

BiodiversityScenario$get_threshold()

Returns

A list with method and value for the threshold.

BiodiversityScenario$get_thresholdvalue()

Duplicate function for internal consistency to return threshold

Usage

BiodiversityScenario$get_thresholdvalue()

Returns

A list with method and value for the threshold.

BiodiversityScenario$apply_threshold()

Apply a new threshold to the projection.

Usage

BiodiversityScenario$apply_threshold(tr = new_waiver())

Arguments

tr

A numeric value with the new threshold.

Returns

This object.

BiodiversityScenario$set_predictors()

Set new predictors to this object.

Usage

BiodiversityScenario$set_predictors(x)

Arguments

x

PredictorDataset object to be supplied.

Returns

This object.

BiodiversityScenario$set_constraints()

Set new constrains

Usage

BiodiversityScenario$set_constraints(x)

Arguments

x

A list object with constraint settings.

Returns

This object.

BiodiversityScenario$get_log()

Returns the output filename of the current log object if set.

Usage

BiodiversityScenario$get_log()

Returns

A character where the output is returned.

BiodiversityScenario$set_log()

Set a new log object

Usage

BiodiversityScenario$set_log(x)

Arguments

x

A Log object.

Returns

This object

BiodiversityScenario$get_simulation()

Get simulation options and parameters if gound

Usage

BiodiversityScenario$get_simulation()

Returns

A list with the parameters.

BiodiversityScenario$set_simulation()

Set simulation objects.

Usage

BiodiversityScenario$set_simulation(x)

Arguments

x

new simulation entries and options as list to be set.

Returns

This object.

BiodiversityScenario$get_predictors()

Get Predictors from the object.

Usage

BiodiversityScenario$get_predictors()

Returns

A predictor dataset.

BiodiversityScenario$rm_predictors()

Remove predictors from the object.

Usage

BiodiversityScenario$rm_predictors(names)

Arguments

names

A character vector with names

Returns

This object.

BiodiversityScenario$get_data()

Get scenario predictions or any other data

Usage

BiodiversityScenario$get_data(what = "scenarios")

Arguments

what

A character vector with names of what

Returns

This object.

BiodiversityScenario$rm_data()

Remove scenario predictions

Usage

BiodiversityScenario$rm_data()

Returns

Invisible

BiodiversityScenario$set_data()

Set new data in object.

Usage

BiodiversityScenario$set_data(x)

Arguments

x

A new data object measuing scenarios.

Returns

This object.

BiodiversityScenario$set_latent()

Adding latent factors to the object.

Usage

BiodiversityScenario$set_latent(latent)

Arguments

latent

A list containing the data object.

Returns

This object.

BiodiversityScenario$get_latent()

Get latent factors if found in object.

Usage

BiodiversityScenario$get_latent()

Returns

A list with the latent settings

BiodiversityScenario$rm_latent()

Remove latent factors if found in object.

Usage

BiodiversityScenario$rm_latent()

Returns

This object.

BiodiversityScenario$plot()

Plot the predictions made here.

Usage

BiodiversityScenario$plot(what = "suitability", which = NULL, ...)

Arguments

what

A character describing the layers to be plotted.

which

A numeric subset to any specific time steps.

...

Any other parameters passed on.

Returns

A graphical representation

BiodiversityScenario$plot_threshold()

Convenience function to plot thresholds if set

Usage

BiodiversityScenario$plot_threshold(which = NULL)

Arguments

which

A numeric subset to any specific time steps.

Returns

A graphical representation

BiodiversityScenario$plot_migclim()

Plot Migclim results if existing.

Usage

BiodiversityScenario$plot_migclim()

Returns

A graphical representation

BiodiversityScenario$plot_animation()

Plot animation of scenarios if possible

Usage

BiodiversityScenario$plot_animation(what = "suitability", fname = NULL)

Arguments

what

A character describing the layers to be plotted.

fname

An optional filename to write the result.

Returns

A graphical representation

BiodiversityScenario$plot_relative_change()

Plot relative change between baseline and projected thresholds

Usage

BiodiversityScenario$plot_relative_change(
  position = NULL,
  variable = "mean",
  plot = TRUE
)

Arguments

position

Which layer to be plotted

variable

A character of the variable to be plotted

plot

logical flag on whether to plot the results or return the object.

Returns

A graphical representation or SpatRaster.

BiodiversityScenario$summary()

Summarize the change in layers between timesteps

Usage

BiodiversityScenario$summary(
  layer = "threshold",
  plot = FALSE,
  relative = FALSE
)

Arguments

layer

A character of the variable to be plotted

plot

logical flag on whether to plot the results or return the coefficients.

relative

logical on coefficients to be converted to relative change.

Returns

Summarized coefficients as data.frame

BiodiversityScenario$summary_beforeafter()

Summarize before-after change of first and last layer.

Usage

BiodiversityScenario$summary_beforeafter()

Returns

Summarized coefficients as data.frame

BiodiversityScenario$plot_scenarios_slope()

Calculate slopes across the projection

Usage

BiodiversityScenario$plot_scenarios_slope(
  what = "suitability",
  oftype = "stars"
)

Arguments

what

A character with layer to be plotted (default: "suitability").

oftype

character of the output type.

Returns

A plot of the scenario slopes

BiodiversityScenario$calc_scenarios_slope()

Calculate slopes across the projection

Usage

BiodiversityScenario$calc_scenarios_slope(
  what = "suitability",
  plot = TRUE,
  oftype = "stars"
)

Arguments

what

A character with layer to be plotted (default: "suitability").

plot

logical flag on whether to plot the results or return the coefficients.

oftype

character of the output type.

Returns

A SpatRaster layer or stars object.

BiodiversityScenario$mask()

Convenience function to mask all input projections.

Usage

BiodiversityScenario$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.

Returns

Invisible

BiodiversityScenario$get_centroid()

Get centroids of projection layers

Usage

BiodiversityScenario$get_centroid(patch = FALSE)

Arguments

patch

A logical if centroid should be calculated weighted by values.

Returns

Returns a sf object.

BiodiversityScenario$save()

Save object as output somewhere

Usage

BiodiversityScenario$save(fname, type = "tif", dt = "FLT4S")

Arguments

fname

An output filename as character.

type

A format as character. Matched against a list of supported formats.

dt

The datatype used, such as float64

Returns

Saved spatial prediction on drive.

BiodiversityScenario$clone()

The objects of this class are cloneable with this method.

Usage

BiodiversityScenario$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.