Skip to contents

This function creates an object that contains all the data, parameters and settings for building an (integrated) species distribution model. Key functions to add data are add_biodiversity_poipo and the like, add_predictors, add_latent_spatial, engine_glmnet or similar, add_priors and add_offset. It creates a prototype BiodiversityDistribution object with its own functions. After setting input data and parameters, model predictions can then be created via the train function and predictions be created.

Additionally, it is possible to specify a "limit" to any predictions conducted on the background. This can be for instance a buffered layer by a certain dispersal distance (Cooper and Soberon, 2018) or a categorical layer representing biomes or soil conditions. Another option is to create a constraint by constructing a minimum convex polygon (MCP) using the supplied biodiversity data. This option can be enabled by setting "limits_method" to "mcp". It is also possible to provide a small buffer to constructed MCP that way. See the frequently asked question (FAQ) section on the homepage for more information.

See Details for a description of the internal functions available to modify or summarize data within the created object.

Note that any model requires at minimum a single added biodiversity dataset as well as a specified engine.

Usage

distribution(
  background,
  limits = NULL,
  limits_method = "none",
  mcp_buffer = 0,
  limits_clip = FALSE
)

# S4 method for SpatRaster,ANY,character,numeric,logical
distribution(background,limits,limits_method,mcp_buffer,limits_clip)

# S4 method for sf,ANY,character,numeric,logical
distribution(background,limits,limits_method,mcp_buffer,limits_clip)

Arguments

background

Specification of the modelling background. Must be a SpatRaster or sf object.

limits

A SpatRaster or sf object that limits the prediction surface when intersected with input data (Default: NULL).

limits_method

A character of the method used for hard limiting a projection. Available options are "none" (Default), "zones" or "mcp".

mcp_buffer

A numeric distance to buffer the mcp (Default 0). Only used if "mcp" is used.

limits_clip

logical Should the limits clip all predictors before fitting a model (TRUE) or just the prediction (FALSE, default).

Value

BiodiversityDistribution object containing data for building a biodiversity distribution modelling problem.

Details

This function creates a BiodiversityDistribution object that in itself contains other functions and stores parameters and (pre-)processed data. A full list of functions available can be queried via "names(object)". Some of the functions are not intended to be manipulated directly, but rather through convenience functions (e.g. "object$set_predictors()"). Similarly other objects are stored in the BiodiversityDistribution object that have their own functions as well and can be queried (e.g. "names(object)"). For a list of functions see the reference documentation. By default, if some datasets are not set, then a "Waiver" object is returned instead.

The following objects can be stored:

Useful high-level functions to address those objects are for instance:

  • object$show() A generic summary of the BiodiversityDistribution object contents. Can also be called via print.

  • object$get_biodiversity_equations() Lists the equations used for each biodiversity dataset with given id. Defaults to all predictors.

  • object$get_biodiversity_types() Lists the type of each specified biodiversity dataset with given id.

  • object$get_extent() Outputs the terra::ext of the modelling region.

  • object$show_background_info() Returns a list with the terra::ext and the terra::crs.

  • object$get_extent_dimensions() Outputs the terra::ext dimension by calling the "extent_dimensions()" function.

  • object$get_predictor_names() Returns a character vector with the names of all added predictors.

  • object$get_prior_variables() Returns a description of priors added.

There are other functions as well but those are better accessed through their respective wrapper functions.

References

  • Fletcher, R.J., Hefley, T.J., Robertson, E.P., Zuckerberg, B., McCleery, R.A., Dorazio, R.M., (2019) A practical guide for combining data to model species distributions. Ecology 100, e02710. https://doi.org/10.1002/ecy.2710

  • Cooper, Jacob C., and Jorge Soberón. "Creating individual accessible area hypotheses improves stacked species distribution model performance." Global Ecology and Biogeography 27, no. 1 (2018): 156-165.

See also

"bdproto" on the general definition of proto objects and in particular BiodiversityDistribution.

Examples

if (FALSE) {
 # Load background raster
 background <- terra::rast(system.file("inst/extdata/europegrid_50km.tif",package = "ibis.iSDM"))
 # Define model
 x <- distribution(background)
 x
 # Show names of the functions within the object
 names(x)

}