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Get coral habitat suitability data

get_coral_habitat.Rd

This function extracts coral habitat suitability and creates presence (1) or absence (0) grids for three groups of deep-water coral species: antipatharia, cold water corals, and octocorals.

Usage

get_coral_habitat(
  spatial_grid = NULL,
  raw = FALSE,
  antipatharia_threshold = 22,
  octocoral_threshold = 2,
  antimeridian = NULL
)

Arguments

spatial_grid

sf or terra::rast() grid, e.g. created using get_grid(). Alternatively, if raw data is required, an sf polygon can be provided, e.g. created using get_boundary(), and set raw = TRUE.

raw

logical if TRUE, spatial_grid should be an sf polygon, and the raw coral data in that polygon(s) will be returned

antipatharia_threshold

numeric between 0 and 100; the threshold value for habitat suitability for antipatharia corals to be considered present (default is 22, as defined in Yesson et al., 2017)

octocoral_threshold

numeric between 0 and 7; the threshold value for how many species (of 7) should be predicted present in an area for octocorals to be considered present (default is 2)

antimeridian

Does spatial_grid span the antimeridian? If so, this should be set to TRUE, otherwise set to FALSE. If set to NULL (default) the function will try to check if data spans the antimeridian and set this appropriately.

Value

If an area_polygon is supplied, a raster stack of coral habitat suitability data is returned; note this is the raw habitat suitability/ no. of species values. If a spatial_grid is supplied, a raster stack or sf of gridded coral habitat presence/ absence data is returned, depending on spatial_grid format.

Details

Habitat suitability data are from global Maxent species distribution models for the following species groups:

  • Antipatharia: The global extent of black coral habiatat suitability modelled using Maxent. The antipatharia habitat suitability is converted to a presence/absence map "by choosing a threshold value of habitat suitability based on the maximum sum of sensitivity and specificity (threshold mss = 0.23)" (Yesson et al. 2017). This threshold can be altered via the function input. Data from Yesson et al. 2017.

  • Cold water corals: The global habitat suitability for five species of Scleractinia modelled using Maxent. Presence defined using Maxent values above the lowest 10 percent of values. Data from Davies and Guinotte 2011.

  • Octocorals: The global habitat suitability modelled for 7 species of cold-water octocoral found deeper than 50m. Data from and described in Yesson et al. 2012: "A consensus/summary map incorporating all seven octocoral suborders was constructed by generating binary presence/absence maps from the model outputs indicating areas of high suitability using a score threshold that maximized the sum of the specificity and sensitivity based on the validation data (Carroll, 2010). These binary layers were summed to generate a layer containing the number of octocoral suborders predicted to be present per cell."

Examples

# Get EEZ data first 
bermuda_eez <- get_boundary(name = "Bermuda")
# Get raw coral habitat data
coral_habitat <- get_coral_habitat(spatial_grid = bermuda_eez, raw = TRUE)
terra::plot(coral_habitat)

# Get gridded coral habitat data
bermuda_grid <- get_grid(boundary = bermuda_eez, crs = '+proj=laea +lon_0=-64.8108333 +lat_0=32.3571917 +datum=WGS84 +units=m +no_defs', resolution = 10000)
bermuda_coral_gridded <- get_coral_habitat(spatial_grid = bermuda_grid)
terra::plot(bermuda_coral_gridded)