Get coral habitat suitability data

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 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 spatial_grid 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")
#> Cache is fresh. Reading: /tmp/RtmpogSL9g/eez-2205f12f/eez.shp
#> (Last Modified: 2025-01-17 00:01:17.889422)
# 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)