Extract pixel data from selected habitats over a target reef. — extract_point

Extract data from the centroids of pixels that overlap the target reef_polyon. Extraction is performed for two raster layers, one habitat_raster must contain habitat categories that form the basis of the pixel centroids, the other add_var_raster is additional desired data for clustering at later points in the workflow. Output is in the format of H3 cells with a diameter of hex_resolution.

Usage

extract_point_cells(
  reef_polygon,
  habitat_raster,
  add_var_raster,
  habitat_categories,
  hex_resolution = 12,
  unit = "km2",
  additional_variable_name = "depth",
  output_epsg = 3112,
  resample_method = "bilinear",
  interpolation = TRUE
)

Arguments

reef_polygon: sf_object. sf object containing the target reef polygons for data coverage.
habitat_raster: SpatRaster. Terra raster object containing categorical values for habitats covering the target reef area.
add_var_raster: SpatRaster. Terra raster object containing an additional variable to extract for all selected habitat pixels covering the target reef area. Can be continuous or categorical, however the raster will be resampled and the method should be changed for categorical data.
habitat_categories: character. Vector containing the habitat categories to select from habitat_raster.
hex_resolution: integer. Selected H3 resolution of hexagons for pixel representation. Default = 12.
unit: character. Unit used by H3 functions to calculate the area of hexagons. Default = "km2".
additional_variable_name: character. Name to assign the extracted data from add_var_raster. Default = "depth".
output_epsg: integer. EPSG code used for outputting pixels and extracted data. Default = 3112.
resample_method: Method used to resample add_var_raster before extracting pixel data. Default = "bilinear", method should be changed for categorical data. See terra::disagg() for more details.
interpolation: bool. Option to interpolate missing values after extracting data from add_var_raster using nearest neighbour interpolation. Default = TRUE.

Value

data.frame containing points from habitat_raster covering reef_polygon for selected habitats in habitat_categories, converted to H3 cell resolution, alongside extracted data from add_var_raster.