nh_map: Make a suitable/unsuitable binary map, given a continuous SDM...

In VANatHeritage/nhSDM: Tools for Natural Heritage SDMs

Make a suitable/unsuitable binary map, given a continuous SDM output or raster template, burn-in features, and masks

Description

This function performs a reclassification of a continuous map to a binary one, and then performs additional changes to the binary map, depending on inputs. If no continuous map is to be used, then a template raster should be given to rast.

Usage

nh_map(
  rast,
  thresh = NULL,
  feature.occ = NULL,
  feature.burn = NULL,
  feature.mask = NULL,
  raster.mask = NULL,
  patch.drop = NULL
)

Arguments

rast	input raster model output (values between 0 and 1); if no model, a template raster must be provided
thresh	numeric between 0 and 1; 'global' threshold value to apply to rast
feature.occ	input feature occurrences, to burn-in to map (sp or sf spatial object)
feature.burn	input feature(s), to burn-in to map (sp or sf spatial object)
feature.mask	input feature mask to apply to map (sp or sf spatial object)
raster.mask	input raster mask to apply to map (should match rast resolution)
patch.drop	patch size (in rast area units) to remove from map

Details

Reclassification (when thresh is given) is always performed first. After this, optional masks are applied where areas within features (feature.mask) and not NoData (raster.mask) are kept (value = 1). All other cells are given (value = 0).

Patches (contiguous groups of cells = 1) are then be dropped by specifying a minimum patch size to patch.drop in area units of the raster's CRS (see nhSDM::nh_patchdrop).

The final step is to 'burn in' (rasterize with value = 1) features from feature.occ and feature.burn. Because it is the last step, it is not affected by masks or patch dropping.

Value

SpatRaster

Author(s)

David Bucklin

Examples

## Not run: 
spf <- sf::st_read("_data/occurrence/ambymabe.shp")
rast <- terra::rast("_data/species/ambymabe/outputs/model_predictions/ambymabe_20171018_130837.tif")
feature.burn <- st_buffer(spf, 250)
feature.mask <- st_buffer(spf, 50000)
raster.mask <- rast("D:/PSH/inputs/species_masks/no_med_hi_dev/no_med_hi_dev.tif")
map <- nh_map(rast, thresh=0.75, feature.occ=spf, feature.burn=feature.burn, 
   feature.mask=feature.mask, raster.mask=raster.mask, NULL)

## End(Not run)

VANatHeritage/nhSDM documentation built on Feb. 1, 2024, 6:39 a.m.