Skip to contents

Apply InSiGHTS with fractional land-use data

Source: R/insights_fraction.R
insights_fraction.Rd

Apply an area-of-habitat (AOH) refinement to a binary or fractional range estimate using land-use or habitat layers expressed as fractions. Use this method when the land-use values represent cell shares or suitability weights in the interval [0, 1]. For land-use inputs already expressed as area per cell, use insights_area() instead.

If lu has multiple layers or attributes, they are summed before being applied to the range. This is useful when several land-use classes jointly represent suitable habitat. Optional other layers can be supplied as additional suitability or condition masks, but they must already be scaled to [0, 1]; raw environmental layers such as elevation should be converted to a suitability mask before calling this function.

Raster inputs are reprojected, cropped, and resampled to the range geometry when needed. Temporal stars inputs may use a time or Time dimension name. If outfile is supplied, the extension is adjusted to .tif for raster output or .nc for stars output.

Usage

insights_fraction(range, lu, other, outfile = NULL, clamp = FALSE)

# S4 method for class 'SpatRaster,SpatRaster'
insights_fraction(range,lu,other,outfile,clamp)

# S4 method for class 'SpatRaster,stars'
insights_fraction(range,lu,other,outfile,clamp)

# S4 method for class 'stars,stars'
insights_fraction(range,lu,other,outfile,clamp)

# S4 method for class 'stars,SpatRaster'
insights_fraction(range,lu,other,outfile,clamp)

# S4 method for class 'ANY,ANY'
insights_fraction(range,lu,other,outfile,clamp)

Arguments

range

A SpatRaster or temporal stars object describing the estimated distribution of a biodiversity feature (e.g. species). Values must be binary or fractional in [0, 1]. Alternatively a DistributionModel fitted with ibis.iSDM package can be supplied.

lu

A SpatRaster or temporal stars object of the future land-use fractions to be applied to the range. Each layer has to be in fractional units between 0 and 1. Multi-layer inputs are summed.

other

Optional SpatRaster or temporal stars object describing additional suitable conditions for the species. Values must already be suitability weights in [0, 1].

outfile

A writeable character of where the output should be written to. If missing, the function will return a SpatRaster or stars object respectively. Missing .tif or .nc extensions are added as needed.

clamp

A logical on whether lu and summed fractional suitability should be clamped to 0 and 1 beforehand (Default: FALSE).

Value

Either a SpatRaster or temporal stars object or nothing if outputs are written directly to drive.

Note

This function does not infer species-habitat relationships from raw land-use classes. Select, weight, or transform land-use and condition layers before calling insights_fraction().

References

  • Rondinini, Carlo, and Piero Visconti. "Scenarios of large mammal loss in Europe for the 21st century." Conservation Biology 29, no. 4 (2015): 1028-1036.

  • Visconti, Piero, Michel Bakkenes, Daniele Baisero, Thomas Brooks, Stuart HM Butchart, Lucas Joppa, Rob Alkemade et al. "Projecting global biodiversity indicators under future development scenarios." Conservation Letters 9, no. 1 (2016): 5-13.

Author

Martin Jung

Examples

require(terra)
# Load package example rasters
range <- terra::rast(system.file(
  "extdata/example_range.tif", package = "ibis.insights", mustWork = TRUE
))
lu <- c(
  terra::rast(system.file(
    "extdata/Grassland.tif", package = "ibis.insights", mustWork = TRUE
  )),
  terra::rast(system.file(
    "extdata/Sparsely.vegetated.areas.tif", package = "ibis.insights", mustWork = TRUE
  ))
)

# Convert example land-use layers to fractions between 0 and 1.
lu <- lu / 10000

out <- insights_fraction(range = range, lu = lu, clamp = TRUE)
head(insights_summary(out))
#>   time suitability unit
#> 1   NA    38374.68  km2