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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.

Direct ibis.iSDM DistributionModel and BiodiversityScenario methods use thresholded layers. Continuous suitability projections should be extracted from ibis.iSDM as SpatRaster or stars objects before calling this function.

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 'DistributionModel,ANY'
insights_fraction(range,lu,other,outfile,clamp)

# S4 method for class 'BiodiversityScenario,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 or BiodiversityScenario 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