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Apply InSiGHTS with continuous areal land-use data

Source: R/insights_area.R
insights_area.Rd

Apply an area-of-habitat (AOH) refinement to a binary or fractional range estimate using land-use or habitat layers already expressed as area per cell. Use this method when lu values are continuous areal units such as km2. For cell shares or suitability weights in [0, 1], use insights_fraction() instead.

If lu has multiple layers or attributes, they are summed before being applied to the range. 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_area(range, lu, other, outfile = NULL)

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

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

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

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

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

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 areas to be applied to the range. Each layer has to be in area units and greater than or equal to 0. 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.

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_area(). No checks are conducted on whether supplied area layers add up to the area of a grid cell.

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)
range <- terra::rast(system.file(
  "extdata/example_range.tif", package = "ibis.insights", mustWork = TRUE
))
lu_fraction <- terra::rast(system.file(
  "extdata/Grassland.tif", package = "ibis.insights", mustWork = TRUE
)) / 10000

# Convert a fractional land-use layer to area per cell in km2.
lu_km2 <- lu_fraction * terra::cellSize(lu_fraction, unit = "km")
out <- insights_area(range = range, lu = lu_km2)

# The output is already in area units, so do not multiply by cell area again.
insights_summary(out, toArea = FALSE)
#>   time suitability  unit
#> 1   NA    37341.62 input