Skip to contents

Specify elevational preferences as offset

Source: R/add_offset.R
add_offset_elevation.Rd

This function implements the elevation preferences offset defined in Ellis‐Soto et al. (2021). The code here was adapted from the Supporting materials script.

Usage

add_offset_elevation(x, elev, pref, rate = 0.0089, add = TRUE)

# S4 method for class 'BiodiversityDistribution,SpatRaster,numeric'
add_offset_elevation(x, elev, pref, rate = 0.0089, add = TRUE)

Arguments

x

distribution() (i.e. BiodiversityDistribution) object.

elev

A SpatRaster with the elevation for a given background.

pref

A numeric vector of length 2 giving the lower and upper bound of known elevational preferences. Can be set to Inf if unknown.

rate

A numeric for the rate used in the offset (Default: .0089). This parameter specifies the decay to near zero probability at elevation above and below the expert limits.

add

logical specifying whether new offset is to be added. Setting this parameter to FALSE replaces the current offsets with the new one (Default: TRUE).

Value

Adds a elevational offset to a distribution object.

Details

Specifically this functions calculates a continuous decay and decreasing probability of a species to occur from elevation limits. It requires a SpatRaster with elevation information. A generalized logistic transform (aka Richard's curve) is used to calculate decay from the suitable elevational areas, with the "rate" parameter allowing to vary the steepness of decline.

Note that all offsets created by this function are by default log-transformed before export. In addition this function also mean-centers the output as recommended by Ellis-Soto et al.

References

  • Ellis‐Soto, D., Merow, C., Amatulli, G., Parra, J.L., Jetz, W., 2021. Continental‐scale 1 km hummingbird diversity derived from fusing point records with lateral and elevational expert information. Ecography (Cop.). 44, 640–652. https://doi.org/10.1111/ecog.05119

  • Merow, C., Allen, J.M., Aiello-Lammens, M., Silander, J.A., 2016. Improving niche and range estimates with Maxent and point process models by integrating spatially explicit information. Glob. Ecol. Biogeogr. 25, 1022–1036. https://doi.org/10.1111/geb.12453

See also

Other offset: add_offset(), add_offset_bias(), add_offset_range(), rm_offset()

Examples

if (FALSE) { # \dontrun{
 # Adds the offset to a distribution object
 distribution(background) |> add_offset_elevation(dem, pref = c(400, 1200))
} # }