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Probability of occupancy, dispersal model

range_raster.Rd

This function creates the raster map with the expansion simulation, estimating probability of occupancy, at a given time step, based on species dispersal and landscape configuration. range_raster uses the output from range_expansion and a raster map with the species current occupancy.

Usage

range_raster(presences.map, re.out, mask.map=NULL, plot=TRUE)

Arguments

presences.map

string of the raster file name with species occurrence.

re.out

object of class list expansion. Output from range_expansion.

mask.map

default NULL. String of the raster file name with the mask. Usually, 1 over the area where the analyses should be done.

plot

default TRUE. Whether It will (TRUE) or will not (FALSE) return a graphics for the expansion model functions and raster maps with expansion probabilities in all four cardinal points.

Details

The function automatically reads the raster input files (presences.map and mask.map, if present). Usually, 0 for absence and 1 for presence in every square cell over a given resolution. Note that the projection for the raster layer should be one of those supporting metric units (i.e., linear scale is equal in all directions around any point such as Transverse Mercator; see https://spatialreference.org/).

Then, it computes and fits a sigmoidal function for the expansion probability.

The user might have to manually adjust the starting values of the function fit.sigmoid, (defined internally in this function) if it has difficulty adjusting to the output of range_expansion.

Value

Produces the spatial realization of the dispersal model, which is saved in the working directory (named 'PROB').

References

Mestre, F., Risk, B., Mira, A., Beja, P., Pita, R. (2017) <doi:10.1016/j.ecolmodel.2017.06.013>

Author

Frederico Mestre and Fernando Canovas

See also

range_expansion

Examples


if (FALSE) { # \dontrun{

#Loading required packages
library(MetaLandSim)

#Loading the range expansion simulation output and required rasters
data(rg_exp)

presences <- system.file("examples/presences.asc", package="MetaLandSim")
mask <- system.file("examples/landmask.asc", package="MetaLandSim")

range.map <- range_raster(presences.map=presences, re.out=rg_exp, mask.map=mask, plot = FALSE)

#Ploting the results with the terra package 
plot(range.map)

#Ploting the results with the rasterVis package 
require(rasterVis)
levelplot(range.map, contour=TRUE)

} # }