Calculates cost distances for a given landscape (resistance matrix)
calculates a cost distance matrix, to be used with run.popgensim
gl.costdistances(landscape, locs, method, NN)
landscape |
a raster object coding the resistance of the landscape |
locs |
coordinates of the subpopulations. If a genlight object is provided coordinates are taken from @other$latlong and centers for population (pop(gl)) are calculated. In case you want to calculate costdistances between individuals redefine pop(gl) via: |
method |
defines the type of cost distance, types are "least-cost", "rSPDistance" or "commute (Circuitscape type)" |
NN |
number of next neighbours recommendation is 8 |
a costdistance matrix between all pairs of locs
## Not run:
data(possums.gl)
library(raster) #needed for that example
landscape.sim <- readRDS(system.file("extdata","landscape.sim.rdata", package="dartR"))
#calculate mean centers of individuals per population
xy <- apply(possums.gl@other$xy, 2, function(x) tapply(x, pop(possums.gl), mean))
cd <- gl.costdistances(landscape.sim, xy, method="leastcost", NN=8)
round(cd,3)
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