View source: R/hypervolume_project.R
hypervolume_project | R Documentation |
Determines a suitability score by calculating the hypervolume value at each of a set of points in an input raster stack based on either a probability density estimation or inclusion test.
Note that projected values are not normalized and are not necessarily constrained to fall between 0 and 1.
Note also that additional arguments can be passed to this function to enable parallel operation (see ... below).
hypervolume_project(hv, rasters, type = "probability", verbose = TRUE, ...)
hv |
An input hypervolume |
rasters |
A |
type |
If |
... |
Additional arguments to be passed to either |
verbose |
If |
A raster
object of same resolution and extent as the input layers corresponding to suitability values.
hypervolume_estimate_probability
, hypervolume_inclusion_test
## Not run: # load in lat/lon data data('quercus') data_alba = subset(quercus, Species=="Quercus alba")[,c("Longitude","Latitude")] data_alba = data_alba[sample(1:nrow(data_alba),500),] # get worldclim data from internet require(maps) require(raster) climatelayers = getData('worldclim', var='bio', res=10, path=tempdir()) # z-transform climate layers to make axes comparable climatelayers_ss = climatelayers[[c(1,12)]] for (i in 1:nlayers(climatelayers_ss)) { climatelayers_ss[[i]] <- (climatelayers_ss[[i]] - cellStats(climatelayers_ss[[i]], 'mean')) / cellStats(climatelayers_ss[[i]], 'sd') } climatelayers_ss = crop(climatelayers_ss, extent(-150,-50,15,60)) # extract transformed climate values climate_alba = extract(climatelayers_ss, data_alba[1:300,]) # compute hypervolume hv_alba <- hypervolume_gaussian(climate_alba) # do geographical projection raster_alba_projected_accurate <- hypervolume_project(hv_alba, rasters=climatelayers_ss) raster_alba_projected_fast = hypervolume_project(hv_alba, rasters=climatelayers_ss, type='inclusion', fast.or.accurate='fast') # draw map of suitability scores plot(raster_alba_projected_accurate,xlim=c(-100,-60),ylim=c(25,55)) map('usa',add=TRUE) plot(raster_alba_projected_fast,xlim=c(-100,-60),ylim=c(25,55)) map('usa',add=TRUE) ## End(Not run)
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