Nothing
species.richness.main <-
function(dataset.all.species, dataset.landwater, dataset.height, distances=1:10, weight=0.5,
resolution=1, narrow.endemic=FALSE, narrow.endemic.limit=5,
upperbound=5, cross.validation=FALSE, fold=5, loocv.limit=10,
create.image=FALSE, image.title="Interpolated Species Richness",
directory=getwd(), filename="species.richness.png",
evaluation=FALSE, eval.title="Histogramm", adjust=FALSE,
clusterlimit=100, predefinedClusterlist=NULL, all.species=-1,
export=FALSE, exportname="species.richness.tif",
noninterpolatedgrid=NULL, silent=TRUE, do.parallel=FALSE){
#calculating coordinates and dimension of grid
if (!silent) cat("Preparing grid.. ")
dimension <- getDimension(dataset.all.species, resolution)
origin <- getOrigin(dataset.all.species)
if (!silent) cat("Done!\n")
#preparing landwatermask
if (!silent) cat("Preparing land-water-mask.. ")
landwatermask <- createLandwatermask(dataset.landwater, dimension, origin, resolution)
if (!silent) cat("Done!\n")
if (!silent) cat("Preparing height-information.. ")
height.matrix <- createHeightmask(dataset.height, dimension, origin, resolution)
if (!silent) cat("Done!\n")
#add height to landwatermask
height.matrix[which(height.matrix < 0)] <- 0
landwatermask[which(landwatermask >= 0)] <- height.matrix[which(landwatermask >= 0)]
if (narrow.endemic){
if (!silent) cat("Extracting narrow endemic species.. ",sep="")
# search narrow endemic species out of dataset
all.species <- getNarrowEndemics(dataset.all.species, all.species,
narrow.endemic.limit, dimension, origin,
resolution)
if (!silent) cat("Done!\n")
}
if (cross.validation){
if (!silent) cat("Calculating cross-validated species richness.. \n")
species.richness.weighted <- species.richness.cv(dataset.all.species, landwatermask, fold,
loocv.limit, distances, weight, dimension,
origin, resolution, upperbound, all.species,
silent, do.parallel)
} else {
if (!silent) cat("Calculating species richness.. \n")
species.richness.weighted <- species.richness(dataset.all.species, landwatermask, distances,
weight, dimension, origin, resolution,
upperbound, all.species, silent, do.parallel)
}
if (adjust){
if (!silent) cat("Adjusting grid .. ")
if (is.null(noninterpolatedgrid)){
noninterpolatedgrid <- createNonInterpolatedGrid(dataset.all.species,
dimension, origin, resolution, all.species)
}
if (is.null(predefinedClusterlist)){
clusterlist <- searchClusters(species.richness.weighted, dimension, origin,
resolution=1, clusterlimit)
} else {
clusterlist <- predefinedClusterlist
}
species.richness.weighted <- adjustment(species.richness.weighted, noninterpolatedgrid,
clusterlist)
if (!silent) cat("Done!\n")
}
if (create.image){
if (!silent) cat("Creating Map (PNG-File).. ")
if(createImage(species.richness.weighted, landwatermask, image.title, directory,
filename, origin, parts=10, resolution)){
if (!silent) cat("PNG-File successfully created!\n")
} else {
cat("PNG-File-Creation failed!\n")
}
}
if (evaluation) {
if (!silent) cat("Creating Evaluation (PNG-File).. ")
if(evaluate(result.grid.one=species.richness.weighted, result.grid.two=NULL,
title.one=eval.title, title.two=NULL, xmax=400, directory=directory,
filename=paste(substring(filename, 1, nchar(filename)-4),".histogramm.png",sep=""))){
if (!silent) cat("PNG-File successfully created!\n")
} else {
if (!silent) cat("PNG-File-Creation failed!\n")
}
}
if (export) {
if (!silent) cat("Export .. ")
export_tif(species.richness.weighted, origin=origin,
resolution=resolution, epsg_code="4326",
directory=directory, filename=exportname)
if (!silent) cat("Done!\n")
}
return(species.richness.weighted)
}
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