vignettes/biodivMapR_05.Rmd
biodivMapR_05.Rmd
The first step towards \(\alpha\)
and \(\beta\) diversity mapping
corresponds to the computation of a SpectralSpecies
map,
which identifies the cluster (‘spectral species’) assigned to each pixel
in the image, after k-means clustering is performed. Most of the input
parameters are obtained when running perform_PCA
.
Info about K-means clustering and the path for the spectral species file can be obtained as outputs.
print("MAP SPECTRAL SPECIES")
Kmeans_info <- map_spectral_species(Input_Image_File = Input_Image_File,
Input_Mask_File = PCA_Output$MaskPath,
Output_Dir = Output_Dir,
SpectralSpace_Output = PCA_Output,
nbclusters = nbclusters,
nbCPU = nbCPU, MaxRAM = MaxRAM)
SpectralSpecies is then stored in a raster file located here:
Kmeans_info$SpectralSpecies
'RESULTS/S2A_T33NUD_20180104_Subset/SPCA/SpectralSpecies'
\(\alpha\) and \(\beta\) diversity maps can then be computed
based on this SpectralSpecies
raster.
The computation of \(\alpha\) and \(\beta\) diversity maps is performed in the next step.