computes beta diversity metrics

compute_beta_metrics(
  ClusterMap_Path,
  SSD_Dir,
  MinSun,
  Nb_Units_Ordin,
  nb_partitions,
  nbclusters,
  pcelim,
  scaling = "PCO",
  dimMDS = 3,
  nbCPU = 1,
  MaxRAM = 0.25,
  SamplesPerThread = 2000
)

Arguments

ClusterMap_Path: character. File containing spectral species or classes from prior classification
SSD_Dir: character. path for spectral species distribution file to be written
MinSun: numeric. minimum proportion of sunlit pixels required to consider plot
Nb_Units_Ordin: numeric. maximum number of spatial units to be processed in Ordination
nb_partitions: numeric. number of iterations
nbclusters: numeric. number of clusters defined in k-Means
pcelim: numeric. Minimum contribution in percents required for a spectral species
scaling: character. scaling method, PCO or NMDS
dimMDS: numeric. number of dimensions for the scaling.
nbCPU: numeric. Number of CPUs to use in parallel.
MaxRAM: numeric. MaxRAM maximum size of chunk in GB to limit RAM allocation when reading image file.
SamplesPerThread: numeric. number of samples to be processed per thread for dissimilarity matrix

Value

my_list a list of information including results of 3 dimensional ordination with PCoA, PCoA model, map of sunlit windows