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