compute_beta_metrics: computes beta diversity metrics

In jbferet/biodivMapR: biodivMapR: an R package for a- and ß-diversity mapping using remotely-sensed images

computes beta diversity metrics

Description

computes beta diversity metrics

Usage

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

jbferet/biodivMapR documentation built on Jan. 26, 2024, 10:38 p.m.