Computes alpha diversity metrics based on spectral species

compute_alpha_metrics(
  Spectral_Species_Path,
  SSD_Dir,
  window_size,
  Input_Mask_File = FALSE,
  nbclusters,
  MinSun = 0.25,
  pcelim = 0.02,
  nbCPU = 1,
  MaxRAM = 0.25,
  Index_Alpha = "Shannon",
  progressbar = FALSE
)

Arguments

Spectral_Species_Path: character. path for spectral species file
SSD_Dir: character. path for spectral species distribution file to be written
window_size: numeric. size of spatial units (in pixels) to compute diversity
Input_Mask_File: character. Path and name of the mask corresponding to the image to be processed.
nbclusters: numeric. number of clusters defined in k-Means
MinSun: numeric. minimum proportion of sunlit pixels required to consider plot
pcelim: numeric. percentage of occurence of a cluster below which cluster is eliminated
nbCPU: numeric. number of CPUs available
MaxRAM: numeric. maximum RAM available
Index_Alpha: list. list of alpha diversity indices to be computed from spectral species
progressbar: boolean. should progress bar be displayed (set to TRUE only if no conflict of parallel process)

Value

list of mean and SD of alpha diversity metrics