apply biodivMapR (computes clusters + diversity metrics) to an image chunk

biodivMapR_chunk(
  blk,
  r_in,
  window_size,
  Kmeans_info,
  Beta_info = NULL,
  alphametrics = "shannon",
  Hill_order = 1,
  FDmetric = NULL,
  SelectBands = NULL,
  pcelim = 0.02,
  nbCPU = 1,
  MinSun = 0.25,
  p = NULL
)

Arguments

blk: list. rows and number of rows to read from
r_in: list. path of rasters to read from
window_size: numeric. window size for square plots
Kmeans_info: list. kmeans description obtained from function get_kmeans
Beta_info: list. BC dissimilarity & associated beta metrics from training set
alphametrics: list. alpha diversity metrics: richness, shannon, simpson
Hill_order: numeric. Hill order
FDmetric: character. list of functional metrics
SelectBands: numeric. bands selected from input data
pcelim: numeric. minimum proportion of pixels to consider spectral species
nbCPU: numeric. Number of CPUs available
MinSun: numeric. minimum amount of sunlit pixels in the plots
p: list. progressor object for progress bar

Value

Shannon index correspnding to the distribution