apply biodivMapR to a set of plots identified by a field 'id' produced with preprocS2 function get_s2_tiling

run_biodivMapR_plot(
  id,
  feature_dir,
  mask_dir = NULL,
  list_features,
  Kmeans_info,
  Beta_info,
  output_dir,
  SelectBands = NULL,
  window_size,
  alphametrics = "shannon",
  Hill_order = 1,
  FDmetric = NULL,
  pcelim = 0.02,
  maxRows = NULL,
  nbCPU = 1,
  MinSun = 0.25,
  filetype = "GTiff",
  MovingWindow = F,
  p = NULL
)

Arguments

id: character. ID for plot
feature_dir: directory where spectral indices are for each plot
mask_dir: character.
list_features: character.
Kmeans_info: list. kmeans description obtained from function get_kmeans
Beta_info: list. BC dissimilarity & associated beta metrics from training set
output_dir: path where to save outputs
SelectBands: numeric. bands selected from input data
window_size: numeric. window size for square plots
alphametrics: list. alpha diversity metrics: richness, shannon, simpson
Hill_order: numeric. Hill order
FDmetric: character. list of functional metrics
pcelim: numeric. minimum proportion of pixels to consider spectral species
maxRows: numeric. maximum number or rows to process
nbCPU: numeric. Number of CPUs available
MinSun: numeric. minimum amount of sunlit pixels in the plots
filetype: character. gdal driver for output raster
MovingWindow: boolean. should process be moving window (much longer)
p: list. progressbar

Value

none