apply biodivMapR to an individual set of rasters (one site)

run_biodivMapR(
  input_raster_path,
  input_mask_path = NULL,
  Kmeans_info,
  Beta_info,
  output_dir,
  output_raster_name,
  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
)

Arguments

input_raster_path

character.

input_mask_path

directory where spectral indices are for each plot

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

output_raster_name

raster file names

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 proportion of sunlit pixels

filetype

character. gdal driver name

MovingWindow

boolean. should process be moving window (much longer)

Value

none