computes diversity metrics from raster

computes diversity metrics from raster

biodivMapR_full(
  input_raster_path,
  output_dir,
  window_size,
  maxRows = NULL,
  Kmeans_info_save = NULL,
  Kmeans_info_read = NULL,
  Beta_info_save = NULL,
  Beta_info_read = NULL,
  input_mask_path = NULL,
  nbclusters = 50,
  nbSamples_beta = 1000,
  SelectBands = NULL,
  alphametrics = "shannon",
  Hill_order = 1,
  FDmetric = NULL,
  pcelim = 0.02,
  nbCPU = 1,
  nbIter = 20,
  MinSun = 0.25,
  maxPixel_kmeans = 1e+05,
  dimPCoA = 3,
  progressbar = T,
  filetype = "GTiff"
)

Arguments

input_raster_path

character. path for the input rasters

output_dir

character. path for the output files

window_size

numeric. window size for square plots

maxRows

numeric. max number of rows in each block

Kmeans_info_save

character. path where to save Kmeans_info

Kmeans_info_read

character. path where to read Kmeans_info

Beta_info_save

character. path where to save Beta_info

Beta_info_read

character. path where to read Beta_info

input_mask_path

character. path for mask file

nbclusters

numeric. number of clusters used in kmeans

nbSamples_beta

numeric. number of samples to compute beta diversity from

SelectBands

numeric. bands selected from input_rast

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

nbCPU

numeric. Number of CPUs available

nbIter

numeric. nb of iterations averaged to compute diversity indices

MinSun

numeric. minimum amount of sunlit pixels in the plots

maxPixel_kmeans

numeric. max number of pixels extracted for kmeans

dimPCoA

numeric. number of dimensions of PCoA

progressbar

boolean. set true for progress bar during clustering

filetype

character. driver for output diversity raster data

Value

Kmeans_info and Beta_info