initialize PCoA for beta diversity mapping

Source: R/init_PCoA.R

initialize PCoA for beta diversity mapping

init_PCoA(
  input_rast,
  output_dir,
  window_size,
  Kmeans_info,
  SelectBands = NULL,
  input_mask = NULL,
  nbSamples = 1000,
  MinSun = 0.25,
  pcelim = 0.02,
  dimPCoA = 3,
  nbCPU = 1,
  Beta_info_save = NULL,
  Beta_info_read = NULL,
  verbose = T
)

Arguments

input_rast

SpatRaster. raster to extract data from

output_dir

character. Path for output directory

window_size

numeric. window size for square plots

Kmeans_info

list. obtained from prepare_init_kmeans

SelectBands

numeric. bands selected from input_rast

input_mask

SpatRaster. mask corresponding to raster to extract data from

nbSamples

numeric. number of samples to be extracted

MinSun

numeric. minimum percentage of sunlit pixels

pcelim

numeric. minimum proportion of pixels to consider spectral species

dimPCoA

numeric.

nbCPU

numeric. Number of CPUs available

Beta_info_save

character. path where to save Beta_info

Beta_info_read

character. path where to read Beta_info

verbose

boolean. set true for messages

Value

list including spectral species distribution & BC diss matrix per plot, BetaPCO model