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,
  selected_bands = NULL,
  input_mask = NULL,
  nb_samples = 1000,
  min_sun = 0.25,
  pcelim = 0.02,
  dimPCoA = 3,
  nbCPU = 1,
  Beta_info_save = NULL,
  Beta_info_read = NULL,
  verbose = TRUE
)

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

selected_bands

numeric. bands selected from input_rast

input_mask

SpatRaster. mask corresponding to raster to extract data from

nb_samples

numeric. number of samples to be extracted

min_sun

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