initialize PCoA for beta diversity mapping based on samples extracted from images

initialize PCoA for beta diversity mapping based on samples extracted from images

init_PCoA_samples(
  rast_sample,
  output_dir,
  Kmeans_info,
  selected_bands = NULL,
  pcelim = 0.02,
  dimPCoA = 3,
  nbCPU = 1,
  beta_metrics = "bray",
  Beta_info_save = NULL,
  verbose = TRUE
)

Arguments

rast_sample

data frame containing samples to use

output_dir

character. Path for output directory

Kmeans_info

list. obtained from prepare_init_kmeans

selected_bands

numeric. bands selected from input_rast

pcelim

numeric. minimum proportion of pixels to consider spectral species

dimPCoA

numeric.

nbCPU

numeric. Number of CPUs available

beta_metrics

character. name of beta dissimilarity metrics Available options are "bray", "brayturn", "jaccard", "jaccardturn", "sorensen", "simpson_diss"

Beta_info_save

character. path where to save Beta_info

verbose

boolean. set true for messages

Value

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