init_PCoA: initialize PCoA for beta diversity mapping

In jbferet/biodivMapR: biodivMapR: an R package for a- and ß-diversity mapping using remotely-sensed images

initialize PCoA for beta diversity mapping

Description

initialize PCoA for beta diversity mapping

Usage

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

jbferet/biodivMapR documentation built on April 12, 2025, 1:32 p.m.