sample pixels and plots to produce alpha and beta models, including clustering, dissimilarity & PCoA

biodivMapR_sample(
  feature_dir,
  list_features,
  mask_dir = NULL,
  output_dir,
  window_size,
  plots,
  nb_clusters = 50,
  nb_samples_alpha = 1e+05,
  beta_metrics = TRUE,
  nb_samples_beta = 2000,
  pcelim = 0.02,
  nbCPU = 1,
  nb_iter = 10,
  weightIRQ = 4,
  Kmeans_path = NULL,
  Beta_path = NULL
)

Arguments

feature_dir: character. path where to get features
list_features: character. list of features
mask_dir: character. path for masks
output_dir: character. path where to save results
window_size: numeric. number of clusters used in kmeans
plots: list. list of sf plots
nb_clusters: numeric. number of clusters
nb_samples_alpha: numeric. number of samples to compute alpha diversity
beta_metrics: boolean. set TRUE to compute beta diversity
nb_samples_beta: numeric. number of samples to compute beta diversity
pcelim: numeric. minimum proportion of pixels to consider spectral species
nbCPU: numeric. Number of CPUs available
nb_iter: numeric. Number of iterations required to compute diversity
weightIRQ: numeric. IQR applied to filter out features to be used
Kmeans_path: character. path for Kmeans_info
Beta_path: character. path for Beta_info

Value

mosaic_path