computes diversity metrics from raster

Source: R/biodivMapR_full.R

computes diversity metrics from raster

biodivMapR_full(
  input_raster_path,
  input_mask_path = NULL,
  output_dir,
  window_size,
  selected_bands = NULL,
  Kmeans_info_save = NULL,
  Kmeans_info_read = NULL,
  Beta_info_save = NULL,
  Beta_info_read = NULL,
  nbCPU = 1,
  options = NULL
)

Arguments

input_raster_path

character. path for the input rasters

input_mask_path

character. path for mask file

output_dir

character. path for the output files

window_size

numeric. window size for square plots

selected_bands

numeric. bands selected from input_rast

Kmeans_info_save

character. path where to save Kmeans_info

Kmeans_info_read

character. path where to read Kmeans_info

Beta_info_save

character. path where to save Beta_info

Beta_info_read

character. path where to read Beta_info

nbCPU

numeric. Number of CPUs available

options

list. includes options

  • alpha_metrics list. alpha diversity metrics: richness, shannon, simpson

  • Hill_order numeric. Hill order

  • beta_metrics boolean. set TRUE to compute beta diversity

  • fd_metrics character. list of functional metrics

  • nb_samples_alpha numeric. max number of pixels extracted for kmeans

  • nb_samples_beta numeric. number of samples to compute beta diversity

  • nb_clusters numeric. number of clusters used in kmeans

  • nb_iter numeric. nb of iterations averaged to compute diversity indices

  • pcelim numeric. minimum proportion of pixels to consider spectral species

  • maxRows numeric. max number of rows processed once by each CPU

  • moving_window boolean. should diversity be computed on moving window?

  • min_sun numeric. minimum amount of sunlit pixels in the plots

  • dimPCoA numeric. number of dimensions of PCoA

  • progressbar boolean. set true for progress bar during clustering

  • filetype character. driver for output diversity raster data

Value

path for diversity_maps, Kmeans_info and Beta_info