biodivMapR_full: computes diversity metrics from raster

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

computes diversity metrics from raster

Description

computes diversity metrics from raster

Usage

biodivMapR_full(
  input_raster_path,
  output_dir,
  window_size,
  maxRows = NULL,
  Kmeans_info_save = NULL,
  Kmeans_info_read = NULL,
  Beta_info_save = NULL,
  Beta_info_read = NULL,
  input_mask_path = NULL,
  nbclusters = 50,
  nbSamples_beta = 1000,
  SelectBands = NULL,
  alphametrics = "shannon",
  Hill_order = 1,
  FDmetric = NULL,
  pcelim = 0.02,
  nbCPU = 1,
  nbIter = 20,
  MinSun = 0.25,
  maxPixel_kmeans = 1e+05,
  dimPCoA = 3,
  progressbar = T,
  filetype = "GTiff"
)

Arguments

input_raster_path	character. path for the input rasters
output_dir	character. path for the output files
window_size	numeric. window size for square plots
maxRows	numeric. max number of rows in each block
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
input_mask_path	character. path for mask file
nbclusters	numeric. number of clusters used in kmeans
nbSamples_beta	numeric. number of samples to compute beta diversity from
SelectBands	numeric. bands selected from input_rast
alphametrics	list. alpha diversity metrics: richness, shannon, simpson
Hill_order	numeric. Hill order
FDmetric	character. list of functional metrics
pcelim	numeric. minimum proportion of pixels to consider spectral species
nbCPU	numeric. Number of CPUs available
nbIter	numeric. nb of iterations averaged to compute diversity indices
MinSun	numeric. minimum amount of sunlit pixels in the plots
maxPixel_kmeans	numeric. max number of pixels extracted for kmeans
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

Kmeans_info and Beta_info

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