run_biodivMapR: apply biodivMapR to an individual set of rasters (one site)

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

apply biodivMapR to an individual set of rasters (one site)

Description

apply biodivMapR to an individual set of rasters (one site)

Usage

run_biodivMapR(
  input_raster_path,
  input_mask_path = NULL,
  Kmeans_info,
  Beta_info,
  output_dir,
  output_raster_name,
  SelectBands = NULL,
  window_size,
  alphametrics = "shannon",
  Hill_order = 1,
  FDmetric = NULL,
  pcelim = 0.02,
  maxRows = NULL,
  nbCPU = 1,
  MinSun = 0.25,
  filetype = "GTiff",
  MovingWindow = F
)

Arguments

input_raster_path	character.
input_mask_path	directory where spectral indices are for each plot
Kmeans_info	list. kmeans description obtained from function get_kmeans
Beta_info	list. BC dissimilarity & associated beta metrics from training set
output_dir	path where to save outputs
output_raster_name	raster file names
SelectBands	numeric. bands selected from input data
window_size	numeric. window size for square plots
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
maxRows	numeric. maximum number or rows to process
nbCPU	numeric. Number of CPUs available
MinSun	numeric. minimum proportion of sunlit pixels
filetype	character. gdal driver name
MovingWindow	boolean. should process be moving window (much longer)

Value

none

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