run_biodivMapR_plot: apply biodivMapR to a set of plots identified by a field...

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

apply biodivMapR to a set of plots identified by a field 'id' produced with preprocS2 function get_s2_tiling

Description

apply biodivMapR to a set of plots identified by a field 'id' produced with preprocS2 function get_s2_tiling

Usage

run_biodivMapR_plot(
  id,
  feature_dir,
  mask_dir = NULL,
  list_features,
  Kmeans_info,
  Beta_info,
  output_dir,
  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,
  p = NULL
)

Arguments

id	character. ID for plot
feature_dir	directory where spectral indices are for each plot
mask_dir	character.
list_features	character.
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
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 amount of sunlit pixels in the plots
filetype	character. gdal driver for output raster
MovingWindow	boolean. should process be moving window (much longer)
p	list. progressbar

Value

none

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