Convert PCA into SSD based on previous clustering

Convert PCA into SSD based on previous clustering

convert_PCA_to_SSD(
  ReadWrite,
  Spectral_Species_Path,
  HDR_SS,
  HDR_SSD,
  HDR_Sunlit,
  window_size,
  nbclusters,
  Input_Mask_File = FALSE,
  HDR_Mask = FALSE,
  MinSun = 0.25,
  pcelim = 0.02,
  Index_Alpha = c("Shannon"),
  SSD_Path,
  Sunlit_Path,
  p = NULL,
  nbCPU = 1,
  nbPieces = 1,
  progressbar = FALSE
)

Arguments

ReadWrite

list. includes byte coordinates where to read and write from files

Spectral_Species_Path

character. path for Spectral_Species raster file

HDR_SS

list. HDR file for spectral species

HDR_SSD

list. HDR file for spectral species distribution

HDR_Sunlit

list. HDR file for spectral species distribution

window_size

numeric. window size

nbclusters

numeric. number of clusters

Input_Mask_File

character. input mask file (useful when using classification map)

HDR_Mask

list. HDR file for mask

MinSun

numeric. Minimum proportion of sunlit pixels required to consider plot.

pcelim

numeric. Minimum contribution (in %) required for a spectral species.

Index_Alpha

list. list of spectral metrics to be computed

SSD_Path

character. path for spectral species distribution file

Sunlit_Path

character. path for sunlit proportion file

p

list. progressor object for progress bar

nbCPU

numeric. Number of CPUs to use in parallel.

nbPieces

numeric. number of pieces to split file read into

progressbar

boolean. should progress bar be displayed (set to TRUE only if no conflict of parallel process)

Value

list of mean and SD of alpha diversity metrics