Extract spectral indices from RGB at the crown scale

The function extracts RGB indices (red, green, blue, sumrgb, rcc, gcc, bcc, gndvi, gli) for each crown at each date. It extracts the value at the crown scale using the exactextractr::exact_extract function. The mean and / or the variance can be extracted (see 'fun' parameter).

Usage

extract_rgbValues(
  path_images,
  path_crowns,
  out_dir_path = NULL,
  ncor = 1,
  sites = NULL,
  dates = NULL,
  tempdir_custom = NULL,
  file_type = ".RData"
)

Arguments

path_images

list with the full paths to the RGB rasters.

path_crowns

chr. Path to the crown delinetion shapefile

out_dir_path

chr. The path to the directory use to stored the images

ncor

Number of cores use in the parallelisation proccess.

sites

chr. name of the site, p.e 'Mbalmayo'.

dates

chr. vector of dates (format should be 'YYYY_MM_DD', p.e '2022_09_25'). The order of the dates should match with the order of the path_images !

tempdir_custom

chr. Path where to store temporary files

file_type

chr. By default it is '.RData' but can be '.csv' or '.xlsx'

Value

A tibble with the variable site, id, date, family, genus, species, type, metric, band and value.

Examples

if (FALSE) { # \dontrun{

imgs = list.files('my-path-to-images', full.names = T)
path_crowns = "my-path-to-crowns-shapefile"
out_dir_path = "output-directory"

rgb_data <- extract_rgbValues (
  path_images = imgs,
  path_crowns = path_crowns,
  out_dir_path = out_dir_path,
  ncor = 10,
  sites = NULL,
  dates = NULL
)
} # }