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,
  N_cores = 1,
  sites = NULL,
  dates = NULL,
  tempdir_custom = NULL,
  file_type = ".RData"
)

Arguments

path_images

character vector. Path to the target images. Images must be of Geotiff format.

path_crowns

character. Path to the crowns polygons file.

out_dir_path

character. Directory where the outputs are saved.

N_cores

integer. Number of cores use in the parallelisation proccess.

sites

character. Name of the site, p.e 'Mbalmayo'.

dates

character vector. Dates (format of dates should be '%Y-%m-%d', '%Y%m%d' or '%Y_%m_%d').The order should match path_images.

tempdir_custom

character. Directory where the temporary files are saved.

file_type

character. 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,
  N_cores = 10,
  sites = NULL,
  dates = NULL
)
} # }