ED radiative transfer module (EDR) wrapper function

This function provides a convenient way to call the ED radiative transfer module (EDR, which simulates full spectral return of an ED patch for a given point in time) directly from R.

EDR(img_path, ed2in_path, spectra_list, trait.values,
  soil_reflect_path = system.file("extdata", "soil_reflect_par.dat",
  package = "PEcAnRTM"), wood_reflect_path = system.file("extdata",
  "wood_reflect_par.dat", package = "PEcAnRTM"), par.wl = 400:2499,
  nir.wl = 2500, edr_exe_path = NULL,
  output.path = dirname(normalizePath(ed2in_path, mustWork = TRUE)),
  settings = list(model = list(revision = "git", config.header = NULL)),
  singularity_args = list(), clean = FALSE, stderr = TRUE,
  verbose_error = TRUE, ...)

Arguments

img_path	Path to Singularity container (usually a .simg file)
ed2in_path	Path to ED2IN file.
spectra_list	List of spectral data matrices. Names must exactly match the PFTs given in trait.values. Each item must be a matrix of reflectance (labeled 'R' or 'reflectance') and transmittance (labeled 'T' or 'transmittance') values. If the matrix is not of class spectra (see spectra()), it must also have a column of wavelength values (labeled 'wl'). Such a matrix is returned by default by all versions of PROSPECT in this package.
trait.values	Named, hierarchical list of trait values for generating config.xml file. Names must be PFTs, and must exactly match names of spectra_list.
soil_reflect_path	Path to soil reflectance file (defaults to spectra in package extdata)
wood_reflect_path	Path to wood reflectance file (defaults to spectra in package extdata)
par.wl	Vector of wavelengths defining PAR region
nir.wl	Vector of wavelengths defining NIR region
edr_exe_path	If img_path is NULL, a full path to the EDR executable. Ignored otherwise.
output.path	Directory in which to execute the run. Defaults to dirname(ed2in_path).
settings	PEcAn settings list. Default is list(model = list(revision = "git", config.header = NULL)).
singularity_args	Additional arguments to be passed to singularity run (before)
clean	Logical. If TRUE, remove all files generated by this function (e.g. cloned history file, ED2IN, output HDF files).
stderr	Logical. If TRUE (default), internalize system2 results as R character vector. TRUE is recommended because it allows EDR to check its execution and to run more quietly.
verbose_error	Logical. If TRUE (default), spit out the full ED if EDR execution fails.
...	Additional arguments to system2