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

Author

Alexey Shiklomanov