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ED radiative transfer module (EDR) wrapper function

Source: R/edr.wrapper.R
EDR.Rd

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.

Usage

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