Code to convert ED2's -T- HDF5 output into netCDF format

Modified from code to convert ED2's HDF5 output into the NACP Intercomparison format (ALMA using netCDF)

model2netcdf.ED2(
  outdir,
  sitelat,
  sitelon,
  start_date,
  end_date,
  pfts,
  settings = NULL,
  process_partial = FALSE
)

Arguments

outdir: Location of ED model output (e.g. a path to a single ensemble output)
sitelat: Latitude of the site
sitelon: Longitude of the site
start_date: Start time of the simulation
end_date: End time of the simulation
pfts: a named vector of PFT numbers where the names are PFT names
settings: pecan settings object
process_partial: should failed runs be processed? Defaults to FALSE. TRUE will generate .nc files for runs that have generated some, but not all, of the expected outputs

if settings is provided, then values for missing arguments sitelat, sitelon, start_date, end_date, and pfts will be taken from it

Michael Dietze, Shawn Serbin, Rob Kooper, Toni Viskari, Istem Fer