Read Simstrat-AED2 netCDF output — read_simstrat

Reads the consolidated output.nc produced by write_simstrat_nc (Simstrat itself writes one text .dat file per variable; AEME converts these to netCDF as a post-processing step so the same reading approach as GLM-AED/GOTM-WET can be reused).

Usage

read_simstrat_output(
  nc = NULL,
  vars_sim = NULL,
  depths = NULL,
  dates = NULL,
  date_index = NULL,
  incl_fluxes = TRUE,
  output_hour = 0,
  file,
  phyto_pars = NULL,
  load_all = TRUE,
  raw_output = FALSE,
  model = "simstrat_aed2"
)

Arguments

nc: An object of class ncdf4 (as returned by either function nc_open or function nc_create), indicating what file to read from.
vars_sim: Variables to extract in the AEME format e.g. "HYD_temp"
depths: Depths to extract. If NULL, extract all model layer depths. Defaults to NULL.
dates: Dates to extract. If NULL, extract all dates. Defaults to NULL.
date_index: Date index to extract. If NULL, extract all dates. Defaults to NULL.
incl_fluxes: Logical indicating whether to include flux variables. Defaults to TRUE.
output_hour: Hour of the day to extract (0-23). Defaults to 0.
file: File path to netCDF file. Only used if nc is NULL.
phyto_pars: Data frame with phytoplankton parameters from AED.
load_all: logical; also load every other variable present in the netCDF file, beyond the declared vars_sim set. Each such variable is keyed by its AEME var_aeme name if key_naming has a translation for it, or by its raw GLM/netCDF name otherwise. Variables shaped like GLM's usual (time) or (z, time) output are loaded the same way as any declared variable; variables with other dimensions (e.g. nzones, particle, sed_layers, lon, lat) are loaded as a new_grouped_var() object instead of being forced into the depth x time convention. Default TRUE.
raw_output: logical; if TRUE, return output as close to the raw netCDF file as possible instead of AEME's standardised format: (z, time) variables are left on GLM's own, time-varying model layer midpoints (no interpolation onto a common depth grid), variables requested via vars_sim are keyed by their raw GLM/netCDF name (e.g. "temp") rather than the translated AEME var_aeme name (e.g. "HYD_temp"), and no AED unit-conversion factors are applied. depths must not be supplied when raw_output = TRUE, since raw output has no common depth grid to interpolate onto. Default FALSE.
model: character; which Simstrat coupling this output came from, "simstrat_aed2" (default) or "simstrat_aed". Selects the matching key_naming column for variable-name translation – the netCDF file format itself (produced by write_simstrat_nc) is identical either way.

Value

List with AEME output variables