Read model outputs and format to AEME standard

Usage

read_model_outputs(
  nc = NULL,
  lake_dir,
  model,
  vars_sim = NULL,
  depths = NULL,
  dates = NULL,
  date_index = NULL,
  incl_fluxes = TRUE,
  output_hour = 0,
  phyto_pars = NULL,
  load_all = TRUE,
  use_dat = NULL,
  daily_mean = FALSE,
  extra_vars = NULL,
  sed_layers = NULL,
  zone_summary = FALSE
)

Arguments

nc: Open netCDF object. If NULL, will open netCDF from lake_dir. This is useful when reading multiple variables from the same file to avoid reopening the file multiple times. Defaults to NULL.
lake_dir: Directory of lake model outputs
model: Model name. One of "gotm_wet", "glm_aed", or "dy_cd".
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.
phyto_pars: Dataframe of phytoplankton parameters for GLM-AED model. See ?read_glm_output for details. Defaults to NULL.
load_all: logical; for model = "glm_aed", also load every other variable present in the netCDF output beyond the declared vars_sim set – see ?read_glm_output. Ignored for other models. Defaults to TRUE.
use_dat: logical; for the Simstrat models only, read Simstrat's own <var>_out.dat text output via read_simstrat_dat instead of the consolidated output.nc. Every other argument means the same thing either way, so this only changes where the numbers are read from. TRUE is the faster path – it skips the netCDF entirely, and with load_all = FALSE reads only the files the requested vars_sim need, which is what a calibration wants. Defaults to NULL: read output.nc when there is one, and fall back to the text output when there is not (a run whose output was never converted, or converted with write_simstrat_nc(remove_dat = FALSE) and the netCDF since removed). Ignored when nc is supplied.
daily_mean: logical; when TRUE, return one record per calendar day. If a model's daily-mean output_daily.nc companion is present (GOTM writes one natively; GLM-AED and Simstrat get one from run_aeme() when time(aeme)$output_daily_mean is TRUE) it is read directly; otherwise the raw sub-daily output.nc is read and averaged by calendar day. Defaults to FALSE. See set_output_time_step.
extra_vars, sed_layers, zone_summary: for model = "glm_aed", which sediment/flux/diagnostic variables to read and how to reduce them – see ?read_glm_output. Ignored for other models.

Value

List of model outputs in AEME standard format