Set the biogeochemical models to be used in a GLM-AED configuration file.
When the file is located from aeme, the GLM nml is also updated so that the
&init_profiles initial conditions, &inflow inflow_vars and
&mass_balance balance_vars only include variables whose AED module is in
aed_models. When nml is supplied only that aed.nml object is modified.
Usage
set_glm_aed_models(
aeme,
path,
aed_models = c("aed_sedflux", "aed_noncohesive", "aed_oxygen", "aed_silica",
"aed_nitrogen", "aed_phosphorus", "aed_organic_matter", "aed_phytoplankton",
"aed_zooplankton", "aed_macrophyte", "aed_totals"),
file = NULL,
nml = NULL
)Arguments
- aeme
Aeme object.
- path
character; directory where input files are located. Defaults to the path stored in
aeme, or the current working directory if not set.- aed_models
Character vector of GLM-AED models to include. Default includes all available AED models: "aed_sedflux", "aed_noncohesive", "aed_oxygen", "aed_silica", "aed_nitrogen", "aed_phosphorus", "aed_organic_matter", "aed_phytoplankton", "aed_zooplankton", "aed_macrophyte", and "aed_totals".
- file
Path to the GLM-AED configuration file. If NULL, the function will attempt to locate the file based on the provided Aeme object and path.
- nml
GLM-AED nml object. If provided, the function will modify this object directly instead of reading from a file.