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Options for the AED biogeochemistry setup in build_aeme()

Source: R/aed_options.R
aed_options.Rd

With use_bgc = TRUE, build_aeme() configures AED for GLM-AED in several steps. aed_options() lets you choose which of these run. The defaults reproduce the usual build, so only set what you want to change. Every step is also available on its own once the model is built: set_glm_aed_models(), set_aed_sed_const2d() and set_aed_totals().

Usage

aed_options(
  modules = NULL,
  resolve_deps = TRUE,
  initialise = TRUE,
  sed_zones = TRUE,
  totals = TRUE
)

Arguments

modules

character or NULL; the AED modules to activate, from "aed_sedflux", "aed_noncohesive", "aed_oxygen", "aed_silica", "aed_nitrogen", "aed_phosphorus", "aed_alum", "aed_organic_matter", "aed_phytoplankton", "aed_zooplankton", "aed_macrophyte" and "aed_totals". NULL (default) activates the modules needed for the variables set to simulate in model_controls.

resolve_deps

logical; when modules is supplied, also activate the modules they depend on (e.g. aed_nitrogen needs aed_oxygen and aed_sedflux), as the model_controls-driven default does. If FALSE, modules is used exactly as given, and GLM aborts at runtime if a module's prerequisites are missing. Default TRUE.

initialise

logical; write the initial concentrations and active modules to aed.nml from model_controls. If FALSE, aed.nml is left as it is (the shipped template for a new lake, or your own file for an existing one). Default TRUE.

sed_zones

logical; estimate and set the per-zone sediment fluxes (aed_sed_const2d) with set_aed_sed_const2d(). Default TRUE.

totals

logical; derive the aed_totals (TN, TP, TOC and TSS) variable lists with set_aed_totals(). Default TRUE.

Value

An aed_options object, to pass as the aed argument of build_aeme().

See also

build_aeme(), set_glm_aed_models(), set_aed_sed_const2d(), set_aed_totals()

Examples

# Default: everything as usual
aed_options()
#> <aed_options>
#> • Modules: from `model_controls`
#> • Write initial concentrations to aed.nml: TRUE
#> • Estimate sediment zone fluxes: TRUE
#> • Derive aed_totals: TRUE

# Only oxygen and nutrient cycling, and leave the sediment fluxes alone
aed_options(
  modules = c("aed_sedflux", "aed_oxygen", "aed_nitrogen", "aed_phosphorus"),
  sed_zones = FALSE
)
#> <aed_options>
#> • Modules: "aed_sedflux", "aed_oxygen", "aed_nitrogen", and "aed_phosphorus"
#>   plus their dependencies
#> • Write initial concentrations to aed.nml: TRUE
#> • Estimate sediment zone fluxes: FALSE
#> • Derive aed_totals: TRUE