add_custom_reaction: Add a custom reaction

In sebkopf/isocyclr: Model isotope fractionation in biogeochemical cycles and pathways

Description

Anything's allowed for these, just the flux and the isotopic composition of the flux are specified.

Usage

add_custom_reaction(
  ip,
  equation,
  name = default_rxn_name(ip),
  flux = NULL,
  ...,
  abscissa = NULL
)

Arguments

ip	An isopath object to which this reaction should be added.
name	Name of the reaction. Must be unique (i.e. will overwrite an existing reaction of the same name). If omitted (the default), will name the reaction based on the existing number of reactions in the isopath, e.g. "rxn4".
flux	The net flux through the reaction - can be a number or expression (referencing variables and parameters in the system)
...	isotopic composition of the flux transferred in the reaction - can be a number or expression (referencing variables and parameters in the system), naming convention: flux.[<component>.]<isotope> = ... (component can be omitted if the isotopic composition of the flux is the same for each pool)
abscissa	The reaction loaction. This is used purely for graphical representation (see generate_reaction_diagram). By default, a decent value will be guessed from the existing reactions in the isopath. This works fairly well as long as all reactions after the first one are added to the isopath in an order such that at least one reactant or product is already part of a different reaction in the pathway.
eq	Valid equation in chemical format a * A + b * B + ... == x * X + y * Y + ... Note that all components must already be part of the isopath (add components using add_component).

Value

The isopath object with the new reaction added.

Note

Under the hood, this uses the standard evaluation function add_reaction_, which can be used directly if needed.

See Also

Other reaction functions: add_standard_reaction()

sebkopf/isocyclr documentation built on Nov. 9, 2020, 4:18 p.m.