Computing Parameters

While it’s handy that DiffEqRxn can figure out which parameters you need from the parameters passed to macros and as rates to chemical expressions, many systems have a set of parameters, and then compute more parameters from those, to keep the parameter count low / enforce invariants. Additionally, if a parameter is a function, using the rate syntax has no way of really passing arguments, like time.

So, in efforts to avoid writing a full programming language that nobody would like to learn, it was decided to do 80% of the work, and let the user do the non-tedious 20% themselves.

Implicit Parameters

If your model depends on a parameter that is otherwise not mentioned in the model, the syntax to indicate that you would still like that parameter included is written:

implicit k_rx

Where \(k_{rx}\) is the parameter that is used, but not referred to anywhere’s in the actual model definition.

Computed Parameters

A computed parameter is sort of opposite to an implicit parameter, it’s definition is: a parameter that is used in the model, but should not be included in the set of parameters passed the differential equation. This is because this parameter is computable from the other parameters, state, and time. Many times, if there is need for an implicit parameter, then declaring a computed parameter is also required.

The syntax for a computed parameter is (on it’s own line):

computed k_fx

Where \(k_{fx}\) is the parameter that is being computed from any combination of parameters, state, and time.