In rxode2: Facilities for Simulating from ODE-Based Models

You can also append "compartments" to the model. Because of the ODE solving internals, you cannot add fake compartments to the model until after all the differential equations are defined.

For example this is legal:

ode.1c.ka <- function(){
  model({
    C2 = center/V
    d / dt(depot) = -KA * depot
    d/dt(center) = KA * depot - CL*C2
    cmt(eff)
  })
}

ode.1c.ka <- ode.1c.ka()
print(ode.1c.ka)

You can see this more clearly with the underlying classic rxode2 model:

ode.1c.ka$simulationModel

But compartments defined before all the differential equations is not supported; So the model below:

ode.1c.ka <- rxode2({
    cmt(eff)
    C2 = center/V;
    d / dt(depot) = -KA * depot
    d/dt(center) = KA * depot - CL*C2
})

will give an error:

Error in rxModelVars_(obj) : 
  Evaluation error: Compartment 'eff' needs differential equations defined.

rxode2 documentation built on Oct. 30, 2024, 9:06 a.m.