In nlmixr2/rxode2: Facilities for Simulating from ODE-Based Models

The ODE-based model specification may be coded inside four places:

• Inside a rxode2({}) block statements:

library(rxode2)
mod <- rxode2({
  # simple assignment
  C2 <- centr/V2

  # time-derivative assignment
  d/dt(centr) <- F*KA*depot - CL*C2 - Q*C2 + Q*C3;
})

• Inside a rxode2("") string statement:

mod <- rxode2("
  # simple assignment
  C2 <- centr/V2

  # time-derivative assignment
  d/dt(centr) <- F*KA*depot - CL*C2 - Q*C2 + Q*C3;
")

• In a file name to be loaded by rxode2:

writeLines("
  # simple assignment
  C2 <- centr/V2

  # time-derivative assignment
  d/dt(centr) <- F*KA*depot - CL*C2 - Q*C2 + Q*C3;
", "modelFile.rxode2")
mod <- rxode2(filename='modelFile.rxode2')
unlink("modelFile.rxode2")

• In a model function which can be parsed by rxode2:

mod <- function() {
  model({
    # simple assignment
    C2 <- centr/V2

    # time-derivative assignment
    d/dt(centr) <- F*KA*depot - CL*C2 - Q*C2 + Q*C3;
  })
}

mod <- rxode2(mod) # or simply mod() if the model is at the end of the function

# These model functions often have residual components and initial
# (`ini({})`) conditions attached as well. For example the
# theophylline model can be written as:

one.compartment <- function() {
  ini({
    tka <- 0.45 # Log Ka
    tcl <- 1 # Log Cl
    tv <- 3.45    # Log V
    eta.ka ~ 0.6
    eta.cl ~ 0.3
    eta.v ~ 0.1
    add.sd <- 0.7
  })
  model({
    ka <- exp(tka + eta.ka)
    cl <- exp(tcl + eta.cl)
    v <- exp(tv + eta.v)
    d/dt(depot) = -ka * depot
    d/dt(center) = ka * depot - cl / v * center
    cp = center / v
    cp ~ add(add.sd)
  })
}

# after parsing the model
mod <- one.compartment()

For the block statement, character string or text file an internal rxode2 compilation manager translates the ODE system into C, compiles it and loads it into the R session. The call to rxode2 produces an object of class rxode2 which consists of a list-like structure (environment) with various member functions.

For the last type of model (a model function), a call to rxode2 creates a parsed rxode2 ui that can be translated to the rxode2 compilation model.

mod$simulationModel

# or
mod$simulationIniModel

This is the same type of function required for nlmixr2 estimation and can be extended and modified by model piping. For this reason will be focused on in the documentation.

nlmixr2/rxode2 documentation built on Jan. 11, 2025, 8:48 a.m.