knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>")

Introduction

This briefly describes the syntax used to define models that RxODE will translate into R-callable compiled code. It also describes the communication of variables between R and the RxODE modeling specification.

Below is a commented example to quickly show the capabilities of RxODE syntax.

Example

   # An RxODE model specification (this line is a comment).

   if(comed==0){   # concomitant medication (con-med)?
      F = 1.0;     # full bioavailability w.o. con-med
   } 
   else {
      F = 0.80;    # 20% reduced bioavailability
   }

   C2 = centr/V2;  # concentration in the central compartment
   C3 = peri/V3;   # concentration in the peripheral compartment

   # ODE describing the PK and PD

   d/dt(depot) = -KA*depot;
   d/dt(centr) = F*KA*depot - CL*C2 - Q*C2 + Q*C3;
   d/dt(peri)  =                      Q*C2 - Q*C3;
   d/dt(eff)   = Kin - Kout*(1-C2/(EC50+C2))*eff;

Syntax


Interface and data handling between R and the generated C code

Users specify which variables are the dynamic system's state variables via the d/dt(identifier) operator as part of the model specification, and which are model parameters via the params= argument in RxODE solve() method:

m1 <- RxODE(model = ode, modName = "m1")

# model parameters -- a named vector is required
theta <- 
   c(KA=0.29, CL=18.6, V2=40.2, Q=10.5, V3=297, Kin=1, Kout=1, EC50=200)

# state variables and their amounts at time 0 (the use of names is
# encouraged, but not required)
inits <- c(depot=0, centr=0, peri=0, eff=1)

# qd1 is an eventTable specification with a set of dosing and sampling 
# records (code not shown here)

solve(theta, event = qd1, inits = inits)

The values of these variables at pre-specified time points are saved during model fitting/integration and returned as part of the fitted values (see the function eventTable, in particular its member function add.sampling function to define a set of time points when to capture the values of these variables) and returned as part of the modeling output.

The ODE specification mini-language is parsed with the help of the open source tool DParser, Plevyak (2015).

Supported functions

All the supported functions in RxODE can be seen with the rxSupportedFuns().

A brief description of the built-in functions are in the following table:

library(RxODE)
## rxSyntaxFunctions <- read.csv("syntax-functions.csv");usethis::use_data(rxSyntaxFunctions)
library(DT)
datatable(rxSyntaxFunctions, rownames = FALSE, filter="top", options = list(pageLength = 10, scrollX=T) )

Note that lag(cmt) = is equivalent to alag(cmt) = and not the same as = lag(wt)

Reserved keywords

There are a few reserved keywords in a RxODE model. They are in the following table:

## rxReservedKeywords <- read.csv("reserved-keywords.csv");names(rxReservedKeywords)[1] <- "Reserved Name";usethis::use_data(rxReservedKeywords)
datatable(rxReservedKeywords, rownames = FALSE, filter="top", options = list(pageLength = 10, scrollX=T) )

Bugs and/or deficiencies

Note

The ODE specification mini-language is parsed with the help of the open source tool \code{dparser}, Plevyak (2015).



nlmixrdevelopment/RxODE documentation built on April 10, 2022, 5:36 a.m.