Introduction to RxODE
Melissa Hallow and Wenping Wang
2016-11-08
RxODE: A tool for performing simulations from
Ordinary Differential Equation (ODE) models, with applications for pharmacometrics
Introduction
RxODE is an R package that facilitates simulation with ODE models in R. It is designed with pharmacometrics models in mind, but can be applied more generally to any ODE model. Here, a typical pharmacokinetics-pharmacodynamics (PKPD) model is used to illustrate the application of RxODE. This model is illustrated in Figure 1. It is assumed that all model parameters have been estimated previously.
Figure 1. A two compartment pharmacokinetics model with an effect compartment
Description of RxODE illustrated through an example
The model equations are specified through a text string in R. Both differential and algebraic equations are permitted. Differential equations are specified by d/dt(var_name) =. Each equation is separated by a semicolon.
ode <- "
C2 = centr/V2;
C3 = peri/V3;
d/dt(depot) =-KA*depot;
d/dt(centr) = 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;
"To load RxODE package and compile the model:
library(RxODE)
work <- tempfile("Rx_intro-")
mod1 <- RxODE(model = ode, modName = "mod1", wd = work)Model parameters are defined in named vectors. Names of parameters in the vector must be a superset of parameters in the ODE model, and the order of parameters within the vector is not important.
theta <-
c(KA=2.94E-01, CL=1.86E+01, V2=4.02E+01, # central
Q=1.05E+01, V3=2.97E+02, # peripheral
Kin=1, Kout=1, EC50=200) # effects Initial conditions (ICs) are defined through a vector as well. The number of ICs must equal exactly the number of ODEs in the model, and the order must be the same as the order in which the ODEs are listed in the model. Elements may be named if desired:
inits <- c(depot=0, centr=0, peri=0, eff=1) RxODE provides a simple and very flexible way to specify dosing and sampling through functions that generate an event table. First, an empty event table is generated through the “eventTable()” function:
ev <- eventTable(amount.units='mg', time.units='hours')Next, use the add.dosing() and add.sampling() functions of the EventTable object to specify the dosing (amounts, frequency and/or times, etc.) and observation times at which to sample the state of the system. These functions can be called multiple times to specify more complex dosing or sampling regiments. Here, these functions are used to specify 10mg BID dosing for 5 days, followed by 20mg QD dosing for 5 days:
ev$add.dosing(dose=10000, nbr.doses=10, dosing.interval=12)
ev$add.dosing(dose=20000, nbr.doses=5, start.time=120, dosing.interval=24)
ev$add.sampling(0:240)The functions get.dosing() and get.sampling() can be used to retrieve information from the event table.
head(ev$get.dosing())## time evid amt
## 1 0 101 10000
## 2 12 101 10000
## 3 24 101 10000
## 4 36 101 10000
## 5 48 101 10000
## 6 60 101 10000head(ev$get.sampling())## time evid amt
## 16 0 0 NA
## 17 1 0 NA
## 18 2 0 NA
## 19 3 0 NA
## 20 4 0 NA
## 21 5 0 NAThe simulation can now be run by calling the model object’s run function. Simulation results for all variables in the model are stored in the output matrix x.
x <- mod1$solve(theta, ev, inits)
head(x)## time depot centr peri eff C2 C3
## [1,] 0 10000.000 0.000 0.0000 1.000000 0.00000 0.0000000
## [2,] 1 7452.765 1783.897 273.1895 1.084664 44.37555 0.9198298
## [3,] 2 5554.370 2206.295 793.8758 1.180825 54.88296 2.6729825
## [4,] 3 4139.542 2086.518 1323.5783 1.228914 51.90343 4.4564927
## [5,] 4 3085.103 1788.795 1776.2702 1.234610 44.49738 5.9807076
## [6,] 5 2299.255 1466.670 2131.7169 1.214742 36.48434 7.1774981par(mfrow=c(1,2))
matplot(x[,"C2"], type="l", ylab="Central Concentration")
matplot(x[,"eff"], type="l", ylab = "Effect")
Simulation of Variability with RxODE
Variability in model parameters can be simulated by creating a matrix of parameter values for use in the simulation. In the example below, 40% variability in clearance is simulated.
nsub <- 100 #number of subproblems
CL <- 1.86E+01*exp(rnorm(nsub,0,.4^2))
theta.all <-
cbind(KA=2.94E-01, CL=CL, V2=4.02E+01, # central
Q=1.05E+01, V3=2.97E+02, # peripheral
Kin=1, Kout=1, EC50=200) # effects
head(theta.all)## KA CL V2 Q V3 Kin Kout EC50
## [1,] 0.294 18.86280 40.2 10.5 297 1 1 200
## [2,] 0.294 21.72334 40.2 10.5 297 1 1 200
## [3,] 0.294 21.72887 40.2 10.5 297 1 1 200
## [4,] 0.294 19.35053 40.2 10.5 297 1 1 200
## [5,] 0.294 17.18757 40.2 10.5 297 1 1 200
## [6,] 0.294 19.94437 40.2 10.5 297 1 1 200Each subproblem can be simulated by using an explicit loop (or the apply() function) to run the simulation for each set of parameters of in the parameter matrix.
nobs <- ev$get.nobs()
cp.all <- matrix(NA, nobs, nsub)
for (i in 1:nsub)
{
theta <- theta.all[i,]
x <- mod1$solve(theta, ev, inits=inits)
cp.all[, i] <- x[, "C2"]
}
matplot(cp.all, type="l", ylab="Central Concentration")
It is now straightforward to perform calculations and generate plots with the simulated data. Below, the 5th, 50th, and 95th percentiles of the simulated data are plotted.
cp.q <- apply(cp.all, 1, quantile, prob = c(0.05, 0.50, 0.95))
matplot(t(cp.q), type="l", lty=c(2,1,2), col=c(2,1,2), ylab="Central Concentration")
Facilities for generating R shiny applications
An example of creating an R shiny application to interactively explore responses of various complex dosing regimens is available at http://qsp.engr.uga.edu:3838/RxODE/RegimenSimulator. Shiny applications like this one may be programmatically created with the experimental function genShinyApp.template().
The above application includes widgets for varying the dose, dosing regimen, dose cycle, and number of cycles.
genShinyApp.template(appDir = "shinyExample", verbose=TRUE)
library(shiny)
runApp("shinyExample")