monolix2simulx.R

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Overview

Description

Convert a Monolix Project into an executable R script for the simulator Simulx

Usage

monolix2simulx(project, parameter = NULL)

Arguments

model

a Mlxtran or PharmML model used for the simulation.

parameter

string, the type of specific parameters to use: “mode” or “mean”

project

the name of a Monolix project

Value

A folder containing the executable R code for simulx and the data files used for the simulation (parameters, observation design, dosage regimen, covariates).

Examples

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R script: doc_monolix2simulx.R

Monolix project: monolixRuns

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The theophylline example is used to illustrate how to directly simulate the model just by providing the Monolix project as an input to simulx.

project.file <- 'monolixRuns/theophylline_project.mlxtran'
res <- simulx(project = project.file)

We can alternatively use monolix2simulx to create an independent folder with a simulx script for simulation that can easily modified or shared with others.

monolix2simulx(project = project.file)

A new folder theophylline_project_simulx is automatically created in the current working directory. It contains the following files:

• theophylline_project_model.txt: the model Mlxtran
• covariate.txt: the individual covariates
• parameter.txt: the estimated population parameters
• treatment.txt: the individual dosage regimens
• output.txt: the individual observation times
• theophylline_project.R: the simulx R script:

# File generated automatically on 2015-04-15 22:21:02
 
library(mlxR)  
 
setwd(dirname(parent.frame(2)$ofile)) 

# model 
model<-"theophylline_project_model.txt"

# treatment
trt <- read.table("treatment.txt", header = TRUE) 

# parameters 
covariate<- read.table("covariate.txt", header = TRUE) 
pop <- read.vector("parameter.txt") 
param <- list(pop,covariate)
 
# output 
name<-"y1"
time<-read.table("output.txt",header=TRUE)
out<-list(name=name,time=time) 
out<-list(out)

# call the simulator 
res <- simulx(model=model,treatment=trt,parameter=param,output=out)

It is then possible to modify this R script as any simulx script.

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Three other demo examples, with different types of model and data, are available:

• A Monolix project for the warfarin PKPD data. In this example, the individual parameters, estimated by the conditional modes, are used for the simulation of the PKPD data. Replace “mode” by “mean” to use the conditional means instead of the conditional modes.

project.file <- 'monolixRuns/warfarin_project.mlxtran'
monolix2simulx(project = project.file, parameter="mode")

• A Monolix project for joint continuous and categorical data

project.file <- 'monolixRuns/pkcat_project.mlxtran'
monolix2simulx(project = project.file)

• A Monolix project for joint continuous and time to event data

project.file <- 'monolixRuns/pkrtte_project.mlxtran'
monolix2simulx(project = project.file)