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Monolix batch run

For Monolix batch run, we now recommend to use the more recent Monolix R API.

 

It is possible to run calculation of several Monolix projects through a single command line from R or Matlab. For that, you can use the following functions (here for R and here for Matlab). To use it

source('runMonolix.R')
runMonolix(name, mlxInstallDir, display, saveGraphics, scenario)

where

  •  name: Define the Mlxtran files to run in absolute path
    • If it is a list of Mlxtran files, run them
    • If it is a list of directory, run all the Mlxtran files in the folder
    • It can be a combination of both
  • mlxInstallDir : Define where MonolixSuite is installed
    • Typically for windows mlxInstallDir <- ‘C:/ProgramData/Lixoft/MonolixSuite2016R1/bin/’
  • display : Boolean to define if Monolix calculation is displayed or not (FALSE by default)
  • saveGraphics : Boolean to define if the graphics are saved or not (FALSE by default). It is not done by default in the Monolix project configuration.
  • scenario : Monolix scenario could be a list of
    • saem: estimate population parameters
    • indiv: estimate individual parameters
    • fim: estimate the standard errors of the estimates and Fisher information matrix
    • ll: estimate the log-likelihood
    • graphics: generate the result graphics
    • By default, the run option is used to get the scenario from the project

Several examples,

  • source('runMonolix.R') 
runMonolix(name='C:/Users/jonathan/mydemos/1.creating_and_using_models/libraries_of_models',
mlxInstallDir='C:/ProgramData/Lixoft/MonolixSuite2016R1/bin/')

    run all the projects in the defined folder. The scenario will be the one defined in each projects

  • source('runMonolix.R')
runMonolix(name='C:/Users/jonathan/mydemos/1.creating_and_using_models/libraries_of_models',
mlxInstallDir='C:/ProgramData/Lixoft/MonolixSuite2016R1/bin/',scenario=c('saem','ll'))

    run all the projects in the defined folder. The scenario will be the calculation of SAEM and the the Log-Likelihood for each projects

  • source('runMonolix.R')
runMonolix(name=c('C:/Users/jonathan/mydemos/1.creating_and_using_models/libraries_of_models',
'C:/Users/jonathan/mydemos/1.creating_and_using_models/libraries_of_models/2.2.censored_data/censoring1_project.mlxtran'), 
mlxInstallDir='C:/ProgramData/Lixoft/MonolixSuite2016R1/bin/', scenario=c('graphics'), saveGraphics = TRUE)

    run all the projects in the defined folder and the other Mlxtran project. The scenario will only be the calculation of the graphics and they will be saved.