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Description of the R functions associated to the project management

Description of the functions of the API

getData Get a description of the data used in the current project.
getInterpretedData Get the data set interpreted by Monolix.
getStructuralModel Get the model file for the structural model used in the current project.
isProjectLoaded Check if the project is loaded.
loadProject Load a project by parsing the Mlxtran-formated file whose path has been given as an input.
newProject Create a new empty project providing model and data specification.
saveProject Save the current project as an Mlxtran-formated file.
setData Set project data giving a data file and specifying headers and observations types.
setStructuralModel Set the structural model.

[Monolix – PKanalix] Get project data

Description

Get a description of the data used in the current project. Available informations are:

  • dataFile (string): path to the data file
  • header (array<character>): vector of header names
  • headerTypes (array<character>): vector of header types
  • observationNames (vector<string>): vector of observation names
  • observationTypes (vector<string>): vector of observation types
  • nbSSDoses (int): number of doses (if there is a SS column)

Usage

getData()

Value

A list describing project data.

See Also

setData

Click here to see examples

data = getData()

data

-> $dataFile

“/path/to/data/file.txt”

$header

c(“ID”,”TIME”,”CONC”,”SEX”,”OCC”)

$headerTypes

c(“ID”,”TIME”,”OBSERVATION”,”CATEGORICAL COVARIATE”,”IGNORE”)

$observationNames

c(“concentration”)

$observationTypes

c(concentration = “continuous”)

## End(Not run)


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[Monolix – PKanalix] Get interpreted project data

Description

[Monolix – PKanalix] Get interpreted project data

Usage

getInterpretedData()

[Monolix – PKanalix – Simulx] Get structural model file

Description

Get the model file for the structural model used in the current project.
For Simulx, this function will return the structural model only if the project was imported from Monolix, and NULL otherwise.

Usage

getStructuralModel()

Value

A string corresponding to the path to the structural model file.

See Also

setStructuralModel

Click here to see examples

getStructuralModel() => “/path/to/model/inclusion/modelFile.txt”

## End(Not run)


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[Monolix – PKanalix – Simulx] Get current project load status

Description

[Monolix – PKanalix – Simulx] Get current project load status

Usage

isProjectLoaded()

Value

TRUE if a project is currently loaded, FALSE otherwise


[Monolix – PKanalix – Simulx] Load project from file

Description

Load a project by parsing the Mlxtran-formated file whose path has been given as an input.
The extensions are .mlxtran for Monolix, .pkx for PKanalix, and .smlx for Simulx.
WARNING: R is sensitive between ‘\’ and ‘/’, only ‘/’ can be used.

Usage

loadProject(projectFile)

Arguments

projectFile (character) Path to the project file. Can be absolute or relative to the current working directory.

See Also

saveProject

Click here to see examples

loadProject(“/path/to/project/file.mlxtran”) for Linux platform

loadProject(“C:/Users/path/to/project/file.mlxtran”) for Windows platform

## End(Not run)


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[Monolix – PKanalix – Simulx] Create new project

Description

Create a new empty project providing model and data specification. The data specification is:

Monolix, PKanalix
  • dataFile (string): path to the data file
  • headerTypes (array<character>): vector of headers
  • observationTypes [optional] (list): a list, indexed by observation name, giving the type of each observation present in the data file. If omitted, all the observations will be considered as "continuous"
  • nbSSDoses (int): number of steady-state doses (if there is a SS column)
  • mapping [optional](list): a list giving the observation name associated to each y-type present in the data file
    (this field is mandatory when there is a column tagged with the "obsid" headerType)

Please refer to setData documentation for a comprehensive description of the "data" argument structure.

Monolix only
  • projectFile (string): path to the datxplore or pkanalix project file defining the data

Usage

newProject(modelFile = NULL, data = NULL)

Arguments

modelFile (character) Path to the model file. Can be absolute or relative to the current working directory.
To use a model from the libraries, you can set modelFile = "lib:modelName.txt", e.g. modelFile = "lib:oral1_1cpt_kaVCl.txt"
data (list) Structure describing the data.
In case of PKanalix, data is mandatory and modelFile is optional (used only for the CA part and must be from the library).
In case of Monolix, data and modelFile are mandatory. It can be replaced by a projectFile corresponding to a Datxplore or PKanalix project file.
In case of Simulx, modelFile is mandatory and data = NULL. It can be replaced by a projectFile corresponding to a Monolix project. In that case, the Monolix project will be imported into Simulx.

See Also

newProject saveProject

Click here to see examples

newProject(data = list(dataFile = “/path/to/data/file.txt”,

headerTypes = c(“IGNORE”, “OBSERVATION”),

observationTypes = “continuous”),

modelFile = “/path/to/model/file.txt”)

newProject(data = list(dataFile = “/path/to/data/file.txt”,

headerTypes = c(“IGNORE”, “OBSERVATION”, “OBSID”),

observationTypes = list(concentration = “continuous”, effect = “discrete”),

mapping = list(“1” = “concentration”, “2” = “effect”)),

modelFile = “/path/to/model/file.txt”)

[Monolix only]

newProject(data = list(projectFile = “/path/to/project/file.datxplore”),

modelFile = “/path/to/model/file.txt”)

[Simulx only]

newProject(modelFile = “/path/to/model/file.txt”)

new project from an import of a structural model

newProject(modelFile = “/path/to/monolix/project/file.mlxtran”)

new project from an import of a monolix model

## End(Not run)


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[Monolix – PKanalix – Simulx] Save current project

Description

Save the current project as an Mlxtran-formated file.
The extensions are .mlxtran for Monolix, .pkx for PKanalix, and .smlx for Simulx.
WARNING: R is sensitive between ‘\’ and ‘/’, only ‘/’ can be used.

Usage

saveProject(projectFile = "")

Arguments

projectFile [optional](character) Path where to save a copy of the current mlxtran model. Can be absolute or relative to the current working directory.
If no path is given, the file used to build the current configuration is updated.

See Also

newProject loadProject

Click here to see examples

[PKanalix only]

saveProject(“/path/to/project/file.pkx”) # save a copy of the model

[Monolix only]

saveProject(“/path/to/project/file.mlxtran”) # save a copy of the model

[Simulx only]

saveProject(“/path/to/project/file.smlx”) # save a copy of the model

[Monolix – PKanalix – Simulx]

saveProject() # update current model

## End(Not run)


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[Monolix – PKanalix] Set project data

Description

Set project data giving a data file and specifying headers and observations types.

Usage

setData(dataFile, headerTypes, observationTypes, nbSSDoses = NULL)

Arguments

dataFile (character): Path to the data file. Can be absolute or relative to the current working directory.
headerTypes (array<character>): A collection of header types.
The possible header types are: "ignore", "id", "time", "observation", "amount", "contcov", "catcov", "occ", "evid", "mdv", "obsid", "cens", "limit", "regressor","admid", "rate", "tinf", "ss", "ii", "addl", "date".
Notice that these are not the types displayed in the interface, these one are shortcuts.
observationTypes [optional] (list): A list giving the type of each observation present in the data file. If there is only one y-type, the corresponding observation name can be omitted.
The possible observation types are "continuous", "discrete", and "event".
nbSSDoses [optional](int): Number of doses (if there is a SS column).

See Also

getData

Click here to see examples

setData(dataFile = “/path/to/data/file.txt”,

headerTypes = c(“IGNORE”, “OBSERVATION”), observationTypes = “continuous”)

setData(dataFile = “/path/to/data/file.txt”,

headerTypes = c(“IGNORE”, “OBSERVATION”, “YTYPE”),

observationTypes = list(Concentration = “continuous”, Level = “discrete”))

## End(Not run)


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[Monolix – PKanalix] Set structural model file

Description

Set the structural model.
NOTE: In case of PKanalix, the user can only use a structural model from the library for the CA analysis. Thus, the structura model should be written ‘lib:modelFromLibrary.txt’.

Usage

setStructuralModel(modelFile)

Arguments

modelFile (character) Path to the model file. Can be absolute or relative to the current working directory.

See Also

getStructuralModel

Click here to see examples

setStructuralModel(“/path/to/model/file.txt”) # for Monolix

setStructuralModel(“‘lib:oral1_2cpt_kaClV1QV2.txt'”) # for PKanalix or Monolix

## End(Not run)


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