Description of the R functions associated to the project management

Get project data

Description

Get a description of the data used in the current project. Available information 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

## Not run:

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)

Get structural model file

Description

Get the model file for the structural model used in the current project.

Usage

getStructuralModel()

Value

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

See Also

setStructuralModel

## Not run:

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

## End(Not run)

Load project from file

Description

Load a project by parsing the mlxtran-formated file whose path has been given as an input.
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

## Not run:

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

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

## End(Not run)

Create new project

Description

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

• dataFile (string): path to the data file
• headerTypes (array<character>): A vector of header types.
  The possible header types are: “id”, “time”, “observation”, “amount”, “contcov”, “catcov”, “occ”, “evid”, “mdv”, “obsid”, “cens”, “limit”, “regressor”,”admid”, “rate”, “tinf”, “ss”, “ii”, “addl”, “date”, “ignore”.
  Notice that these are not the types displayed in the interface, these one are shortcuts. They are not case-sensitive.
• observationTypes (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).
• 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)

Usage

newProject(modelFile, data)

Arguments

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

data
(list) Structure describing the data.

See Also

newProject saveProject

## Not run:

newProject(data = list(dataFile = "/path/to/data/file.txt",
           headerTypes = c("IGNORE","OBSERVATION"),
           observationTypes = "continuous"),
           modelFile = "/path/to/model/file.txt")

## End(Not run)

## Example with warfarin_data.txt from demos and oral1_1cpt_kaVCl.txt from libraries in the current directory
data = list(dataFile= "./warfarin_data.txt",
            headerTypes =c("id", "time", "amount", "observation", "obsid", "contcov", "catcov", "ignore"),
            observationTypes = list(y1 = "continuous", y2 = "continuous" ),
            mapping = list("1" = "y1", "2" = "y2"))
modelFile <- './oral1_1cpt_kaVCl.txt' 
newProject(modelFile = modelFile, data = data)

Save current project

Description

Save the current project as an Mlxtran-formated file.

Usage

saveProject(projectFile = "")

Arguments

projectFile
<a href="character“>optional 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

## Not run:

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

saveProject() # update current model

## End(Not run)

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: “id”, “time”, “observation”, “amount”, “contcov”, “catcov”, “occ”, “evid”, “mdv”, “obsid”, “cens”, “limit”, “regressor”,”admid”, “rate”, “tinf”, “ss”, “ii”, “addl”, “date”, “ignore”
Notice that these are not the types displayed in the interface, these one are shortcuts. They are not case-sensitive.

observationTypes
(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
<a href="int“>optional: Number of doses (if there is a SS column).

See Also

getData

## Not run:

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)

Set structural model file

Description

Set the structural model.

Usage

setStructuralModel(modelFile)

Arguments

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

See Also

getStructuralModel

## Not run:

setStructuralModel("/path/to/model/file.txt")

## End(Not run)