| getData | Get a description of the data used in the current project. |
| getStructuralModel | Get the model file for the structural model used in the current project. |
| 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. |
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
Click here to see examples
## 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)
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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
Click here to see examples
## Not run:
getStructuralModel() => “/path/to/model/inclusion/modelFile.txt”
## End(Not run)
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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
Click here to see examples
## 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)
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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>): vector of headers
- 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)
- nbSSDoses (int): number of steady-state doses (if there is a SS column)
Please refer to setData documentation for a comprehensive description of the “data” argument structure.
Usage
newProject(modelFile = NULL, 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
Click here to see examples
## 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)
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Save current project
Description
Save the current project as an Mlxtran-formated file.
Usage
saveProject(projectFile = "")
Arguments
projectFile
newProject loadProject
Click here to see examples
## Not run:
saveProject(“/path/to/project/file.mlxtran”) # save a copy of the model
saveProject() # update current model
## End(Not run)
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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 (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
Click here to see examples
## 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)
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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
Click here to see examples
## Not run:
setStructuralModel(“/path/to/model/file.txt”) # for Monolix
setStructuralModel(“‘lib:oral1_2cpt_kaClV1QV2.txt'”) # for PKanalix
## End(Not run)
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