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Study

Study.Rd

Description of a study

Public fields

ID

of the study

Active bindings

Compounds

List of administered compounds (with administration protocol), object of class Compound

Individual

Individual used in the study.

Methods

Public methods

Method new()

Initialize a new instance of the class

Usage

Study$new(ID, compounds, individual, genericModel = NULL)

Arguments

ID

ID of the study

compounds

list of administered compounds, compounds must be object of class Compound.

individual

individual used in the study

genericModel

path to a generic model to use if pre-generated (for example from MoBi with PD). Keep to NULL if a generic model should be automatically generated.

Returns

A new Study object.

Method getAllParameterPaths()

Get the paths of all parameters defined for the study. This is a union of all compounds and administration protocol parameters.

Usage

Study$getAllParameterPaths()

Returns

A character vector with the paths of all parameters

Method addDataSets()

Add DataSet objects to the study

Usage

Study$addDataSets(dataSets)

Arguments

dataSets

a DataSet object

Method getDataSets()

Get the DataSet objects of the study

Usage

Study$getDataSets()

Returns

A list of DataSet objects

Method setOutputInterval()

Clears the output interval from the simulation and adds a new one.

Usage

Study$setOutputInterval(startTime, endTime, timeUnit, resolution)

Arguments

startTime

start time of the interval in time units

endTime

end time of the interval in time units

timeUnit

time unit of the interval

resolution

resolution of the interval in pts/time units

Method addOutputInterval()

Adds an interval to the output schema of the study

Usage

Study$addOutputInterval(startTime, endTime, timeUnit, resolution)

Arguments

startTime

start time of the interval in time units

endTime

end time of the interval in time units

timeUnit

time unit of the interval

resolution

resolution of the interval in pts/time units

Method toSnapshot()

Convert study to a snapshot

Usage

Study$toSnapshot()

Method exportSnapshot()

Convert study to a snapshot

Usage

Study$exportSnapshot(file)

Arguments

file

file path to save the snapshot

Method exportPKML()

Convert study to a pkml

Usage

Study$exportPKML(file, overwrite = FALSE)

Arguments

file

file path to save the pkml

overwrite

if TRUE, overwrite existing file

Method setGenericModel()

Set generic model to use if pre-generated (for example from MoBi with PD)

Usage

Study$setGenericModel(modelPath)

Arguments

modelPath

path of the pkml model to use for the study. Keep to NULL if a generic model should be automatically generated.

Method getGenericModel()

Get generic model path assigned to the study (either from automatic pkml creation or preassigned by user).

Usage

Study$getGenericModel(silent = FALSE)

Arguments

silent

if TRUE, do not print a message if the model is not set.

Returns

path of the pkml model used for the study, or NULL if not set. If path is not valid the model is unset.

Method setSimulation()

Set simulation model to use if pre-generated (for example from MoBi with PD)

Usage

Study$setSimulation(simulation)

Arguments

simulation

simulation loaded from pkml (to check )

Method getSimulation()

Get simulation model used for the study

Usage

Study$getSimulation()

Method print()

Print the object to the console

Usage

Study$print(...)

Arguments

...

Rest arguments.