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TestProjectBuilder

TestProjectBuilder.Rd

Manages the creation and writing test project, which can be used for this package or packages which use the reporting framework as base to build a test project

Super class

ospsuite.utils::Printable -> TestProjectBuilder

Active bindings

rootDirectory

root directory of test project. This function synchronizes files from one directory to another, copying only the files that are not already present. This function updates the display names for scenarios and output paths in the project configuration.

Methods

Public methods

Method new()

Initialize a new instance of the class.

Usage

TestProjectBuilder$new()

Method iniTestProject()

A short description...

This function initializes the project structure and configuration for the test project.

Usage

TestProjectBuilder$iniTestProject(rootDirectory, verbose = FALSE)

Arguments

rootDirectory

A character string specifying the root directory for the test project.

verbose

A logical value indicating whether to print messages about the process.

Returns

A ProjectConfiguration object containing the details of the initialized project.

Method setupRandomPopulations()

This function sets up populations for the test project by copying necessary files and exporting defined populations.

Usage

TestProjectBuilder$setupRandomPopulations(
  projectConfiguration,
  populationNames,
  writeTestData = FALSE,
  templateDir = NULL
)

Arguments

projectConfiguration

A ProjectConfiguration object containing the project configuration details.

populationNames

A character vector of population names to be copied.

writeTestData

A logical value indicating whether newly created test data should be filed to the inst directory of the package.

templateDir

character string specifying the installation directory for the package.

Returns

NULL

Method setupSimulations()

This function sets up simulations for the test project by synchronizing necessary directories and running initialized scenarios to calculate pharmacokinetic (PK) parameters.

Usage

TestProjectBuilder$setupSimulations(
  projectConfiguration,
  scenarioList,
  writeTestData,
  templateDir = NULL
)

Arguments

projectConfiguration

A ProjectConfiguration object containing the project configuration details.

scenarioList

A list of scenarios initialized for the project.

writeTestData

A logical value indicating whether newly created test data should be filed to the inst directory of the package.

templateDir

A character string specifying the installation directory for the package.

Returns

A list containing the results from running the scenarios. Set Up Sensitivity Analysis

This function sets up sensitivity analysis for the test project based on the defined scenarios.

Method setUpSensitivity()

Usage

TestProjectBuilder$setUpSensitivity(
  projectConfiguration,
  scenarioList,
  scenarioName,
  writeTestData,
  parameterList,
  sensitivitySheet = "smallSelection",
  templateDir = NULL
)

Arguments

projectConfiguration

A ProjectConfiguration object containing project configuration details.

scenarioList

A list of scenarios initialized for the project.

scenarioName

The name of the scenario used for sensitivity

writeTestData

A logical value indicating whether newly created test data should be filed to the inst directory of the package.

parameterList

A named list where each name corresponds to a parameter in the Excel sheet, and each value is the new value to set for that parameter.

sensitivitySheet

Name of sheet with parameter selection

templateDir

A character string specifying the installation directory for the package.

Returns

A ProjectConfiguration object containing the updated project configuration.

Method addRandomTPData()

This function adds random time profile data to the test project for selected individuals.

Usage

TestProjectBuilder$addRandomTPData(
  projectConfiguration,
  scenarioResults,
  ids,
  timePoints = c(15, 30, 45, 60, 90, c(3, 6, 9, 12, 18, 24) * 60),
  outputPathIds = c("Plasma", "CYP3A4total", "CYP3A4Liver"),
  sdShift = 0.05,
  lloqValue = 0.1
)

Arguments

projectConfiguration

A ProjectConfiguration object containing project configuration details.

scenarioResults

List of scenario results.

ids

A vector of individual IDs to include in the random data.

timePoints

A numeric vector specifying the time points at which to generate data (default is c(15, 30, 45, 60, 90, c(3, 6, 9, 12, 18, 24) * 60)).

outputPathIds

A character vector specifying the output path IDs to include in the random data (default is c('Plasma', 'CYP3A4total', 'CYP3A4Liver')).

sdShift

A numeric value indicating the standard deviation shift applied to the random values (default is 0.05).

lloqValue

A numeric value representing the lower limit of quantification (default is 0.1).

Returns

Invisible NULL. This function adds random pharmacokinetic (PK) data to the test project, including shifting values and calculating statistics for selected individuals.

Method addRandomPKData()

Usage

TestProjectBuilder$addRandomPKData(
  projectConfiguration,
  pkParameterDT,
  ids,
  outputPathIds = c("Plasma", "CYP3A4total", "CYP3A4Liver"),
  sdShift = 0.05
)

Arguments

projectConfiguration

A ProjectConfiguration object containing project configuration details.

pkParameterDT

A data.table containing PK parameters and values.

ids

A vector of individual IDs to include in the random data.

outputPathIds

A character vector specifying the output path IDs to include in the random data (default is c('Plasma', 'CYP3A4total', 'CYP3A4Liver')).

sdShift

A numeric value indicating the standard deviation shift applied to the random values (default is 0.05).

Returns

Invisible NULL.

Method mockManualEditingsCleanup()

This function cleans up the project configuration files by clearing existing data from relevant Excel sheets.

Usage

TestProjectBuilder$mockManualEditingsCleanup(projectConfiguration)

Arguments

projectConfiguration

A ProjectConfiguration object containing project configuration details.

Returns

NULL

Method mockManualEditingsPopulation()

This function adds biometric ranges for virtual pediatric and one adult populations to the configuration files

Usage

TestProjectBuilder$mockManualEditingsPopulation(
  projectConfiguration,
  randomPops = data.table(populationName = c("adults", "toddler", "children",
    "school-children", "adolescents"), species = "Human", population =
    "European_ICRP_2002", numberOfIndividuals = 100, proportionOfFemales = 50, ageMin =
    c(20, 0.5, 2, 6, 12), ageMax = c(40, 2, 6, 12, 18), weightUnit = "kg", heightUnit =
    "cm", bMIUnit = "kg/m²", `protein Ontogenies` = "CYP3A4:CYP3A4, UGT1A4:UGT1A4")
)

Arguments

projectConfiguration

A ProjectConfiguration object containing project configuration details.

randomPops

data.table with content for sheet Demographics in Population.xlsx

Returns

NULL

Method mockManualEditingsScenario()

This function sets up scenarios based on the defined populations and adds PK Parameters and output paths to the project configuration.

Usage

TestProjectBuilder$mockManualEditingsScenario(
  projectConfiguration,
  dtTestScenarios,
  pKParameter = NULL
)

Arguments

projectConfiguration

A ProjectConfiguration object containing project configuration details.

dtTestScenarios

`data.table` with content for scenarios

pKParameter

vector with pkParameter sheets

Returns

NULL

Method mockManualEditingsPKParameter()

This function adds PK parameters to the project configuration based on templates.

Usage

TestProjectBuilder$mockManualEditingsPKParameter(projectConfiguration)

Arguments

projectConfiguration

A ProjectConfiguration object containing project configuration details.

Returns

NULL

Method mockManualEditingsIndividuals()

This function adjust the bio-metrics with in individuals and exports virtual twin populations.

Usage

TestProjectBuilder$mockManualEditingsIndividuals(projectConfiguration)

Arguments

projectConfiguration

A `ProjectConfiguration` object containing project configuration details.

Returns

`data.table` with content of sheet `VirtualTwinPopulation`

Method mockManualEditingsSensitivity()

This function modifies specific parameters in a given Excel sheet based on the provided parameter list and saves the changes back to the workbook.

Usage

TestProjectBuilder$mockManualEditingsSensitivity(
  projectConfiguration,
  sheetName,
  parameterList
)

Arguments

projectConfiguration

A list containing project configuration details, including the path to the sensitivity file.

sheetName

A string representing the name of the sheet in the Excel workbook that will be edited.

parameterList

A named list where each name corresponds to a parameter in the Excel sheet, and each value is the new value to set for that parameter.

Returns

NULL This function is called for its side effects (i.e., modifying the Excel file).

Method clone()

The objects of this class are cloneable with this method.

Usage

TestProjectBuilder$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.