Package index • esqlabsR

Project workflow

ProjectConfiguration: ProjectConfiguration
createDefaultProjectConfiguration(): Create a default ProjectConfiguration
createProjectConfiguration(): Create a ProjectConfiguration
exampleProjectConfigurationPath(): Get the path to example ProjectConfiguration.xlsx
initProject(): Initialize esqlabsR Project Folders and required Files
isProjectInitialized(): Check if a directory contains an esqlabsR project
restoreProjectConfiguration(): Import project configuration from JSON to Excel files
snapshotProjectConfiguration(): Export project configuration Excel files to JSON
Scenario: Scenario
ScenarioConfiguration: ScenarioConfiguration
addScenarioConfigurationsToExcel(): Add scenario configurations to project Excel files
createScenarioConfigurationsFromPKML(): Create scenario configurations from PKML files
createScenarios(): Create Scenario objects from ScenarioConfiguration objects
loadScenarioResults(): Load simulated scenarios from csv and pkml.
readScenarioConfigurationFromExcel(): Read scenario definition(s) from Excel file
runScenarios(): Run a set of scenarios.
saveScenarioResults(): Save results of scenario simulations to csv.
projectConfigurationStatus(): Check if Excel configuration files are in sync with JSON snapshot
createPlotsFromExcel(): Generate plots as defined in excel file projectConfiguration$plotsFile

readExcel(): Read XLSX files using readxl::read_excel with suppressed warnings
readIndividualCharacteristicsFromXLS(): Read individual characteristics from file
readParametersFromXLS(): Read parameter values from a structured Excel file. Each excel sheet must consist of columns 'Container Path', 'Parameter Name', 'Value', and 'Units'
readPopulationCharacteristicsFromXLS(): Read an excel file containing information about population and create a PopulationCharacteristics object
readScenarioConfigurationFromExcel(): Read scenario definition(s) from Excel file
extendParameterStructure(): Extend parameters structure with new entries
extendPopulationByUserDefinedParams(): Add user defined variability on parameters to a population.
extendPopulationFromXLS(): Add user defined variability on parameters to a population from an excel file.
setApplications(): Set an application protocol in a Simulation from the Excel file
setParameterValuesByPathWithCondition(): Set the values of parameters in the simulation by path, if the condition is true.
writeIndividualToXLS(): Create a parameter set describing an individual and write it to the Excel file
writeParameterStructureToXLS(): Write parameter structure to excel that can be loaded in MoBi
exportParametersToXLS(): Export simulation parameters to excel
createDataCombinedFromExcel(): Generate DataCombined objects as defined in excel file

compareSimulations(): Compare two simulations
compareWithNA(): Compare values including NA
calculateMeanDataSet(): Calculate mean and standard deviation for the yValues of the given DataSet objects
initializeSimulation(): Load a simulation and apply a set of parameters.
geomean(): Calculate geometric mean of a numeric vector
geosd(): Calculate geometric standard deviation of a numeric vector
sampleRandomValue(): Sample a random value from a distribution
applyIndividualParameters(): Apply an individual to the simulation. For human species, only parameters that do not override formulas are applied. For other species, all parameters returned by createIndividual are applied.
Distributions: Supported distributions for sampling
LLOQMode: Possible entries for the lloqMode argument of calculateMeans()
ULOQMode: Possible modes to treat values above the upper limit of quantification.
loadObservedData(): Load data from excel
loadObservedDataFromPKML(): Load data from pkml

col2hsv(): Returns the HSV values for a given R color name
esqlabsColors(): esqLABS color palette
createEsqlabsExportConfiguration(): Create an instance of ExportConfiguration R6 class
createEsqlabsPlotConfiguration(): Create an instance of DefaultPlotConfiguration R6 class
createEsqlabsPlotGridConfiguration(): Create an instance of PlotGridConfiguration R6 class
createDataCombinedFromExcel(): Generate DataCombined objects as defined in excel file

isParametersEqual(): Check if two parameters are equal with respect to certain properties.
isProjectInitialized(): Check if a directory contains an esqlabsR project
isTableFormulasEqual(): Check if two table formulas are equal.
stringToNum(): Convert string to numeric
GenderInt: Possible gender entries as integer values

loadSensitivityCalculation(): Load Sensitivity Calculation Results
saveSensitivityCalculation(): Save Sensitivity Calculation Results
sensitivityCalculation(): Carry out and visualize sensitivity analysis (with OSPSuite)
sensitivitySpiderPlot(): Sensitivity Spider Plot for Pharmacokinetic Parameters
sensitivityTimeProfiles(): Time Profile plots for Sensitivity Analysis
sensitivityTornadoPlot(): Tornado Plot for Sensitivity Analysis

enumPutList(): Add a new key-value pairs to an enum, where the value is a list.
getAllApplicationParameters(): Get parameters of applications in the simulation
getEsqlabsRSetting(): Get the value of a global esqlabsR setting.
getIndexClosestToValue(): Find value in an array
getMoleculeNameFromQuantity(): Get the name of the molecule from a quantity
executeInParallel(): Parallelize the execution of a function over a list of arguments values
pathFromClipboard(): Convert Windows filepaths for R
removeFromList(): Remove an entry from a list
sourceAll(): Source all .R files located in a specific folder
esqlabsRSettingNames: Names of the settings stored in esqlabsEnv Can be used with getEsqlabsRSetting()