Package index • esqlabsR

Project workflow

ProjectConfiguration: ProjectConfiguration

createDefaultProjectConfiguration(): Create a default ProjectConfiguration

example_ProjectConfiguration(): Get the path to example ProjectConfiguration.xlsx

Scenario: Scenario

ScenarioConfiguration: ScenarioConfiguration

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.

createPlotsFromExcel(): Generate plots as defined in excel file projectConfiguration$plotsFile

init_project(): Initialize esqlabsR Project Folder

Helpers for data import, wrangling, and export

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

Helpers for modeling and simulation

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.

foldChangeFunction(): Function returning the fold difference between x and x_0

hillFunction(): Hill equation, transforming a value of an effector (e.g. concentration) to a saturable function value.

sineFunction(): Sine function

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

Helpers for plotting

col2hsv(): Returns the HSV values for a given R color name

esqLABS_colors(): 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

Input validation

isParametersEqual(): Check if two parameters are equal with respect to certain properties.

isTableFormulasEqual(): Check if two table formulas are equal.

stringToNum(): Convert string to numeric

GenderInt: Possible gender entries as integer values

escapeForRegex(): Escape a string for possible regular expression match

Sensitivity analysis

sensitivityCalculation(): Carry out and visualize sensitivity analysis (with OSPSuite)

sensitivitySpiderPlot(): Sensitivity Spider Plot for Pharmacokinetic Parameters

sensitivityTimeProfiles(): Sensitivity Time Profiles for Pharmacokinetic Parameters

sensitivityTornadoPlot(): Tornado Plot for Sensitivity Analysis

Shiny applications

startFunctionVisualizer(): Start function visualizer

startUnitConverter(): Start unit converter

Miscellaneous

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()

Inherited classes

ExportConfiguration: ExportConfiguration