Package: esqlabsR 5.7.0.9005

Pavel Balazki

esqlabsR: ESQlabs utilities package

The `{esqlabsR}` package facilitates and standardizes the modeling and simulation of physiologically based kinetic (PBK) and quantitative systems pharmacology/toxicology (QSP/T) models implemented in the [Open Systems Pharmacology Software](https://www.open-systems-pharmacology.org/) (OSPS).

Authors:ESQlabs GmbH [cph, fnd], Pavel Balazki [cre, aut], Johanna Eitel [aut], Indrajeet Patil [aut], Sergei Vavilov [aut], Felix Mil [aut], Sia Mirza [aut]

esqlabsR_5.7.0.9005.tar.gz
esqlabsR_5.7.0.9005.zip(r-4.7-any)esqlabsR_5.7.0.9005.zip(r-4.6-any)esqlabsR_5.7.0.9005.zip(r-4.5-any)
esqlabsR_5.7.0.9005.tgz(r-4.6-any)esqlabsR_5.7.0.9005.tgz(r-4.5-any)
esqlabsR_5.7.0.9005.tar.gz(r-4.7-any)esqlabsR_5.7.0.9005.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
esqlabsR/json (API)

# Install 'esqlabsR' in R:
install.packages('esqlabsR', repos = c('https://esqlabs.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/esqlabs/esqlabsr/issues

Pkgdown/docs site:https://esqlabs.github.io

On CRAN:

Conda:

pbpkpbpk-modelingsimulationquarto

7.02 score 45 stars 1 packages 50 scripts 79 exports 98 dependencies

Last updated from:3a5c2c6f5a (on additional-repos-osp-universe). Checks:5 ERROR, 3 WARNING, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develERROR300
source / vignettesERROR328
linux-releaseERROR300
macos-releaseERROR200
macos-oldrelERROR311
windows-develWARNING697
windows-releaseWARNING532
windows-oldrelWARNING670
wasm-releaseFAIL266

Exports:addScenarioConfigurationsToExcelapplyIndividualParameterscalculateMeanDataSetcol2hsvcompareSimulationscompareWithNAcreateDataCombinedFromExcelcreateDefaultProjectConfigurationcreateEsqlabsExportConfigurationcreateEsqlabsPlotConfigurationcreateEsqlabsPlotGridConfigurationcreatePITaskscreatePlotsFromExcelcreateProjectConfigurationcreateScenarioConfigurationsFromPKMLcreateScenariosDistributionsenumPutListesqlabsColorsesqlabsRSettingNamesexampleProjectConfigurationPathexecuteInParallelExportConfigurationexportParametersToXLSextendParameterStructureextendPopulationByUserDefinedParamsextendPopulationFromXLSGenderIntgeomeangeosdgetAllApplicationParametersgetEsqlabsRSettinggetIndexClosestToValuegetMoleculeNameFromQuantityinitializeSimulationinitProjectisAnyCriticalErrorsisParametersEqualisProjectInitializedisTableFormulasEqualLLOQModeloadObservedDataloadObservedDataFromPKMLloadScenarioResultsloadSensitivityCalculationpathFromClipboardPITaskConfigurationProjectConfigurationprojectConfigurationStatusreadExcelreadIndividualCharacteristicsFromXLSreadParametersFromXLSreadPITaskConfigurationFromExcelreadPopulationCharacteristicsFromXLSreadScenarioConfigurationFromExcelremoveFromListrestoreProjectConfigurationrunPIrunScenariossampleRandomValuesaveScenarioResultssaveSensitivityCalculationScenarioScenarioConfigurationsensitivityCalculationsensitivitySpiderPlotsensitivityTimeProfilessensitivityTornadoPlotsetApplicationssetParameterValuesByPathWithConditionsnapshotProjectConfigurationsourceAllstringToNumULOQModevalidateAllConfigurationsvalidationResultvalidationSummarywriteIndividualToXLSwriteParameterStructureToXLS

Dependencies:askpassbackportsbitbit64cellrangercheckmateclicliprcolorspacecommonmarkcowplotcpp11crayoncredentialscurldata.tableDEoptimdescdfoptimDiceKrigingdplyrfarverfitdistrplusfsgenericsgertggh4xggnewscaleggplot2ggtextgitcredsgluegridtextgtablehmshttr2iniisobandjpegjsonlitelabelinglatticelifecyclelitedownloggermagrittrmarkdownMASSMatrixnloptrnumDerivopensslopenxlsxospsuiteospsuite.parameteridentificationospsuite.plotsospsuite.utilspatchworkpillarpkgconfigpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppreadrreadxlrematchrlangrprojrootrSharprstudioapiS7scalesstringistringrsurvivalsystibbletidyrtidyselecttlftzdbusethisutf8vctrsviridisLitevroomwhiskerwithrwritexlxfunxml2yamlzip

Readme and manuals

Help Manual

Help pageTopics
Add scenario configurations to project Excel filesaddScenarioConfigurationsToExcel
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.applyIndividualParameters
Calculate mean and standard deviation for the yValues of the given 'DataSet' objectscalculateMeanDataSet
Returns the HSV values for a given R color namecol2hsv
Compare two simulationscompareSimulations
Compare values including 'NA'compareWithNA
Generate DataCombined objects as defined in excel filecreateDataCombinedFromExcel
Create a default 'ProjectConfiguration'createDefaultProjectConfiguration
Create an instance of 'ExportConfiguration' R6 classcreateEsqlabsExportConfiguration
Create an instance of 'DefaultPlotConfiguration' R6 classcreateEsqlabsPlotConfiguration
Create an instance of 'PlotGridConfiguration' R6 classcreateEsqlabsPlotGridConfiguration
Create Parameter Identification taskscreatePITasks
Generate plots as defined in excel file 'projectConfiguration$plotsFile'createPlotsFromExcel
Create a 'ProjectConfiguration'createProjectConfiguration
Create scenario configurations from PKML filescreateScenarioConfigurationsFromPKML
Create 'Scenario' objects from 'ScenarioConfiguration' objectscreateScenarios
Supported distributions for samplingDistributions
Add a new key-value pairs to an enum, where the value is a list.enumPutList
esqLABS color paletteesqlabsColors
Names of the settings stored in esqlabsEnv Can be used with 'getEsqlabsRSetting()'esqlabsRSettingNames
Get the path to example ProjectConfiguration.xlsxexampleProjectConfigurationPath
Parallelize the execution of a function over a list of arguments valuesexecuteInParallel
ExportConfigurationExportConfiguration
Export simulation parameters to excelexportParametersToXLS
Extend parameters structure with new entriesextendParameterStructure
Add user defined variability on parameters to a population.extendPopulationByUserDefinedParams
Add user defined variability on parameters to a population from an excel file.extendPopulationFromXLS
Possible gender entries as integer valuesGenderInt
Calculate geometric mean of a numeric vectorgeomean
Calculate geometric standard deviation of a numeric vectorgeosd
Get parameters of applications in the simulationgetAllApplicationParameters
Get the value of a global esqlabsR setting.getEsqlabsRSetting
Find value in an arraygetIndexClosestToValue
Get the name of the molecule from a quantitygetMoleculeNameFromQuantity
Load a simulation and apply a set of parameters.initializeSimulation
Initialize esqlabsR Project Folders and required FilesinitProject
Check if validation results contain any critical errorsisAnyCriticalErrors
Check if two parameters are equal with respect to certain properties.isParametersEqual
Check if a directory contains an esqlabsR projectisProjectInitialized
Check if two table formulas are equal.isTableFormulasEqual
Possible entries for the 'lloqMode' argument of 'calculateMeans()'LLOQMode
Load data from excelloadObservedData
Load data from pkmlloadObservedDataFromPKML
Load simulated scenarios from csv and pkml.loadScenarioResults
Load Sensitivity Calculation ResultsloadSensitivityCalculation
Convert Windows filepaths for RpathFromClipboard
PITaskConfigurationPITaskConfiguration
ProjectConfigurationProjectConfiguration
Check if Excel configuration files are in sync with JSON snapshotprojectConfigurationStatus
Read XLSX files using 'readxl::read_excel' with suppressed warningsreadExcel
Read individual characteristics from filereadIndividualCharacteristicsFromXLS
Read parameter values from a structured Excel file. Each excel sheet must consist of columns 'Container Path', 'Parameter Name', 'Value', and 'Units'readParametersFromXLS
Read Parameter Identification configurations from ExcelreadPITaskConfigurationFromExcel
Read an excel file containing information about population and create a 'PopulationCharacteristics' objectreadPopulationCharacteristicsFromXLS
Read scenario definition(s) from Excel filereadScenarioConfigurationFromExcel
Remove an entry from a listremoveFromList
Import project configuration from JSON to Excel filesrestoreProjectConfiguration
Run Parameter Identification tasksrunPI
Run a set of scenarios.runScenarios
Sample a random value from a distributionsampleRandomValue
Save results of scenario simulations to csv.saveScenarioResults
Save Sensitivity Calculation ResultssaveSensitivityCalculation
ScenarioScenario
ScenarioConfigurationScenarioConfiguration
Carry out and visualize sensitivity analysis (with OSPSuite)sensitivityCalculation
Sensitivity Spider Plot for Pharmacokinetic ParameterssensitivitySpiderPlot
Time Profile plots for Sensitivity AnalysissensitivityTimeProfiles
Tornado Plot for Sensitivity AnalysissensitivityTornadoPlot
Set an application protocol in a 'Simulation' from the Excel filesetApplications
Set the values of parameters in the simulation by path, if the 'condition' is true.setParameterValuesByPathWithCondition
Export project configuration Excel files to JSONsnapshotProjectConfiguration
Source all .R files located in a specific foldersourceAll
Convert string to numericstringToNum
Possible modes to treat values above the upper limit of quantification.ULOQMode
Validate all configuration files in a projectvalidateAllConfigurations
validationResultvalidationResult
Get summary of all validation resultsvalidationSummary
Create a parameter set describing an individual and write it to the Excel filewriteIndividualToXLS
Write parameter structure to excel that can be loaded in MoBiwriteParameterStructureToXLS