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Changelog

Source: NEWS.md

esqlabsR (development version)

esqlabsR 5.1.3

Minor improvements and bug fixes

esqlabsR 5.1.2

Minor improvements and bug fixes

  • Fixes a bug where scenario results could not be saved or loaded when scenario name contains a slash or a backslash (#548, 1)
  • Add support for nsd argument from ospsuite::plotPopulationTimeProfile() aggregation methods. A new column nsd was added to the PlotConfiguration sheet in the example Plot.xlsx (#544, @Felixmil).
  • Documentation includes PK-Sim installation instructions (#537, @Felixmil).
  • Better error message if some ids are not uniques in the excel configuration files (#568, @Felixmil)
  • Handles better empty rows in the excel configuration files (#569, @Felixmil)
  • Cleaner NEWS file (#527).

esqlabsR 5.1.1

  • Update required dependencies versions

esqlabsR 5.1.0

Breaking Changes

  • When importing observed data using the default importer configuration, data set naming is grouped by StudyId at the first place.

    • Before: {Molecule}_{Study Id}_{Subject Id}_{Species}_{Organ}_{Compartment}_{Dose}_{Route}_{Group Id}
    • After: {Study Id}_{Molecule}_{Subject Id}_{Species}_{Organ}_{Compartment}_{Dose}_{Route}_{Group Id}

    This will result in different data set names, and plots specifying the data sets by the old naming will fail. For compatibility, use custom importer configuration with the old naming:

      importerConfiguration <- ospsuite::loadDataImporterConfiguration(
    configurationFilePath = projectConfiguration$dataImporterConfigurationFile
    )
    importerConfiguration$namingPattern <- "{Molecule}_{Study Id}_{Subject Id}_{Species}_{Organ}_{Compartment}_{Dose}_{Route}_{Group Id}"

Major changes

  • loadObservedData() gets a new argument importerConfiguration. The user can now provide a custom importer configuration for loading the data.

  • Plots.xlsx, sheet ‘plotConfiguration’, now uses xValuesLimits and yValuesLimits to set axis limits of the plots by default. This approach filters data outside of the limits. See https://ggplot2.tidyverse.org/reference/coord_cartesian.html#ref-examples for more details. The user can still use xAxisLimits and yAxisLimits.

  • Sheet ‘plotConfiguration’ in the Excel file ‘Plots’ gets additional column ‘aggregation’. The value is passed to the function plotPopulationTimeProfile(). Supported values are listed in ospsuite::DataAggregationMethods.

    • arithmetic: population results are plotted as arithmetic mean +- arithmetic standard deviation
    • geometric: population results are plotted as geometric mean +- geometric standard deviation
    • quantiles (default): population results are plotted as quantiles defined in the column quantiles.

  • Protein ontogenies can be defined for populations and individuals. To specify ontogenies for proteins in the simulation, list the proteins you want to define ontogenies for in the column ‘Protein’ of files ‘PopulationParameters.xlsx’ or ‘Individuals.xlsx’, separated by a ‘,’. Speficy the ontogenies available in PK-Sim (see article https://www.open-systems-pharmacology.org/OSPSuite-R/articles/create-individual.html#adding-enzyme-ontogenies) in the column ‘Ontogenies’. The number of entries in the both columns must be equal.

  • Excel file ‘PopulationParameters.xlsx’ gets additional columns ‘Protein’ and ‘Ontogeny’.

  • Excel file ‘Individuals.xlsx’ gets additional columns ‘Protein’ and ‘Ontogeny’.

Minor improvements and bug fixes

  • When a scenario fails, runScenarios() does not crash any more, but a warning is shown with the name of the failed scenario. The returned outputValues is NULL.

  • Throw a warning instead of an error if a path specified in ProjectConfiguration does not exist. $outputFolder existence is not checked anymore.

  • stringToNum() does not show a warning NAs introduced by coercion when a value cannot be converted to a numeric any more. For such values, NA is silently returned.

  • exportParametersToXLS - ignore parameters with NaN (#480)

  • Show a meaningful error when no time unit is specified for a scenario (#483)

  • New vignette/article about figure creation.

  • Plots are using new color palette.

  • Some modifications to plot configuration files for better plots. (#456,

esqlabsR 5.0.0

Breaking Changes

  • Field setTestParameters removed from ScenarioConfiguration

  • Function initializeScenario() has been removed.

  • Definition of simulation time in the Scenarios.xlsx file changed. The new expected format is a triplet of values <StartTime, EndTime, Resolution>, where Resolution is the number of simulated points per time unit defined in the column TimeUnit.

  • Field poinstPerMinute of ScenarioConfiguration has been removed.

  • Function compareSimulationParameters() has been removed and replaced by compareSimulations()

  • Scenarios excel file gets additional columns SteadyStateTime, SteadyStateTimeUnit, PopulationId, OutputPathsIds.

  • readScenarioConfigurationFromExcel() has a new signature and requires a list of scenarioNames and a ProjectConfiguration. The output is a named list of ScenarioConfiguration objects.

  • Output paths are not set from global variable OutputPaths any more but from the respective field of ScenarioConfgiruation

  • ProjectConfiguration does not have field $outputDevice any more.

  • ScenarioConfiguration does not store SimulationRunOptions any more. Simulation run options must be passed to the runScenarios() function. Different run options cannot be used within one scenarios run.

  • Enum GraphicsDevices has been removed.

  • Function initializeSimulation() does not have arguments simulateSteadyState, steadyStateTime and simulationRunOptions any more.

Major changes

  • New class Scenario that represents a scenario created from a ScenarioConfiguration.

  • ScenarioConfiguration gets a new field outputPaths which is a list of output paths for which the results will be calculated. If NULL (default), outputs as defined in the simulation are used.

  • Paths of model outputs are defined in the excel file Scenarios.xlsx. In the sheet OutputPaths, create an entry for each output. The column OutputPath is the full path to the output, while OutputPathId is an identifier that conveniently allows to select the correct output.
    In the Scenarios sheet, enter the IDs of all paths the outputs should be generated for, separated by a ,, e.g. Aciclovir_PVB, Aciclovir_fat_cell. If no outputs are specified, the outputs as defined in the simulation .pkml file will be produced.

  • ScenarioConfiguration gets a new field populationId, specifying the id of the population as defined in the PopulationParameters.xlsx file, sheet Demographics. If the field is NULL, the scenario is simulated as an individual simulation, otherwise a population simulation is performed.

  • ScenarioConfiguration gets a new field readPopulationFromCSV. If FALSE (default), a new population is created from defined population demographics. If TRUE, a simulation will be imported from a csv sheet located in the folder Parameters/Populations and named as the PopulationId.

  • runScenarios() supports scenario configurations for population simulations.

  • Target folder for saving *.pkml simulations when runScenarios(scenarioConfigurations, saveSimulationsToPKML = TRUE) changed from Models/Simulations/<DateSuffix> to Results/SimulationResults/<DateSuffix>.

  • sensitivityCalculation() - fixed bug in wrong calculation of sensitivity values. Please be aware that the results produced by earlier versions are wrong.

  • The workflow for running scenarios changed to:

    • Create a ProjectConfiguration with createDefaultProjectConfiguration()
    • Create ScenarioConfigurations, e.g. with readScenarioConfigurationFromExcel(scenarioNames, projectConfiguration)`
    • Run scenarios with runScenarios(scenarioConfigurations) Alternatively:
    • Create a ProjectConfiguration with createDefaultProjectConfiguration()
    • Create ScenarioConfigurations, e.g. with

readScenarioConfigurationFromExcel(scenarioNames, projectConfiguration)

  • ProjectConfiguration gets a new field plotsFile. It is the name of the excel file with plot definitions and must be located in the paramsFolder.

  • When defining an individual of other species than human in ScenarioConfiguration and applying it to a human model, missing species-specific parameters are applied and the scaling works properly. Supported scalingsa are: Human to rat, human to monkey, human to rabbit.

  • initializeSimulation() does not perform steady-state run any more. This is done as part of the runScenarios() function.

  • New function loadObservedDataFromPKML() to load data from *.pkml located in the “PKML” sub-folder of the “Data” folder.

  • New function createScenarios() to create Scenario objects from ScenarioConfiguration objects.

  • Plots can be created by calling the new function createPlotsFromExcel(). It requires as input parameters simulatedScenarios (a list of simulated scenarios as returned by runScenarios()), observedData (a list of DataSet objects) and a ProjectConfiguration object projectConfiguration.

  • New function createDataCombinedFromExcel() creates DataCombined objects as defined in the Plots.xlsx file.

  • New function saveScenarioResults() to save results produced by the runScenarios() function to csv files and corresponding simulations to pkml files.

  • New function loadScenarioResults() to load results from csv files into a structure as produced by the runScenarios() function.

  • New function compareSimulation() to compare two simulations for differences.

  • runScenarios() also returns a Population object for population simulations.

  • runScenarios() gets a new argument savePopulationToCSV, with default value FALSE.

  • esqlabsR extends the tlf::ExportConfiguration class to dynamically calculate the height of the exported figure from the number of rows and the new parameter heightPerRow.

Minor changes and bug fixes

  • Function stringToNum() gets additional arguments lloqMode and uloqMode that determine how entries of type “<number” and “>number” will be treated.

  • readScenarioConfigurationFromExcel() will read all scenarios defined in the Scenarios.xlsx file if no scenario names are specified (argument scenarioNames = NULL).

  • Function setApplications() is deprecated.

  • Dark grey frame around legends by default.

esqlabsR 4.0.0

Breaking changes

Major changes

esqlabsR 3.0.0

Major changes

esqlabsR 2.0.0

  • Maintenance and bug fixes.

esqlabsR 1.0.0

  • Initial release of the package.