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ospsuite (development version)

Minor improvements and bug fixes

  • plotTimeProfile() now defaults to showLegendPerDataset = "all", showing individual dataset names for both observed and simulated data by default (#1844).
  • DataSet$setValues() and plotting functions (plotTimeProfile(), plotPredictedVsObserved(), plotResidualsVsCovariate(), plotResidualsAsHistogram(), plotQuantileQuantilePlot()) now warn and replace negative yErrorValues with NA instead of silently accepting them (#1756).
  • Fixed plotPredictedVsObserved() error bar mapping: when predictedAxis = "x", error bars are now correctly placed on the y-axis (#1715).

ospsuite 12.4.2

Major changes

  • Added five new plotting functions powered by {ospsuite.plots}: plotTimeProfile(), plotPredictedVsObserved(), plotResidualsVsCovariate(), plotResidualsAsHistogram(), and plotQuantileQuantilePlot(). These functions accept DataCombined objects or data frames and handle mixed error types and unit conversion directly, without requiring data preprocessing (#1652).
  • The {tlf}-based plotting functions plotIndividualTimeProfile(), plotPopulationTimeProfile(), plotObservedVsSimulated(), plotResidualsVsTime(), and plotResidualsVsSimulated() are now soft-deprecated in favor of the {ospsuite.plots}-based equivalents and will be removed in version 14.0. (#1739)

Minor improvements and bug fixes

  • Fixed validateDimension() error message not showing the actual dimension name (#1822).
  • Plotting functions based on {ospsuite.plots} now produce a warning and return NULL when DataCombined has no plottable entries (#1709).
  • Updated {ospsuite.plots} option key references to match camelCase naming convention (e.g., watermarkEnabled, defaultPercentiles) (#1818).
  • Added addResidualColumn() to unify residual computation across calculateResiduals() and the residual plot functions. Supports "log", "linear" (or "lin"), and "ratio" scaling. For log scaling, zero or negative values now produce NaN with a warning instead of an epsilon-based approximation (#1713).
  • Plotting functions now document all passable ... arguments via @inheritDotParams, improving IDE autocompletion for plotPredictedVsObserved() and plotResidualsAsHistogram() (#1817).
  • Added dataSetsFromDataFrame() function that creates a list of DataSet objects from a data.frame with the same structure as returned by dataSetToDataFrame(). This is the inverse operation of dataSetToDataFrame() and allows creating DataSet objects from data frames without requiring an Excel file. (#1495)
  • Added populationFromDataFrame() function to create a Population object from a data.frame, the reverse of populationToDataFrame(). If no IndividualId column is present, sequential IDs are automatically generated. (#1807)
  • loadDataSetsFromExcel() now accepts a sheets parameter to specify which sheets to load. When sheets = NULL (default), the function uses sheets defined in the importer configuration. If the configuration has no sheets defined, all sheets are loaded. When sheets is a character vector, those specific sheets are loaded, overriding any sheets in the configuration. The importAllSheets parameter is now deprecated and will be removed in version 14 (#1760).
  • toDisplayUnit() now accepts an optional unit parameter to specify the source unit of the values, consistent with toUnit() and toBaseUnit() functions. When not specified, values are assumed to be in base unit (maintaining backward compatibility). (#1762)
  • addOutputs() and setOutputs() now throw an error by default when the provided path is not found. This behavior can be disabled by setting stopIfNotFound = FALSE (#1734).
  • ospUnits$Dimensionless$Unitless and ospUnits$Fraction$Unitless now return an empty string "" instead of the literal string "Unitless" (#1754).
  • Added read-only valueOrigin property to Quantity class (including Parameter and other derived classes) to access the value origin from the underlying .NET object. This is useful for generating automated reports that track parameter value provenance (#1751).
  • createImporterConfigurationForFile() now automatically sets the sheets attribute when a sheet parameter is provided, eliminating the need to manually set it before using loadDataSetsFromExcel() (#1755).
  • Fixed getSteadyState() to correctly apply lowerThreshold for both positive and negative values. The threshold now filters values in the interval [-lowerThreshold, lowerThreshold] instead of only values below the threshold (#1792).
  • runSimulations() now throws an error if any simulation has no output selections defined, instead of silently returning empty results. (#1404)
  • exportResultsToCSV() now validates that the input is a single SimulationResults object and rejects lists of results, preventing downstream .NET interop failures (#1752).

ospsuite 12.4.1

Breaking changes

  • R version >=4.4 is required
  • ospsuite.utils version >=1.10.0 is required
  • This package no longer re-exports %||%. ospsuite::%||% will not work.

Major changes

  • Computational core libraries updated to match OSPS Version 12 update 2 release.

Minor changes

  • Using native operator %||% instead of importing from the ospsuite.utils package.

ospsuite 12.4.0

Major changes

  • Added support for macOS (both Intel and Apple Silicon architectures). (#1621)

Minor improvements and bug fixes

  • Added optional names parameter to dataSetToTibble() function to support custom naming of datasets. This is particularly useful when multiple datasets have the same original name. The naming logic has been moved from the private .dataSetToDataFrame() method in DataCombined to dataSetToTibble() for better code reuse and maintainability. (#1627)

ospsuite 12.3.2

Minor improvements and bug fixes

  • OSPSuite binaries were updated to match OSPSuite v12.1 release.

ospsuite 12.3.1

Minor improvements and bug fixes

ospsuite 12.3.0

Breaking changes

  • {ospsuite} now requires {ospsuite.utils} version >= 1.7.0.
  • Classes SimulationBatchRunValues and SimulationBatchOptions are not exported any more. They should not be used directly.

Major changes

  • DataImporterConfiguration now supports getting and setting of the Lower Limit of Quantification (LLOQ) column name via a new field lloqColumn. If the column name is not set (value NULL), LLOQ values will be imported from the measurement column if values are written in the form '< xxx' (e.g., '<0.001'). Otherwise, the values will be imported from the specified column (#722)

Minor improvements and bug fixes

  • Added showLegendPerDataset parameter to plotIndividualTimeProfile() and plotPopulationTimeProfile() to optionally display separate legend entries for each dataset. This is experimental.
  • Improved print outputs for all classes
  • Classes do not inherit from the deprecated Printable class from the {ospsuite.utils} package.
  • Print methods for all classes are now implemented using the ospPrint\* functions introduced in version 1.6.2. of the {ospsuite.utils} package.
  • ParameterRange$printValue() is deprecated. Use getPrintValue() in conjunction with a print method of your choice.
  • Private method Quantity$printQuantity() removed. Quantity$printValue() and Quantity$printQuantityValue() are deprecated. Use getPrintValue() in conjunction with a print method of your choice.
  • SnapshotParameter$printValue() is deprecated. Use getPrintValue() in conjunction with a print method of your choice.
  • Added snapshot tests for all print methods.
  • calculateResiduals() for DataCombined now supports full pairwise residual computation between multiple observed and simulated datasets within a group.
  • The name property of a Simulation can now be changed (#1245)
  • calculateResiduals now handles single-point simulated datasets via direct x-value matching instead of interpolation. Unmatched observed x-values return NA (#1559).

ospsuite 12.2.0

Major Changes

  • New runSimulationsFromSnapshot() to run simulations from .json snapshots files,
  • New convertSnapshot() to convert project snapshots between .json and .pksim5 files.
  • New getMolWeightFor() to retrieve molecular weight for molecule of Quantity.

ospsuite 12.1.0

Major Changes

  • The package fully supports Linux.
  • The package loses dependency {rClr} and gains {rSharp}.
  • The package does not require a local installation of PK-Sim any more. All required dependencies are shipped with the package.

ospsuite 12.0.0

Breaking Changes

  • The single argument of the getBaseUnit() function is now named quantityOrDimension (was dimension previously). It can now use objects of class Quantity as inputs, to be consistent with the toBaseUnit() function.

Major Changes

  • The package gains {openxlsx} and {lifecycle} dependencies.
  • Added a function getSteadyState() to calculate steady state values for simulations. This function is of particular use for models of endogenous substrates, where changing a parameter value (e.g., the production rate) will change the steady-state values of the substrate. The steady-state is considered to be the last values of the molecules amounts and state variable parameters in the simulation with sufficiently long simulation time, i.e., where the rates of the processes do not (significantly) change. The steady-state is NOT analytically calculated or estimated in any other way than simulating for the given time.
  • Added a function exportSteadyStateToXLS() to export steady state values calculated for one simulation using the getSteadyState() to an Excel file that can be imported in MoBi.
  • Lower limit of quantification (LLOQ) is plotted as dotted lines for plotIndividualTimeProfile() and plotPopulationTimeProfile().
  • plotPopulationTimeProfile() provides two new aggregations methods: arithmetic and geometric average and the ability to chose the number of standard deviations to display around the mean through the nsd argument.
  • Function calculateResiduals() uses natural logarithm (log()) when calculating residuals with scaling = "log" as opposed to log10() as it was done before. This also affects figures created by plotObservedVsSimulated(), plotResidualsVsSimulated(), and plotResidualsVsTime(). (#1091, #1087).
  • plotPopulationTimeProfile() has a new aggregation argument that allow the user to choose between quantiles, arithmetic and geometric aggregations of y.

Minor improvements and bug fixes

  • Named Simulation lists can be passed to runSimulations() so that the results are returned as a named list using the same names instead of the simulation id. If no name is provided, the simulation id is used as before. (#1383)
  • The order of columns of the data frame returned by DataCombined$toDataFrame() has changed.
  • DataCombined$toDataFrame() shows the data in the order as the data sets were added and not alphabetically sorted.
  • DataCombined$removeGroupAssignment() does not show a warning if specified name is not present in the DataCombined.
  • DataCombined$removeGroupAssignment() does not produce an error if specified names are not unique.
  • Fixed Passing font size options from plotConfiguration objects to tlf objects (#1198)
  • Legend now have transparent background by default and can be customized through new DefaultPlotConfiguration fields (#1216)
  • plotObsVsPred() now have foldDistance argument set to NULL by default (previously 2). The function will not add any fold lines on the plot by default but display identity line. Set this argument to FALSE to not draw any lines.
  • DefaultPlotConfiguration has a new setting: displayLLOQ (default TRUE) to control plotting of LLOQ lines.
  • DefaultPlotConfiguration's xLimits and yLimits arguments are deprecated and replaced by xAxisLimits and yAxisLimits. Use them to zoom in the plot while preserving all data points. Use xValuesLimits and yValuesLimits to filter out data point outside of these range. More detailed explanations in the ggplot2 coord_cartesian documentation.
  • addSimulationResults and addDataSets methods of the DataCombined class now support an optional silent argument which silences the checks for data set names. If you expect to replace data sets in DataCombined objects repeatedly, consider switching the parameter from the default FALSE value to TRUE.
  • simulationResultsToDataFrame() is faster than before (#1317, @Felixmil).
  • DataCombined gets a new method setDataTypes() to change data types (observed or simulated) for existing data sets. This method is useful when you want to enforce a certain data type, e.g., for adding artificial data set as simulated results.
  • New function setOutputs() to change outputs of SimulationBatch objects. It combines clearOutputs() and setOutputs() in one function.
  • New simulations life cycle flowcharts in the vignette("efficient-calculations") vignette.
  • New internal function .setEndSimulationTime() to set the end time of the simulation. The function will either extend or shorten the simulation time to the specified end time.
  • Using runSimulation() is now soft deprecated in favor of runSimulations().

ospsuite 11.1.197

Major Changes

  • Adds new visualization functions:

    • plotObservedVsSimulated() for observed versus simulated data scatter plot.
    • plotResidualsVsTime() for time versus residuals data scatter plot.
    • plotResidualsVsSimulated() for simulated versus residuals data scatter plot.

  • Adds new helper functions to work with DataCombined objects:

    • convertUnits() to convert datasets in DataCombined to common units.
    • calculateResiduals() to calculate residuals for datasets in DataCombined.

  • The class SimulationBatch gets a new property id.

  • The output of runSimulationBatches() is now a named list with names being the ids of SimulationBatch.

  • calculateResiduals() now uses log(base = 10) for calculation of residuals in logarithmic scale instead if log(base = exp(1))

  • calculateResiduals() does also return residuals for entries where simulated or observed value is 0 in logarithmic scale. These values were ignored in previous versions. If the observed or simulated value is zero or negative, it is replaced by an arbitrary small value getOSPSuiteSetting("LOG_SAFE_EPSILON") (1e-20 by default).

Minor improvements and bug fixes

  • SimulationBatch$addRunValues() will throw an error when any start value is NaN.
  • SimulatioBatch gets methods getVariableParameters() and getVariableMolecules() that return list of parameter resp. molecule paths that are defined variable.

ospsuite 11.0.123

Breaking changes

  • Signature for toUnit function has changed. molWeight is now the fifth, while sourceUnit is the fourth parameter (#837).

  • DataImporterConfiguration: fields timeUnitFromColumn and measurementUnitFromColumn are renamed to isTimeUnitFromColumn and isMeasurementUnitFromColumn

  • The constructor for DataImporterConfiguration does not accept a path to a configuration file any more. Use the function loadDataImporterConfiguration() to create a configuration object from a file.

  • The constructor for DataSet objects requires a name argument.

  • All validate*() helper functions and "%||%" infix operators are no longer exported. Please have a look at the new utility package, from which these functions are now exported: https://www.open-systems-pharmacology.org/OSPSuite.RUtils/.

  • The pkAnalysesAsDataFrame() function changes column data types for QuantityPath, Parameter, and Unit from factor to character (#673).

Major Changes

  • Adds new DataCombined class that combines observed data (DataSet) and simulated data (SimulationResults) into a single object. Especially important is the $toDataFrame() method of this object that returns a data frame containing combined data from observed and simulated data, which can be further used for visualizations or other analysis.

  • Adds new visualization functions:

  • plotIndividualTimeProfile() and plotPopulationTimeProfile() to create time-profile plots.

  • Adds a new class DefaultPlotConfiguration to provide plot configurations for plotting functions.

  • Adds simulationResultsToDataFrame() function to convert SimulationResults objects into a data frame.

  • All *ToDataFrame() functions also get *ToTibble() variants to extract a tibble data frame instead of a classical data frame.

  • Following functions are marked for deprecation and will be removed in future releases:

    • pkAnalysesAsDataFrame() is now pkAnalysesToDataFrame()
    • populationAsDataFrame() is now populationToDataFrame()

ospsuite 10.0

Version compatible with the OSPSuite V10.

Major Changes

  • Enable Batch Simulation Run (#444).
  • Export of population to CSV (#423).
  • Support aging data for population calculation (#295).
  • Enums to look up units and dimensions (#478).
  • Support R4 (#531).
  • extend setParameterValuesByPath function (#541).
  • DataSet: load from PKML (#575).
  • Efficient calculations, see this vignette.

Minor improvements and bug fixes

  • Cannot calculate PK-Parameters of a population when one individual simulation failed (#436).
  • Usability issue when creating a population (#473).
  • Unnecessary Debug output in some plot tasks (#503).
  • uniqueEntities: Error when passing only one entity (#515).
  • R-Toolbox bug? getAllParametersMatching(). (#428).
  • Add CL parameter to the list of StandardPKPArameters (#582).
  • toBaseUnit and toUnit should support null as input (and return null). (#583).
  • ospsuite::toBaseUnit should be case insensitive (#614).
  • Integer variables not handled by some functions (#553).

ospsuite 9.0

  • Version compatible with the OSPSuite V9.
  • Initial Release