NEWS.md

ospsuite (development version)

Major Changes

• New runSimulationsFromSnapshot() to run simulations from .json snapshots files,
• New convertSnapshot() to convert project snapshots between .json and .pksim5 files.

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 {lifecyle} 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 here.
• 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