ospsuite 12.1.0

Warning: Simulations saved with this pre-release (and all versions >=12) with saveSimulation() cannot be opened with MoBi versions >12! Currently, only a non-qualified development version 12 of MoBi is available.

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

• Based on the Open Systems Pharmacology Suite v12
• 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().