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Releases: Open-Systems-Pharmacology/OSPSuite-R

ospsuite 12.1.0

26 Jul 12:40
@Felixmil Felixmil
v12.1.0
3b49493
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ospsuite 12.1.0 Pre-release
Pre-release

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().

Contributors

Felixmil
Assets 4
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Version 11.3.520

11 Apr 17:05
@Yuri05 Yuri05
v11.3.520
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Version 11.3.520 Latest
Latest

Installation

Documentation

https://www.open-systems-pharmacology.org/OSPSuite-R/

What's Changed

Full Changelog: v11.2.251...v11.3.520

Contributors

rwmcintosh and Yuri05
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Version 11.2.251

19 Apr 14:07
@Yuri05 Yuri05
v11.2.251
c3ae574
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Version 11.2.251

Installation

Documentation

https://www.open-systems-pharmacology.org/OSPSuite-R/

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Version 11.1.197

31 Jan 10:28
@Yuri05 Yuri05
v11.1.197
b8427a7
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Version 11.1.197

Installation

Documentation

https://www.open-systems-pharmacology.org/OSPSuite-R/

New features

  • 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.

Major Changes

  • 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 Changes

  • 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.

Full Changelog: v11.0.123...v11.1.197

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Version 11.0.123

20 May 13:45
@Yuri05 Yuri05
v11.0.123
cf12170
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Version 11.0.123

Installation

Documentation

https://www.open-systems-pharmacology.org/OSPSuite-R/

New features

  • 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.

Major Changes

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

    • pkAnalysesAsDataFrame() is now pkAnalysesToDataFrame()

    • populationAsDataFrame() is now populationToDataFrame()

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).

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Version 10.0.72

19 Oct 13:13
@msevestre msevestre
v10.0.72
dea6065
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Version 10.0.72

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msevestre, IndrajeetPatil, and 5 other contributors
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Version 10.0.70

13 Oct 13:27
@msevestre msevestre
v10.0.70
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Version 10.0.70 Pre-release
Pre-release

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Contributors

msevestre, IndrajeetPatil, and 5 other contributors
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Version 10.0.25

20 Apr 09:41
@Yuri05 Yuri05
v10.0.25
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Version 10.0.25 Pre-release
Pre-release

This release includes some bug fixes and minor new features (s. the list of modifications)

Installation

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Version 9.1.4

03 Dec 18:30
@msevestre msevestre
v9.1.4
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Version 9.1.4

Version 9.1.4.. This can be used as replacement of existing 9.1.x release

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Version 9.1.2

09 Oct 15:19
@msevestre msevestre
v9.1.2
366c963
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Version 9.1.2

This is the same version as 9.1. The only change is that the default version in the description file was updated
If you are using 9.1.1 already, there is no need to update to this package

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