ospsuite 12.4.3

Major changes

• Computational core libraries updated to match OSPS Version 12 update 3 release.

Minor improvements and bug fixes

• plotPredictedVsObserved() and plotResidualsVsCovariate() gain a showLegendPerDataset argument ("none", "observed", "all", default "all") to differentiate observed datasets within a group by point shape, consistent with plotTimeProfile() (#1839).
• plotResidualsVsCovariate(), plotResidualsAsHistogram(), and plotQuantileQuantilePlot() now compute residuals consistently with calculateResiduals(), producing NaN with a warning for zero or negative values on the log scale instead of extreme values (#1713).
• 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

• Fixed tests expectations for better compatibility with latest version of
  {ospsuite.utils} package. #1570
• Revised "get started" (https://www.open-systems-pharmacology.org/OSPSuite-R/articles/ospsuite.html) documentation page to make it more accesible to new users. #1571

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
  plotPupulationTimeProfile() 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).

Built Packages (R 4.5.1)

• Windows
• Linux

ospsuite 12.2.0

Note

If you are upgrading from version 11 of the package, read the release notes 12.1 for the full list of changes.

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

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().

Version 11.3.520

Installation

• Option 1 - install from scratch.

  • Windows: package (How to install)
  • Ubuntu 18: package (How to install)
  • CentOS 7: package (How to install)

• Option 2 - use docker images (NOTE: Version 11.0 is included; docker images for the version 11.3 not yet available)

  • R 4.1.0
    • Ubuntu 18
    • CentOS 7

Documentation

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

What's Changed

• update core by @rwmcintosh in #1379
• Hotfix/11.3 by @Yuri05 in #1385

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