esqlabsR 5.0.0

New functionalities

• New function loadObservedDataFromPKML() to load data from *.pkml located in
  the "PKML" sub-folder of the "Data" folder.

• New function createScenarios() to create Scenario objects from ScenarioConfiguration objects

• Plots can be created by calling the new function createPlotsFromExcel(). It requires as input parameters simulatedScenarios (a list of simulated scenarios as returned by runScenarios()), observedData (a list of DataSet objects) and a ProjectConfiguration object projectConfiguration.

• New function createDataCombinedFromExcel() creates DataCombined objects as
  defined in the Plots.xlsx file.

• New function saveScenarioResults() to save results produced by the runScenarios()
  function to csv files and corresponding simulations to pkml files.

• New function loadScenarioResults() to load results from csv files into a structure
  as produced by the runScenarios() function.

• New function compareSimulation() to compare two simulations for differences.

• runScenarios() also returns a Population object for population simulations.

• runScenarios() gets a new argument savePopulationToCSV, with default value FALSE.

BREAKING CHANGES

• Field setTestParameters removed from ScenarioConfiguration
• Function initializeScenario() has been removed
• Definition of simulation time in the Scenarios.xlsx file changed. The new expected format
  is a triplet of values <StartTime, EndTime, Resolution>, where Resolution is the number of
  simulated points per time unit defined in the column TimeUnit.
• Field poinstPerMinute of ScenarioConfiguration has been removed.
• Function compareSimulationParameters() has been removed and replaced by compareSimulations()
• Scenarios excel file gets additional columns SteadyStateTime, SteadyStateTimeUnit,
  PopulationId, OutputPathsIds.
• readScenarioConfigurationFromExcel() has a new signature and requires a list of
  scenarioNames and a ProjectConfiguration. The output is a named list of ScenarioConfiguration
  objects.
• Output paths are not set from global variable OutputPaths any more but
  from the respective field of ScenarioConfgiruation
• ProjectConfiguration does not have field $outputDevice any more.
• ScenarioConfiguration does not store SimulationRunOptions any more. Simulation run options must be passed to the runScenarios() function. Different run options cannot be used within one scenarios run.
• Enum GraphicsDevices has been removed.
• Function initializeSimulation() does not have arguments simulateSteadyState, steadyStateTime and simulationRunOptions any more.

MAJOR CHANGES

• New class Scenario that represents a scenario created from a ScenarioConfiguration

• ScenarioConfiguration gets a new field outputPaths which is a list of
  output paths for which the results will be calculated. If NULL (default),
  outputs as defined in the simulation are used.

• Paths of model outputs are defined in the excel file Scenarios.xlsx. In the
  sheet OutputPaths, create an entry for each output. The column OutputPath is the full
  path to the output, while OutputPathId is an identifier that conveniently allows
  to select the correct output.
  In the Scenarios sheet, enter the IDs of all paths the outputs should be generated for,
  separated by a ,, e.g. Aciclovir_PVB, Aciclovir_fat_cell.

If no outputs are specified, the outputs as defined in the simulation .pkml file
will be produced.

• ScenarioConfiguration gets a new field populationId, specifying the id of
  the population as defined in the PopulationParameters.xlsx file, sheet Demographics.
  If the field is NULL, the scenario is simulated as an individual simulation,
  otherwise a population simulation is performed.

• ScenarioConfiguration gets a new field readPopulationFromCSV. If FALSE (default),
  a new population is created from defined population demographics. If TRUE, a simulation
  will be imported from a csv sheet located in the folder Parameters/Populations and
  named as the PopulationId.

• runScenarios() supports scenario configurations for population simulations

• Target folder for saving *.pkml simulations when runScenarios(scenarioConfigurations, saveSimulationsToPKML = TRUE)
  changed from Models/Simulations/<DateSuffix> to Results/SimulationResults/<DateSuffix>.

• sensitivityCalculation() - fixed bug in wrong calculation of sensitivity values.
  Please be aware that the results produced by earlier versions are wrong.

• The workflow for running scenarios changed to:

  • Create a ProjectConfiguration with createDefaultProjectConfiguration()

  • Create ScenarioConfigurations, e.g. with readScenarioConfigurationFromExcel(scenarioNames, projectConfiguration)

  • Run scenarios with runScenarios(scenarioConfigurations)

  • Alternatively:

  • Create a ProjectConfiguration with createDefaultProjectConfiguration()

  • Create ScenarioConfigurations, e.g. with readScenarioConfigurationFromExcel(scenarioNames, projectConfiguration)

• ProjectConfiguration gets a new field plotsFile. It is the name of the excel file with plot definitions and must be located in the paramsFolder.

• When defining an individual of other species than human in ScenarioConfiguration
  and applying it to a human model, missing species-specific parameters are applied and the
  scaling works properly. Supported scalingsa are: Human to rat, human to monkey,
  human to rabbit.

• initializeSimulation() does not perform steady-state run any more. This is done as part of the runScenarios() function.

MINOR CHANGES

• Function stringToNum() gets additional arguments lloqMode and uloqMode
  that determine how entries of type "<number" and ">number" will be treated.

• readScenarioConfigurationFromExcel() will read all scenarios defined in the
  Scenarios.xlsx file if no scenario names are specified (argument scenarioNames = NULL).

• Function setApplications() is deprecated.

• Dark grey frame around legends by default.

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