Improvements to profile plots when multiple datasets of a given type present per group

[IndrajeetPatil]

TODO:

• Closes plotIndividualTimeProfile - multiple observed data within one group should get different symbols #980
• Closes plotIndividualTimeProfile multiple simulation results within one group are connected #982
• Closes plotSimulatedVsObserved y and x axis limits should be identical #1051
• Closes plotObservedVsSimulated wrong results #1052
• Closes Don't run simulation each time for tests; use a stored example instead #1056
• Closes Add more tests for plotPopulationTimeProfile() #1058
• Closes plotPopulationTimeProfile: Error bars not shown #1059
• Closes Nighty failing because of some snapshots outdated #1060
• Closes plotPopulationTimeProfile - upper quantile is not shown #1062
• Closes plotPopulationTimeProfile range color does not match line color if multiple results are assigned to the same group #1064
• Closes Add examples in the manual for DataCombined and related plotting functions #1065
• Closes unnecessary files in .tar.gz packages #1066
• Closes Fix failing tests #1076
• Refactor to DRY up code
• Revert interpolation implemented for Add function to interpolate predicted data #804, since it was giving incorrect results, and there was a simpler method available that gives almost identical results
• Remove all unnecessary internal utilities
• Update snapshots for plot to catch up with {tlf} changes

[IndrajeetPatil]

Best to review the changes in how plot look will be by checking how snapshots for plots have changed:

https://github.com/Open-Systems-Pharmacology/OSPSuite-R/pull/1054/files

[PavelBal]

I see that interpolation has been removed completely? I would like to test how it behaves now, but require this feature first #1067

[IndrajeetPatil]

Why is #1067 needed to check that? We haven't had it thus far and have trusted the results from interpolation anyway.

Here are two examples that can be used to check if the observed and simulated data are being paired properly:

Example-1

# load the simulation
sim <- loadTestSimulation("MinimalModel")
simResults <- importResultsFromCSV(
  simulation = sim,
  filePaths = getTestDataFilePath("Stevens_2012_placebo_indiv_results.csv")
)

# import observed data (will return a list of `DataSet` objects)
dataSet <- loadDataSetsFromExcel(
  xlsFilePath = getTestDataFilePath("CompiledDataSetStevens2012.xlsx"),
  importerConfiguration = loadDataImporterConfiguration(getTestDataFilePath("ImporterConfiguration.xml"))
)

# create a new instance and add datasets
myCombDat <- DataCombined$new()
myCombDat$addDataSets(dataSet)
myCombDat$addSimulationResults(
  simResults,
  quantitiesOrPaths = c(
    "Organism|Lumen|Stomach|Metformin|Gastric retention",
    "Organism|Lumen|Stomach|Metformin|Gastric retention distal",
    "Organism|Lumen|Stomach|Metformin|Gastric retention proximal"
  )
)

myCombDat$setGroups(
  names = c(
    "Organism|Lumen|Stomach|Metformin|Gastric retention",
    "Organism|Lumen|Stomach|Metformin|Gastric retention distal",
    "Organism|Lumen|Stomach|Metformin|Gastric retention proximal",
    "Stevens_2012_placebo.Placebo_total",
    "Stevens_2012_placebo.Placebo_distal",
    "Stevens_2012_placebo.Placebo_proximal"
  ),
  groups = c("Solid total", "Solid distal", "Solid proximal", "Solid total", "Solid distal", "Solid proximal")
)

plotObservedVsSimulated(myCombDat)

Example-2

  simFilePath <- system.file("extdata", "Aciclovir.pkml", package = "ospsuite")
  sim <- loadSimulation(simFilePath)

  simResults <- runSimulation(sim)

  obsData <- lapply(
    c("ObsDataAciclovir_1.pkml", "ObsDataAciclovir_2.pkml", "ObsDataAciclovir_3.pkml"),
    function(x) loadDataSetFromPKML(system.file("extdata", x, package = "ospsuite"))
  )

  names(obsData) <- lapply(obsData, function(x) x$name)

  outputPath <- "Organism|PeripheralVenousBlood|Aciclovir|Plasma (Peripheral Venous Blood)"
  myDataCombined <- DataCombined$new()

  # Add simulated results
  myDataCombined$addSimulationResults(
    simulationResults = simResults,
    quantitiesOrPaths = outputPath,
    groups = "Aciclovir PVB"
  )

  # Add observed data set
  myDataCombined$addDataSets(obsData$`Vergin 1995.Iv`, groups = "Aciclovir PVB")

  plotObservedVsSimulated(myDataCombined)

[IndrajeetPatil]

@PavelBal Builds passing now.

Skipping a few tests on CI that won't pass until Open-Systems-Pharmacology/TLF-Library#367 is resolved. But since the PR has already grown to a monstrous size, there is no reason to postpone this until all issues are resolved.

I will make a new PR once that issue is resolved.