Fixes #1086 remove group_by to optimize computation and suggest paral…

…lel (#1130)

* Fixes #1086 remove group_by to optimize computation and suggest parallel

- If parallel is not installed, the regular code is used.
- Regular code tries not to run group_by that slow down the computation by a lot
- The number of cores is identified from the SimulationSettings already set up for the PK parameter calculation task

* Remove ave which did not work as expected

* Fixes #1086 ratios data.frame is pivoted into matrix

* Remove simulation set name from test data

DESCRIPTION

@@ -49,7 +49,8 @@ Suggests:
     styler,
     rClr,
     crayon,
-    webshot
+    webshot,
+    parallel
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.2.3

tests/testthat/test-monte-carlo-sampling.R

@@ -9,7 +9,6 @@ comparisonParams <- list(meanlog = 1, sdlog = 2)
 set.seed(1111)
 
 referenceData <- data.frame(
-  simulationSetName = "reference",
   IndividualId = 1:popSize,
   QuantityPath = "a",
   Parameter = "Cmax",
@@ -21,7 +20,6 @@ referenceData <- data.frame(
 )
 
 comparisonData <- data.frame(
-  simulationSetName = "test",
   IndividualId = 1:popSize,
   QuantityPath = "a",
   Parameter = "Cmax",
@@ -63,7 +61,7 @@ test_that("Monte Carlo Solution is close to known solution", {
     referencePKData = referenceData, 
     simulationSetName = "test",
     # With 10000 repetitions the method runs longer
-    settings = list(showProgress = FALSE, mcRepetitions = 200)
+    settings = list(showProgress = FALSE, numberOfCores = 1, mcRepetitions = 200)
   )
 
   expect_equal(
@@ -84,13 +82,13 @@ test_that("Monte Carlo Solution is repeatable", {
     pkData = comparisonData, 
     referencePKData = referenceData, 
     simulationSetName = "test",
-    settings = list(showProgress = FALSE, mcRepetitions = 100, mcRandomSeed = 3333)
+    settings = list(showProgress = FALSE, numberOfCores = 1, mcRepetitions = 100, mcRandomSeed = 3333)
   )
   mcSolution2 <- ospsuite.reportingengine:::getPKRatioSummaryFromMCSampling(
     pkData = comparisonData, 
     referencePKData = referenceData, 
     simulationSetName = "test",
-    settings = list(showProgress = FALSE, mcRepetitions = 100, mcRandomSeed = 3333)
+    settings = list(showProgress = FALSE, numberOfCores = 1, mcRepetitions = 100, mcRandomSeed = 3333)
   )
 
   expect_equal(mcSolution1, mcSolution2)

tests/testthat/test-pop-pk-parameters.R

@@ -150,4 +150,4 @@ updatePKParameter("AUC_tEnd", displayName = "AUC_tEnd", displayUnit = "µmol*min
 # Clear test workflow folders
 unlink(workflowPediatric$workflowFolder, recursive = TRUE)
 unlink(workflowParallel$workflowFolder, recursive = TRUE)
-#unlink(workflowRatio$workflowFolder, recursive = TRUE)
+unlink(workflowRatio$workflowFolder, recursive = TRUE)