SensitivityAnalysis - use "by path" methods (#271)

* Use unlist

* Assign condition to a variable

* Skipping tests that rely on PK-Sim

* fix `createEsqlabsPlotConfiguration()`

Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>

R/sensitivityCalculation.R

@@ -104,16 +104,21 @@ sensitivityCalculation <- function(simulation,
     # Initialize `batchResultsIdMap` for the current parameter
     batchResultsIdMap[[parameterPath]] <- vector("list", length(variationRange))
     names(batchResultsIdMap[[parameterPath]]) <- variationRange
-
-    param <- getParameter(parameterPath, simulation)
-
-    if (param$isConstant) {
-      constantParamPaths <- c(constantParamPaths, parameterPath)
-    } else {
+    # Check if the parameter is given by an explicit formula
+    isExplicitFormulaByPath <- ospsuite::isExplicitFormulaByPath(
+      path = parameterPath,
+      simulation = simulation
+    )
+    if (isExplicitFormulaByPath) {
       formulaParamPaths <- c(formulaParamPaths, parameterPath)
+    } else {
+      constantParamPaths <- c(constantParamPaths, parameterPath)
     }
 
-    initialValues[[parameterPath]] <- param$value
+    initialValues[[parameterPath]] <- ospsuite::getQuantityValuesByPath(
+      quantityPaths = parameterPath,
+      simulation = simulation
+    )
   }
 
   constantParamPaths <- unlist(constantParamPaths)

R/utilities-figures.R

@@ -151,7 +151,7 @@ createEsqlabsPlotConfiguration <- function() {
   defaultPlotConfiguration$yLabelSize <- 8
   defaultPlotConfiguration$xAxisLabelTicksSize <- 8
   defaultPlotConfiguration$yAxisLabelTicksSize <- 8
-  defaultPlotConfiguration$legendCaptionSize <- 6
+  defaultPlotConfiguration$legendTitleSize <- 6
   defaultPlotConfiguration$legendPosition <- tlf::LegendPositions$outsideTop
 
   return(defaultPlotConfiguration)

appveyor.yml

@@ -18,6 +18,8 @@ environment:
   R_ARCH: x64
   KEEP_VIGNETTES: true
   NOT_CRAN: true
+  #We use this variale to skip some tests that depend on PK-Sim using "skip_on_ci"
+  CI: true
 
 version: "$(app_version).{build}"
 

tests/testthat/test-utilities-individual.R

@@ -1,4 +1,5 @@
 ## context("readIndividualCharacteristicsFromXLS")
+skip_on_ci()
 
 test_that("It returns NULL if the specified individual Id cannot be found in
           the file and nullIfNotFound is TRUE", {