diff --git a/R/utilities-mass-balance.R b/R/utilities-mass-balance.R
index ccc5e270..327d44eb 100644
--- a/R/utilities-mass-balance.R
+++ b/R/utilities-mass-balance.R
@@ -32,7 +32,7 @@ plotMeanMassBalance <- function(structureSet, settings = NULL) {
   for (plotSettings in massBalanceSettings) {
     compoundNames <- as.character(plotSettings$Molecules)
     # Sub section using settings name
-    if(!isEmpty(plotSettings$Name)){
+    if (!isEmpty(plotSettings$Name)) {
       sectionId <- defaultFileNames$resultID(length(massBalanceResults) + 1, "mass_balance")
       massBalanceResults[[sectionId]] <- saveTaskResults(
         id = sectionId,
@@ -198,7 +198,7 @@ plotMeanMassBalance <- function(structureSet, settings = NULL) {
       "mass_balance",
       structureSet$simulationSet$simulationSetName
     )
-    
+
     pieChartData <- massBalanceData %>%
       filter(Time == max(Time)) %>%
       mutate(LegendWithPercent = paste(
@@ -227,10 +227,10 @@ plotMeanMassBalance <- function(structureSet, settings = NULL) {
       id = pieChartID,
       plot = pieChartPlot,
       plotCaption = captions$massBalance$pieChart(
-        timeCaption, 
+        timeCaption,
         metaData$Time$unit,
         compoundNames
-        )
+      )
     )
 
     # Table of mass balance time profiles
@@ -326,9 +326,9 @@ getMassBalanceDataMapping <- function(plotType) {
 }
 
 #' @title getApplicationResults
-#' @description Get a data.frame of application results corresponding to 
+#' @description Get a data.frame of application results corresponding to
 #' total drug mass as a function of time.
-#' @param applications 
+#' @param applications
 #' list of `Application` objects queried by the method `simulation$allApplicationsFor()`
 #' @return A data.frame that includes `time`, `drugMass` and `totalDrugMass` as variables
 #' @import ospsuite
@@ -339,13 +339,13 @@ getApplicationResults <- function(applications) {
   applicationResults <- data.frame()
   for (application in applications) {
     applicationResults <- rbind.data.frame(
-        applicationResults,
-        data.frame(
-          time = application$startTime$value,
-          drugMass = application$drugMass$value
-        )
+      applicationResults,
+      data.frame(
+        time = application$startTime$value,
+        drugMass = application$drugMass$value
       )
-    }
+    )
+  }
   # Total drug mass is cumulative sum of all the applied drug mass
   applicationResults <- applicationResults %>%
     mutate(totalDrugMass = cumsum(drugMass))
@@ -376,25 +376,27 @@ getMassBalanceData <- function(groupings, compoundNames, simulation, simulationR
     # Exclusion criteria
     excludedMoleculePaths <- NULL
     # If ExcludePreviousGroupings is TRUE, exclude molecules from previous groupings
-    if(group$ExcludePreviousGroupings %||% TRUE){
+    if (group$ExcludePreviousGroupings %||% TRUE) {
       excludedMoleculePaths <- previouslyIncludedMoleculePaths
     }
     if (!is.null(group$Exclude)) {
       excludedMolecules <- ospsuite::getAllMoleculesMatching(group$Exclude, simulation)
       excludedMoleculePaths <- c(
         excludedMoleculePaths,
-        sapply(excludedMolecules, function(molecule){molecule$path})
+        sapply(excludedMolecules, function(molecule) {
+          molecule$path
+        })
       )
     }
     includedMolecules <- includedMolecules[!includedMoleculePaths %in% excludedMoleculePaths]
     includedMoleculePaths <- setdiff(includedMoleculePaths, excludedMoleculePaths)
-    if(isEmpty(includedMoleculePaths)) {
+    if (isEmpty(includedMoleculePaths)) {
       warning(messages$noMoleculePathsIncluded(group$Name), call. = FALSE)
       next
     }
     validateMoleculesFromCompounds(includedMolecules, compoundNames)
     checkMoleculesAlreadyIncluded(includedMoleculePaths, previouslyIncludedMoleculePaths)
-    
+
     previouslyIncludedMoleculePaths <- c(
       previouslyIncludedMoleculePaths,
       includedMoleculePaths
@@ -408,7 +410,7 @@ getMassBalanceData <- function(groupings, compoundNames, simulation, simulationR
       }
     )
     moleculeAmounts <- rowSums(as.data.frame(moleculeAmounts))
-    
+
     massBalanceData <- rbind.data.frame(
       massBalanceData,
       data.frame(
@@ -424,7 +426,7 @@ getMassBalanceData <- function(groupings, compoundNames, simulation, simulationR
 
 #' @title defaultMassBalanceGrouping
 #' @description Get mass balance default inclusion/exclusion defined as groupings list
-#' Default groups are 
+#' Default groups are
 #' \itemize{
 #' \item Plasma
 #' \item BloodCells
@@ -440,9 +442,8 @@ getMassBalanceData <- function(groupings, compoundNames, simulation, simulationR
 #' @import ospsuite
 #' @keywords internal
 defaultMassBalanceGroupings <- function(compoundNames) {
-  
   groupNames <- c(
-    "Plasma", 
+    "Plasma",
     "BloodCells",
     "Interstitial",
     "Intracellular",
@@ -450,8 +451,8 @@ defaultMassBalanceGroupings <- function(compoundNames) {
     "Gallbladder",
     "Urine",
     "Feces"
-    )
-  
+  )
+
   defaultGroupings <- c(
     lapply(
       groupNames,
diff --git a/man/CalculatePKParametersTask.Rd b/man/CalculatePKParametersTask.Rd
index 9b5a06a2..4e9d409a 100644
--- a/man/CalculatePKParametersTask.Rd
+++ b/man/CalculatePKParametersTask.Rd
@@ -8,7 +8,7 @@ R6 class for defining how pk parameters are calculated and save
 }
 \keyword{internal}
 \section{Super classes}{
-\code{ospsuite.reportingengine::Task} -> \code{ospsuite.reportingengine::SimulationTask} -> \code{CalculatePKParametersTask}
+\code{\link[ospsuite.reportingengine:Task]{ospsuite.reportingengine::Task}} -> \code{\link[ospsuite.reportingengine:SimulationTask]{ospsuite.reportingengine::SimulationTask}} -> \code{CalculatePKParametersTask}
 }
 \section{Public fields}{
 \if{html}{\out{<div class="r6-fields">}}
diff --git a/man/GofPlotTask.Rd b/man/GofPlotTask.Rd
index 05956913..be247a99 100644
--- a/man/GofPlotTask.Rd
+++ b/man/GofPlotTask.Rd
@@ -32,7 +32,7 @@ Other workflow tasks:
 }
 \concept{workflow tasks}
 \section{Super classes}{
-\code{ospsuite.reportingengine::Task} -> \code{ospsuite.reportingengine::PlotTask} -> \code{GofPlotTask}
+\code{\link[ospsuite.reportingengine:Task]{ospsuite.reportingengine::Task}} -> \code{\link[ospsuite.reportingengine:PlotTask]{ospsuite.reportingengine::PlotTask}} -> \code{GofPlotTask}
 }
 \section{Methods}{
 \subsection{Public methods}{
diff --git a/man/GofTaskSettings.Rd b/man/GofTaskSettings.Rd
index b4e588d3..f37803b2 100644
--- a/man/GofTaskSettings.Rd
+++ b/man/GofTaskSettings.Rd
@@ -39,7 +39,7 @@ workflow$plotTimeProfilesAndResiduals$settings$getStatistics()
 }
 \keyword{internal}
 \section{Super class}{
-\code{ospsuite.reportingengine::TaskSettings} -> \code{GofTaskSettings}
+\code{\link[ospsuite.reportingengine:TaskSettings]{ospsuite.reportingengine::TaskSettings}} -> \code{GofTaskSettings}
 }
 \section{Public fields}{
 \if{html}{\out{<div class="r6-fields">}}
diff --git a/man/MeanModelWorkflow.Rd b/man/MeanModelWorkflow.Rd
index 4c6a11f7..341fb0fa 100644
--- a/man/MeanModelWorkflow.Rd
+++ b/man/MeanModelWorkflow.Rd
@@ -13,7 +13,7 @@ Other workflows:
 }
 \concept{workflows}
 \section{Super class}{
-\code{ospsuite.reportingengine::Workflow} -> \code{MeanModelWorkflow}
+\code{\link[ospsuite.reportingengine:Workflow]{ospsuite.reportingengine::Workflow}} -> \code{MeanModelWorkflow}
 }
 \section{Public fields}{
 \if{html}{\out{<div class="r6-fields">}}
diff --git a/man/PlotTask.Rd b/man/PlotTask.Rd
index 9b2d86bf..42ed480d 100644
--- a/man/PlotTask.Rd
+++ b/man/PlotTask.Rd
@@ -32,7 +32,7 @@ Other workflow tasks:
 }
 \concept{workflow tasks}
 \section{Super class}{
-\code{ospsuite.reportingengine::Task} -> \code{PlotTask}
+\code{\link[ospsuite.reportingengine:Task]{ospsuite.reportingengine::Task}} -> \code{PlotTask}
 }
 \section{Public fields}{
 \if{html}{\out{<div class="r6-fields">}}
diff --git a/man/PopulationPlotTask.Rd b/man/PopulationPlotTask.Rd
index 357d6ac2..7e6fc2d0 100644
--- a/man/PopulationPlotTask.Rd
+++ b/man/PopulationPlotTask.Rd
@@ -32,7 +32,7 @@ Other workflow tasks:
 }
 \concept{workflow tasks}
 \section{Super classes}{
-\code{ospsuite.reportingengine::Task} -> \code{ospsuite.reportingengine::PlotTask} -> \code{PopulationPlotTask}
+\code{\link[ospsuite.reportingengine:Task]{ospsuite.reportingengine::Task}} -> \code{\link[ospsuite.reportingengine:PlotTask]{ospsuite.reportingengine::PlotTask}} -> \code{PopulationPlotTask}
 }
 \section{Public fields}{
 \if{html}{\out{<div class="r6-fields">}}
diff --git a/man/PopulationSensitivityAnalysisTask.Rd b/man/PopulationSensitivityAnalysisTask.Rd
index f277871f..c20a58ac 100644
--- a/man/PopulationSensitivityAnalysisTask.Rd
+++ b/man/PopulationSensitivityAnalysisTask.Rd
@@ -32,7 +32,7 @@ Other workflow tasks:
 }
 \concept{workflow tasks}
 \section{Super classes}{
-\code{ospsuite.reportingengine::Task} -> \code{ospsuite.reportingengine::SensitivityAnalysisTask} -> \code{PopulationSensitivityAnalysisTask}
+\code{\link[ospsuite.reportingengine:Task]{ospsuite.reportingengine::Task}} -> \code{\link[ospsuite.reportingengine:SensitivityAnalysisTask]{ospsuite.reportingengine::SensitivityAnalysisTask}} -> \code{PopulationSensitivityAnalysisTask}
 }
 \section{Public fields}{
 \if{html}{\out{<div class="r6-fields">}}
diff --git a/man/PopulationSimulationSet.Rd b/man/PopulationSimulationSet.Rd
index cd398618..69127fd4 100644
--- a/man/PopulationSimulationSet.Rd
+++ b/man/PopulationSimulationSet.Rd
@@ -7,7 +7,7 @@
 R6 class representing Reporting Engine Population Model Set
 }
 \section{Super class}{
-\code{ospsuite.reportingengine::SimulationSet} -> \code{PopulationSimulationSet}
+\code{\link[ospsuite.reportingengine:SimulationSet]{ospsuite.reportingengine::SimulationSet}} -> \code{PopulationSimulationSet}
 }
 \section{Public fields}{
 \if{html}{\out{<div class="r6-fields">}}
diff --git a/man/PopulationWorkflow.Rd b/man/PopulationWorkflow.Rd
index 02b9d278..76fc9850 100644
--- a/man/PopulationWorkflow.Rd
+++ b/man/PopulationWorkflow.Rd
@@ -13,7 +13,7 @@ Other workflows:
 }
 \concept{workflows}
 \section{Super class}{
-\code{ospsuite.reportingengine::Workflow} -> \code{PopulationWorkflow}
+\code{\link[ospsuite.reportingengine:Workflow]{ospsuite.reportingengine::Workflow}} -> \code{PopulationWorkflow}
 }
 \section{Public fields}{
 \if{html}{\out{<div class="r6-fields">}}
diff --git a/man/QualificationTask.Rd b/man/QualificationTask.Rd
index bf1a7e22..71b8df58 100644
--- a/man/QualificationTask.Rd
+++ b/man/QualificationTask.Rd
@@ -32,7 +32,7 @@ Other workflow tasks:
 }
 \concept{workflow tasks}
 \section{Super classes}{
-\code{ospsuite.reportingengine::Task} -> \code{ospsuite.reportingengine::PlotTask} -> \code{QualificationTask}
+\code{\link[ospsuite.reportingengine:Task]{ospsuite.reportingengine::Task}} -> \code{\link[ospsuite.reportingengine:PlotTask]{ospsuite.reportingengine::PlotTask}} -> \code{QualificationTask}
 }
 \section{Methods}{
 \subsection{Public methods}{
diff --git a/man/QualificationWorkflow.Rd b/man/QualificationWorkflow.Rd
index 476cd45c..95d5de8d 100644
--- a/man/QualificationWorkflow.Rd
+++ b/man/QualificationWorkflow.Rd
@@ -13,7 +13,7 @@ Other workflows:
 }
 \concept{workflows}
 \section{Super class}{
-\code{ospsuite.reportingengine::Workflow} -> \code{QualificationWorkflow}
+\code{\link[ospsuite.reportingengine:Workflow]{ospsuite.reportingengine::Workflow}} -> \code{QualificationWorkflow}
 }
 \section{Public fields}{
 \if{html}{\out{<div class="r6-fields">}}
diff --git a/man/SensitivityAnalysisTask.Rd b/man/SensitivityAnalysisTask.Rd
index 4d9c8e74..0519313c 100644
--- a/man/SensitivityAnalysisTask.Rd
+++ b/man/SensitivityAnalysisTask.Rd
@@ -32,7 +32,7 @@ Other workflow tasks:
 }
 \concept{workflow tasks}
 \section{Super class}{
-\code{ospsuite.reportingengine::Task} -> \code{SensitivityAnalysisTask}
+\code{\link[ospsuite.reportingengine:Task]{ospsuite.reportingengine::Task}} -> \code{SensitivityAnalysisTask}
 }
 \section{Public fields}{
 \if{html}{\out{<div class="r6-fields">}}
diff --git a/man/SimulationTask.Rd b/man/SimulationTask.Rd
index 9ffd3656..49160e85 100644
--- a/man/SimulationTask.Rd
+++ b/man/SimulationTask.Rd
@@ -8,7 +8,7 @@ R6 class for SimulationTask settings
 }
 \keyword{internal}
 \section{Super class}{
-\code{ospsuite.reportingengine::Task} -> \code{SimulationTask}
+\code{\link[ospsuite.reportingengine:Task]{ospsuite.reportingengine::Task}} -> \code{SimulationTask}
 }
 \section{Public fields}{
 \if{html}{\out{<div class="r6-fields">}}
diff --git a/man/defaultMassBalanceGroupings.Rd b/man/defaultMassBalanceGroupings.Rd
index 9dbac988..3a4f06c3 100644
--- a/man/defaultMassBalanceGroupings.Rd
+++ b/man/defaultMassBalanceGroupings.Rd
@@ -11,7 +11,7 @@ defaultMassBalanceGroupings(compoundNames)
 }
 \description{
 Get mass balance default inclusion/exclusion defined as groupings list
-Default groups are 
+Default groups are
 \itemize{
 \item Plasma
 \item BloodCells
diff --git a/man/getApplicationResults.Rd b/man/getApplicationResults.Rd
index cb5cfbc2..a361694c 100644
--- a/man/getApplicationResults.Rd
+++ b/man/getApplicationResults.Rd
@@ -13,7 +13,7 @@ getApplicationResults(applications)
 A data.frame that includes `time`, `drugMass` and `totalDrugMass` as variables
 }
 \description{
-Get a data.frame of application results corresponding to 
+Get a data.frame of application results corresponding to
 total drug mass as a function of time.
 }
 \keyword{internal}