Version 9.1.4

Open-Systems-Pharmacology · Dec 3, 2020 · 380690b · 380690b
2 parents c42a506 + 576aea6
commit 380690b
Show file tree

Hide file tree

Showing 57 changed files with 96 additions and 38 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -27,7 +27,7 @@ Suggests:
     pander
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
 Collate: 

diff --git a/R/simulation-results.R b/R/simulation-results.R
@@ -47,6 +47,7 @@ SimulationResults <- R6::R6Class(
     #' @param path Path for which values should be retrieved
     #' @param individualIds One or more individual ids for which values should be returned
     #' @param stopIfNotFound If \code{TRUE} (default) an error is thrown if no values could be found for the `path`/
+    #' If \code{FALSE}, a list of \code{NA} values is returned
     getValuesByPath = function(path, individualIds, stopIfNotFound = TRUE) {
       validateIsNumeric(individualIds)
       individualIds <- c(individualIds)

diff --git a/R/utilities-container.R b/R/utilities-container.R
@@ -49,8 +49,8 @@ getAllContainerPathsIn <- function(container) {
 #'
 #' @inherit getAllContainersMatching
 #' @param path A string representing the path relative to the \code{container}
-#' @param stopIfNotFound Boolean. If TRUE and no container exist for the given path,
-#' an error is thrown. Default is TRUE.
+#' @param stopIfNotFound Boolean. If \code{TRUE} (default) and no container exists for the given path,
+#' an error is thrown. If \code{FALSE}, \code{NULL} is returned.
 
 #' @return The \code{Container} with the given path. If the container for the path
 #' does not exist, an error is thrown if \code{stopIfNotFound} is TRUE (default),

diff --git a/R/utilities-entity.R b/R/utilities-entity.R
@@ -149,8 +149,8 @@ getAllEntityPathsIn <- function(container, entityType, method = NULL) {
 #'
 #' @inherit getAllEntitiesMatching
 #' @param path A string representing the path relative to the \code{container}
-#' @param stopIfNotFound Boolean. If TRUE and no parameter exist for the given path,
-#' an error is thrown. Default is TRUE.
+#' @param stopIfNotFound Boolean. If \code{TRUE} (default) and no entity exists for the given path,
+#' an error is thrown. If \code{FALSE}, \code{NULL} is returned.
 #' @param entityType Class of the type that should be returned. Supported types are Container, Quantity, and Parameter
 #'
 #' @return The \code{Entity} with the given path coerced to the \code{entityType}.

diff --git a/R/utilities-molecule.R b/R/utilities-molecule.R
@@ -49,8 +49,8 @@ getAllMoleculePathsIn <- function(container) {
 #'
 #' @inherit getAllMoleculesMatching
 #' @param path A string representing the path relative to the \code{container}
-#' @param stopIfNotFound Boolean. If TRUE and no molecule exist for the given path,
-#' an error is thrown. Default is TRUE.
+#' @param stopIfNotFound Boolean. If \code{TRUE} (default) and no molecule exist for the given path,
+#' an error is thrown. If \code{FALSE}, \code{NULL} is returned.
 #'
 #' @return The \code{Molecule} with the given path. If the molecule for the path
 #' does not exist, an error is thrown if \code{stopIfNotFound} is TRUE (default),

diff --git a/R/utilities-parameter.R b/R/utilities-parameter.R
@@ -48,8 +48,8 @@ getAllParameterPathsIn <- function(container) {
 #'
 #' @inherit getAllParametersMatching
 #' @param path A string representing the path relative to the \code{container}
-#' @param stopIfNotFound Boolean. If TRUE and no parameter exist for the given path,
-#' an error is thrown. Default is TRUE.
+#' @param stopIfNotFound Boolean. If \code{TRUE} (default) and no parameter exist for the given path,
+#' an error is thrown. If \code{FALSE}, \code{NULL} is returned.
 #'
 #' @return The \code{Parameter} with the given path. If the parameter for the path
 #' does not exist, an error is thrown if \code{stopIfNotFound} is TRUE (default),

diff --git a/R/utilities-pk-parameter.R b/R/utilities-pk-parameter.R
@@ -75,7 +75,8 @@ updatePKParameter <- function(name, displayName = NULL, displayUnit = NULL) {
 #' @title Returns an instance of a PK-Parameter by name or NULL if the parameter by name is not found
 #'
 #' @param name Name of PK-Parameter to update
-#' @param stopIfNotFound Indicates whether an exception is thrown when the PK-Parameter was not found. Default is \code{TRUE}
+#' @param stopIfNotFound Boolean. If \code{TRUE} (default) and no pk parameter exist for the given name,
+#' an error is thrown. If \code{FALSE}, \code{NULL} is returned.
 #'
 #' @examples
 #'

diff --git a/R/utilities-quantity.R b/R/utilities-quantity.R
@@ -48,8 +48,8 @@ getAllQuantityPathsIn <- function(container) {
 #'
 #' @inherit getAllQuantitiesMatching
 #' @param path A string representing the path relative to the \code{container}
-#' @param stopIfNotFound Boolean. If TRUE and no quantity exist for the given path,
-#' an error is thrown. Default is TRUE.
+#' @param stopIfNotFound Boolean. If \code{TRUE} (default) and no quantity exists for the given path,
+#' an error is thrown. If \code{FALSE}, \code{NULL} is returned.
 #'
 #' @return The \code{Quantity} with the given path. If the quantity for the path
 #' does not exist, an error is thrown if \code{stopIfNotFound} is TRUE (default),

diff --git a/R/utilities-simulation-results.R b/R/utilities-simulation-results.R
@@ -18,6 +18,8 @@
 #' @param population population used to calculate the simulationResults (optional). This is used only to add the population covariates to the resulting data table.
 #'
 #' @param stopIfNotFound Boolean. If TRUE and no result exist for the given path, an error is thrown. Default is \code{TRUE}
+#' @param stopIfNotFound If \code{TRUE} (default) an error is thrown if no results exist for any `path`
+#' If \code{FALSE}, a list of \code{NA} values is returned for the repsecitve path.
 #' @export
 getOutputValues <- function(simulationResults,
                             quantitiesOrPaths = NULL,
@@ -77,7 +79,7 @@ getOutputValues <- function(simulationResults,
 
 
   for (path in paths) {
-    quantity <- getQuantity(path, simulationResults$simulation)
+    quantity <- getQuantity(path, simulationResults$simulation, stopIfNotFound = stopIfNotFound)
     metaData[[path]] <- list(unit = quantity$unit, dimension = quantity$dimension)
     values[[path]] <- simulationResults$getValuesByPath(path, individualIds, stopIfNotFound)
   }

diff --git a/inst/lib/OSPSuite.Assets.dll b/inst/lib/OSPSuite.Assets.dll
diff --git a/inst/lib/OSPSuite.Core.dll b/inst/lib/OSPSuite.Core.dll
diff --git a/inst/lib/OSPSuite.Infrastructure.Autofac.dll b/inst/lib/OSPSuite.Infrastructure.Autofac.dll
diff --git a/inst/lib/OSPSuite.Infrastructure.Import.dll b/inst/lib/OSPSuite.Infrastructure.Import.dll
diff --git a/inst/lib/OSPSuite.Infrastructure.dll b/inst/lib/OSPSuite.Infrastructure.dll
diff --git a/inst/lib/OSPSuite.R.dll b/inst/lib/OSPSuite.R.dll
diff --git a/man/ApiConfig.Rd b/man/ApiConfig.Rd
diff --git a/man/Application.Rd b/man/Application.Rd
diff --git a/man/Container.Rd b/man/Container.Rd
diff --git a/man/DotNetWrapper.Rd b/man/DotNetWrapper.Rd
diff --git a/man/Formula.Rd b/man/Formula.Rd
diff --git a/man/IndividualCharacteristics.Rd b/man/IndividualCharacteristics.Rd
diff --git a/man/Interval.Rd b/man/Interval.Rd
diff --git a/man/Molecule.Rd b/man/Molecule.Rd
diff --git a/man/OutputSchema.Rd b/man/OutputSchema.Rd
diff --git a/man/OutputSelections.Rd b/man/OutputSelections.Rd
diff --git a/man/PKParameter.Rd b/man/PKParameter.Rd
diff --git a/man/PKParameterSensitivity.Rd b/man/PKParameterSensitivity.Rd
diff --git a/man/Parameter.Rd b/man/Parameter.Rd
diff --git a/man/ParameterRange.Rd b/man/ParameterRange.Rd
diff --git a/man/Population.Rd b/man/Population.Rd
diff --git a/man/PopulationCharacteristics.Rd b/man/PopulationCharacteristics.Rd
diff --git a/man/Quantity.Rd b/man/Quantity.Rd
diff --git a/man/QuantityPKParameter.Rd b/man/QuantityPKParameter.Rd
diff --git a/man/QuantitySelection.Rd b/man/QuantitySelection.Rd
diff --git a/man/SensitivityAnalysis.Rd b/man/SensitivityAnalysis.Rd
diff --git a/man/SensitivityAnalysisResults.Rd b/man/SensitivityAnalysisResults.Rd
diff --git a/man/SensitivityAnalysisRunOptions.Rd b/man/SensitivityAnalysisRunOptions.Rd
diff --git a/man/Simulation.Rd b/man/Simulation.Rd
diff --git a/man/SimulationPKAnalyses.Rd b/man/SimulationPKAnalyses.Rd