diff --git a/DESCRIPTION b/DESCRIPTION index db051ccf5..6a1f071ee 100644 --- 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 index 7ba7606b2..042c2ddba 100644 --- 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 index fa210106e..246db35ef 100644 --- 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 index 1b88b31da..cf2f14bc4 100644 --- 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 index 7c69225b7..451a914eb 100644 --- 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 index df81a1931..d7e2e9de0 100644 --- 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 index 2c9599b6a..7e4c253f2 100644 --- 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 index 21a891a3d..1cd01bdbf 100644 --- 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 index f07b8a6ea..46c1fb424 100644 --- 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$getValuesByPath(path, individualIds, stopIfNotFound) } diff --git a/inst/lib/OSPSuite.Assets.dll b/inst/lib/OSPSuite.Assets.dll index b5f505c6e..786512c77 100644 Binary files a/inst/lib/OSPSuite.Assets.dll and b/inst/lib/OSPSuite.Assets.dll differ diff --git a/inst/lib/OSPSuite.Core.dll b/inst/lib/OSPSuite.Core.dll index b11c7effe..237f33c52 100644 Binary files a/inst/lib/OSPSuite.Core.dll and b/inst/lib/OSPSuite.Core.dll differ diff --git a/inst/lib/OSPSuite.Infrastructure.Autofac.dll b/inst/lib/OSPSuite.Infrastructure.Autofac.dll index 5ea862156..e5129f49e 100644 Binary files a/inst/lib/OSPSuite.Infrastructure.Autofac.dll and b/inst/lib/OSPSuite.Infrastructure.Autofac.dll differ diff --git a/inst/lib/OSPSuite.Infrastructure.Import.dll b/inst/lib/OSPSuite.Infrastructure.Import.dll index 60864fb8e..58595e61e 100644 Binary files a/inst/lib/OSPSuite.Infrastructure.Import.dll and b/inst/lib/OSPSuite.Infrastructure.Import.dll differ diff --git a/inst/lib/OSPSuite.Infrastructure.dll b/inst/lib/OSPSuite.Infrastructure.dll index e20d9367f..48b8dda92 100644 Binary files a/inst/lib/OSPSuite.Infrastructure.dll and b/inst/lib/OSPSuite.Infrastructure.dll differ diff --git a/inst/lib/OSPSuite.R.dll b/inst/lib/OSPSuite.R.dll index 66aef657f..3024627d6 100644 Binary files a/inst/lib/OSPSuite.R.dll and b/inst/lib/OSPSuite.R.dll differ diff --git a/man/ApiConfig.Rd b/man/ApiConfig.Rd index e2c075e4c..581b8fcdd 100644 --- a/man/ApiConfig.Rd +++ b/man/ApiConfig.Rd @@ -28,6 +28,7 @@ Global configuration for the OSPSuite .NET API \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} } \out{
} } diff --git a/man/Application.Rd b/man/Application.Rd index 79e35eb80..78cdbab12 100644 --- a/man/Application.Rd +++ b/man/Application.Rd @@ -30,6 +30,7 @@ Application representing one instance of an application in a Simulation \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} \item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-initialize}{\code{ospsuite::DotNetWrapper$initialize()}}\out{} } \out{
} diff --git a/man/Container.Rd b/man/Container.Rd index 066eddbef..add59b032 100644 --- a/man/Container.Rd +++ b/man/Container.Rd @@ -26,6 +26,7 @@ Contains other entities such as Parameter or containers \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} \item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-initialize}{\code{ospsuite::DotNetWrapper$initialize()}}\out{} } \out{
} diff --git a/man/DotNetWrapper.Rd b/man/DotNetWrapper.Rd index f92f06a73..1b7259f4a 100644 --- a/man/DotNetWrapper.Rd +++ b/man/DotNetWrapper.Rd @@ -29,6 +29,7 @@ Wrapper class for .net Object \subsection{Public methods}{ \itemize{ \item \href{#method-new}{\code{DotNetWrapper$new()}} +\item \href{#method-finalize}{\code{DotNetWrapper$finalize()}} } } \if{html}{ @@ -56,5 +57,14 @@ Initialize a new instance of the class \subsection{Returns}{ A new \code{DotNetWrapper} object. } +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-finalize}{}}} +\subsection{Method \code{finalize()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DotNetWrapper$finalize()}\if{html}{\out{
}} +} + } } diff --git a/man/Formula.Rd b/man/Formula.Rd index e4ab38816..5ed78dfd7 100644 --- a/man/Formula.Rd +++ b/man/Formula.Rd @@ -44,6 +44,7 @@ A table formula of the model (Typically related to a \code{Quantity} such as a p \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} \item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-initialize}{\code{ospsuite::DotNetWrapper$initialize()}}\out{} } \out{
} @@ -105,6 +106,7 @@ Print the formula to the console without the name of the class \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} \item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-initialize}{\code{ospsuite::DotNetWrapper$initialize()}}\out{} } \out{
} diff --git a/man/IndividualCharacteristics.Rd b/man/IndividualCharacteristics.Rd index d025964d6..cf8b623ec 100644 --- a/man/IndividualCharacteristics.Rd +++ b/man/IndividualCharacteristics.Rd @@ -42,6 +42,7 @@ Characteristics of an individual describing its origin \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} } \out{
} } diff --git a/man/Interval.Rd b/man/Interval.Rd index ea404da34..d4011b08e 100644 --- a/man/Interval.Rd +++ b/man/Interval.Rd @@ -32,6 +32,7 @@ Simulation Interval (typically associated with an instace of \code{OutputSchema} \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} \item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-initialize}{\code{ospsuite::DotNetWrapper$initialize()}}\out{} } \out{
} diff --git a/man/Molecule.Rd b/man/Molecule.Rd index 378cfee18..d657115f6 100644 --- a/man/Molecule.Rd +++ b/man/Molecule.Rd @@ -32,8 +32,9 @@ see https://docs.open-systems-pharmacology.org/working-with-mobi/mobi-documentat } } \if{html}{ -\out{
Inherited methods} +\out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} \item \out{}\href{../../ospsuite/html/Quantity.html#method-hasUnit}{\code{ospsuite::Quantity$hasUnit()}}\out{} \item \out{}\href{../../ospsuite/html/Quantity.html#method-printQuantityValue}{\code{ospsuite::Quantity$printQuantityValue()}}\out{} \item \out{}\href{../../ospsuite/html/Quantity.html#method-printValue}{\code{ospsuite::Quantity$printValue()}}\out{} diff --git a/man/OutputSchema.Rd b/man/OutputSchema.Rd index 28960f064..c0881814c 100644 --- a/man/OutputSchema.Rd +++ b/man/OutputSchema.Rd @@ -34,6 +34,7 @@ Output schema associated with a given simulation \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} \item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-initialize}{\code{ospsuite::DotNetWrapper$initialize()}}\out{} } \out{
} diff --git a/man/OutputSelections.Rd b/man/OutputSelections.Rd index f592d8f58..748fa7d57 100644 --- a/man/OutputSelections.Rd +++ b/man/OutputSelections.Rd @@ -29,6 +29,7 @@ List of selected quantities selected as output for a given simulation \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} \item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-initialize}{\code{ospsuite::DotNetWrapper$initialize()}}\out{} } \out{
} diff --git a/man/PKParameter.Rd b/man/PKParameter.Rd index 73d9862b3..df35fefae 100644 --- a/man/PKParameter.Rd +++ b/man/PKParameter.Rd @@ -35,6 +35,7 @@ Standard PK Parameters defined in the OSPSuite \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} \item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-initialize}{\code{ospsuite::DotNetWrapper$initialize()}}\out{} } \out{
} diff --git a/man/PKParameterSensitivity.Rd b/man/PKParameterSensitivity.Rd index 4ba014b5a..ba7829053 100644 --- a/man/PKParameterSensitivity.Rd +++ b/man/PKParameterSensitivity.Rd @@ -32,6 +32,7 @@ Sensitivity of a PK Parameter for one output for a given parameter \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} \item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-initialize}{\code{ospsuite::DotNetWrapper$initialize()}}\out{} } \out{
} diff --git a/man/Parameter.Rd b/man/Parameter.Rd index e6fda34cf..3f88ab381 100644 --- a/man/Parameter.Rd +++ b/man/Parameter.Rd @@ -31,8 +31,9 @@ Derived from \link{Quantity}, please see base class documentation. } } \if{html}{ -\out{
Inherited methods} +\out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} \item \out{}\href{../../ospsuite/html/Quantity.html#method-hasUnit}{\code{ospsuite::Quantity$hasUnit()}}\out{} \item \out{}\href{../../ospsuite/html/Quantity.html#method-printQuantityValue}{\code{ospsuite::Quantity$printQuantityValue()}}\out{} \item \out{}\href{../../ospsuite/html/Quantity.html#method-printValue}{\code{ospsuite::Quantity$printValue()}}\out{} diff --git a/man/ParameterRange.Rd b/man/ParameterRange.Rd index 071d79588..c96fd81ff 100644 --- a/man/ParameterRange.Rd +++ b/man/ParameterRange.Rd @@ -33,6 +33,7 @@ A parameter rnage typically used in the definition of \code{PopulationCharacteri \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} } \out{
} } diff --git a/man/Population.Rd b/man/Population.Rd index 27018eb8e..c7d4c395f 100644 --- a/man/Population.Rd +++ b/man/Population.Rd @@ -39,6 +39,7 @@ List of individuals used in a population simulation \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} \item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-initialize}{\code{ospsuite::DotNetWrapper$initialize()}}\out{} } \out{
} diff --git a/man/PopulationCharacteristics.Rd b/man/PopulationCharacteristics.Rd index 28b43ecc8..ba5ccdcc8 100644 --- a/man/PopulationCharacteristics.Rd +++ b/man/PopulationCharacteristics.Rd @@ -46,6 +46,7 @@ Characteristics of a population used for population creation \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} } \out{
} } diff --git a/man/Quantity.Rd b/man/Quantity.Rd index a8e8e9f42..09dfdff0f 100644 --- a/man/Quantity.Rd +++ b/man/Quantity.Rd @@ -56,6 +56,7 @@ A quantity of the model (with unit, value) such as a Parameter or an Amount \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} } \out{
} } diff --git a/man/QuantityPKParameter.Rd b/man/QuantityPKParameter.Rd index 4cb6eeda7..1ee189b37 100644 --- a/man/QuantityPKParameter.Rd +++ b/man/QuantityPKParameter.Rd @@ -36,6 +36,7 @@ pK-Parameter values for all indiviudals of a simulation (1 or more) calculated f \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} } \out{
} } diff --git a/man/QuantitySelection.Rd b/man/QuantitySelection.Rd index 9631af3b6..19aa4c3a7 100644 --- a/man/QuantitySelection.Rd +++ b/man/QuantitySelection.Rd @@ -28,6 +28,7 @@ List of quantities selected as output for a given simulation \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} \item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-initialize}{\code{ospsuite::DotNetWrapper$initialize()}}\out{} } \out{
} diff --git a/man/SensitivityAnalysis.Rd b/man/SensitivityAnalysis.Rd index 1d4c7d71e..7446c5ed1 100644 --- a/man/SensitivityAnalysis.Rd +++ b/man/SensitivityAnalysis.Rd @@ -37,6 +37,7 @@ with a value that was overriden by the user} \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} } \out{
} } diff --git a/man/SensitivityAnalysisResults.Rd b/man/SensitivityAnalysisResults.Rd index 264d9f408..1b773bf42 100644 --- a/man/SensitivityAnalysisResults.Rd +++ b/man/SensitivityAnalysisResults.Rd @@ -36,6 +36,7 @@ This will be a subset of all potential PK-Parameters available in the system} \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} } \out{
} } diff --git a/man/SensitivityAnalysisRunOptions.Rd b/man/SensitivityAnalysisRunOptions.Rd index 1f9021274..8e26217a6 100644 --- a/man/SensitivityAnalysisRunOptions.Rd +++ b/man/SensitivityAnalysisRunOptions.Rd @@ -29,6 +29,7 @@ Options to be passed to the sensitivity analysis engine \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} } \out{
} } diff --git a/man/Simulation.Rd b/man/Simulation.Rd index 3901848ec..c8d543236 100644 --- a/man/Simulation.Rd +++ b/man/Simulation.Rd @@ -43,6 +43,7 @@ An OSPSuite simulation \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} } \out{
} } diff --git a/man/SimulationPKAnalyses.Rd b/man/SimulationPKAnalyses.Rd index c3b6d26ba..df35ec68c 100644 --- a/man/SimulationPKAnalyses.Rd +++ b/man/SimulationPKAnalyses.Rd @@ -33,6 +33,7 @@ pK-Analyses of a simulation (either individual or population simulation). \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} } \out{
} } diff --git a/man/SimulationResults.Rd b/man/SimulationResults.Rd index 4016a5295..eaec050e2 100644 --- a/man/SimulationResults.Rd +++ b/man/SimulationResults.Rd @@ -38,6 +38,7 @@ Results of a simulation run (either individual or population simulation) \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} } \out{
} } @@ -96,7 +97,8 @@ Returns \code{TRUE} if results are available for the individual with id \code{in \item{\code{individualIds}}{One or more individual ids for which values should be returned} -\item{\code{stopIfNotFound}}{If \code{TRUE} (default) an error is thrown if no values could be found for the \code{path}/} +\item{\code{stopIfNotFound}}{If \code{TRUE} (default) an error is thrown if no values could be found for the \code{path}/ +If \code{FALSE}, a list of \code{NA} values is returned} } \if{html}{\out{}} } diff --git a/man/SimulationRunOptions.Rd b/man/SimulationRunOptions.Rd index 5b5a6d2fc..e055edd9b 100644 --- a/man/SimulationRunOptions.Rd +++ b/man/SimulationRunOptions.Rd @@ -32,6 +32,7 @@ Default is \code{getOSPSuiteSetting("numberOfCores")}.} \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} } \out{
} } diff --git a/man/SimulationSettings.Rd b/man/SimulationSettings.Rd index 2c5b52b66..eff4f38c4 100644 --- a/man/SimulationSettings.Rd +++ b/man/SimulationSettings.Rd @@ -30,6 +30,7 @@ Settings associated with a given simulation \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} \item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-initialize}{\code{ospsuite::DotNetWrapper$initialize()}}\out{} } \out{
} diff --git a/man/SnapshotParameter.Rd b/man/SnapshotParameter.Rd index 83415290d..50bc482d1 100644 --- a/man/SnapshotParameter.Rd +++ b/man/SnapshotParameter.Rd @@ -31,6 +31,7 @@ A parameter typically used in the definition of \code{IndividualCharacteristics} \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} } \out{
} } diff --git a/man/SolverSettings.Rd b/man/SolverSettings.Rd index f9e0b5809..fb99bb741 100644 --- a/man/SolverSettings.Rd +++ b/man/SolverSettings.Rd @@ -38,6 +38,7 @@ Solver settings associated with a given simulation \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} \item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-initialize}{\code{ospsuite::DotNetWrapper$initialize()}}\out{} } \out{
} diff --git a/man/UserDefinedPKParameter.Rd b/man/UserDefinedPKParameter.Rd index 94b9e44b2..87f1c59fa 100644 --- a/man/UserDefinedPKParameter.Rd +++ b/man/UserDefinedPKParameter.Rd @@ -50,6 +50,7 @@ See \code{StandardPKParameter} enum for all possible pk parameters} \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} \item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-initialize}{\code{ospsuite::DotNetWrapper$initialize()}}\out{} } \out{
} diff --git a/man/ValuePoint.Rd b/man/ValuePoint.Rd index 640fcdb9c..e8007202f 100644 --- a/man/ValuePoint.Rd +++ b/man/ValuePoint.Rd @@ -30,6 +30,7 @@ An entry (x, y) in a table formula \if{html}{ \out{
Inherited methods} \itemize{ +\item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-finalize}{\code{ospsuite::DotNetWrapper$finalize()}}\out{} \item \out{}\href{../../ospsuite/html/DotNetWrapper.html#method-initialize}{\code{ospsuite::DotNetWrapper$initialize()}}\out{} } \out{
} diff --git a/man/createIndividualCharacteristics.Rd b/man/createIndividualCharacteristics.Rd index bbbe35775..45cb80efb 100644 --- a/man/createIndividualCharacteristics.Rd +++ b/man/createIndividualCharacteristics.Rd @@ -8,7 +8,7 @@ createIndividualCharacteristics( species, population = NULL, gender = NULL, - weight, + weight = NULL, weightUnit = "kg", height = NULL, heightUnit = "cm", diff --git a/man/getContainer.Rd b/man/getContainer.Rd index ff3917df8..10db105b8 100644 --- a/man/getContainer.Rd +++ b/man/getContainer.Rd @@ -11,8 +11,8 @@ getContainer(path, container, stopIfNotFound = TRUE) \item{container}{A Container or Simulation used to find the containers} -\item{stopIfNotFound}{Boolean. If TRUE and no container exist for the given path, -an error is thrown. Default is TRUE.} +\item{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.} } \value{ The \code{Container} with the given path. If the container for the path diff --git a/man/getEntity.Rd b/man/getEntity.Rd index e79d85cf7..8e0c378bf 100644 --- a/man/getEntity.Rd +++ b/man/getEntity.Rd @@ -13,8 +13,8 @@ getEntity(path, container, entityType, stopIfNotFound = TRUE) \item{entityType}{Class of the type that should be returned. Supported types are Container, Quantity, and Parameter} -\item{stopIfNotFound}{Boolean. If TRUE and no parameter exist for the given path, -an error is thrown. Default is TRUE.} +\item{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.} } \value{ The \code{Entity} with the given path coerced to the \code{entityType}. diff --git a/man/getMolecule.Rd b/man/getMolecule.Rd index 2944b964d..fcc5e4f2a 100644 --- a/man/getMolecule.Rd +++ b/man/getMolecule.Rd @@ -11,8 +11,8 @@ getMolecule(path, container, stopIfNotFound = TRUE) \item{container}{A Container or Simulation used to find the molecules} -\item{stopIfNotFound}{Boolean. If TRUE and no molecule exist for the given path, -an error is thrown. Default is TRUE.} +\item{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.} } \value{ The \code{Molecule} with the given path. If the molecule for the path diff --git a/man/getOutputValues.Rd b/man/getOutputValues.Rd index f243b88c8..c1f037618 100644 --- a/man/getOutputValues.Rd +++ b/man/getOutputValues.Rd @@ -26,7 +26,8 @@ If quantitiesOrPaths is \code{NULL} (default value), returns the results for all \item{individualIds}{\code{numeric} IDs of individiuals for which the results should be extracted. By default, all individuals from the results are considered. If the individual with the provided ID is not found, the ID is ignored} -\item{stopIfNotFound}{Boolean. If TRUE and no result exist for the given path, an error is thrown. Default is \code{TRUE}} +\item{stopIfNotFound}{If \code{TRUE} (default) an error is thrown if no results exist for any \code{path} +If \code{FALSE}, a list of \code{NA} values is returned for the repsecitve path.} } \description{ The function receives an object of simulation results generated by running the simulation diff --git a/man/getParameter.Rd b/man/getParameter.Rd index d1125cb46..7d36a1d10 100644 --- a/man/getParameter.Rd +++ b/man/getParameter.Rd @@ -11,8 +11,8 @@ getParameter(path, container, stopIfNotFound = TRUE) \item{container}{A Container or Simulation used to find the parameters} -\item{stopIfNotFound}{Boolean. If TRUE and no parameter exist for the given path, -an error is thrown. Default is TRUE.} +\item{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.} } \value{ The \code{Parameter} with the given path. If the parameter for the path diff --git a/man/getQuantity.Rd b/man/getQuantity.Rd index bda8fbddf..36854b859 100644 --- a/man/getQuantity.Rd +++ b/man/getQuantity.Rd @@ -11,8 +11,8 @@ getQuantity(path, container, stopIfNotFound = TRUE) \item{container}{A Container or Simulation used to find the parameters} -\item{stopIfNotFound}{Boolean. If TRUE and no quantity exist for the given path, -an error is thrown. Default is TRUE.} +\item{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.} } \value{ The \code{Quantity} with the given path. If the quantity for the path diff --git a/man/pkParameterByName.Rd b/man/pkParameterByName.Rd index e315c5707..a42f29be0 100644 --- a/man/pkParameterByName.Rd +++ b/man/pkParameterByName.Rd @@ -9,7 +9,8 @@ pkParameterByName(name, stopIfNotFound = TRUE) \arguments{ \item{name}{Name of PK-Parameter to update} -\item{stopIfNotFound}{Indicates whether an exception is thrown when the PK-Parameter was not found. Default is \code{TRUE}} +\item{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.} } \description{ Returns an instance of a PK-Parameter by name or NULL if the parameter by name is not found diff --git a/packages.config b/packages.config index a4ec6a39e..8106772b0 100644 --- a/packages.config +++ b/packages.config @@ -1,11 +1,11 @@ - - - - - - + + + + + + diff --git a/tests/testthat/test-utilities-parameter.R b/tests/testthat/test-utilities-parameter.R index f0ff9b695..80b124de7 100644 --- a/tests/testthat/test-utilities-parameter.R +++ b/tests/testthat/test-utilities-parameter.R @@ -198,6 +198,7 @@ test_that("It return the full path for a parameter that does not exist", { test_that("It return the display paths for a vector of parameters", { path1 <- toPathString(c("Organism", "Liver", "Intracellular", "Volume")) path2 <- toPathString(c("Organism", "Liver", "Volume")) - displayPath <- getParameterDisplayPaths(c(path1, path2), sim) - expect_identical(displayPath, c("Liver-Intracellular-Volume", "Liver-Volume")) + path3 <- toPathString(c("Organism", "Age")) + displayPath <- getParameterDisplayPaths(c(path1, path2, path3), sim) + expect_identical(displayPath, c("Liver-Intracellular-Volume", "Liver-Volume", "Age")) }) diff --git a/tests/testthat/test-utilities-simulation-results.R b/tests/testthat/test-utilities-simulation-results.R index c25d0fae7..3eb90bfc0 100644 --- a/tests/testthat/test-utilities-simulation-results.R +++ b/tests/testthat/test-utilities-simulation-results.R @@ -13,7 +13,16 @@ NUMBER_OF_EXTRA_COLUMNS <- NUMBER_OF_STATIC_COLUMNS + NUMBER_OF_COVARIATES_COLUM context("getOutputValues") test_that("It throws an error when no valid simulation results are provided", { - expect_error(getOutputValues(sim, resultsPaths)) + expect_error(getOutputValues(individualResults, "NoPath")) +}) + +test_that("It returns an array of NA if specific result is not found and stopIfNotFound = FALSE", { + res <- getOutputValues(individualResults, "NoPath", stopIfNotFound = FALSE) + + data <- res$data + expect_equal(length(data), 1 + NUMBER_OF_STATIC_COLUMNS) + + expect_true(all(is.na(data$NoPath))) }) test_that("It can retrieve values without a population specified", {