313 time offset (#651)

* Fixes #313 time offset variable in simulation set for shifting time While fixing this issue, I imported ospsuite.utils in NAMESPACE so ospsuite.utils:: should not be necessary any longer * Integrate timeOffset in excel template * Document timeOffset in vignette
Open-Systems-Pharmacology · Jan 6, 2022 · 9776ad2 · 9776ad2
1 parent 426962f
commit 9776ad2
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Showing 13 changed files with 331 additions and 145 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -138,6 +138,7 @@ export(updateSimulationIndividualParameters)
 export(vpcParameterPlot)
 import(ggplot2)
 import(ospsuite)
+import(ospsuite.utils)
 import(stats)
 import(tlf)
 import(utils)

diff --git a/R/messages.R b/R/messages.R
@@ -180,11 +180,10 @@ messages <- list(
     return(paste0(callingFunction(), "Values '", paste0(data[duplicated(data)], collapse = "', '"), "' in ", dataName, " are not unique"))
   },
 
-  dataIncludedInTimeRange = function(finalSize, initialSize, timeRange, timeUnit, dataType) {
+  dataIncludedInTimeRange = function(finalSize, timeRange, timeUnit, dataType) {
     paste0(
       finalSize, " ", dataType,
-      " data were included in the analysis between ", min(timeRange), " and ", max(timeRange), " ", timeUnit,
-      ". Initial size was ", initialSize, "."
+      " data were included in the analysis between ", min(timeRange), " and ", max(timeRange), " ", timeUnit, "."
     )
   }
 )

diff --git a/R/population-simulation-set.R b/R/population-simulation-set.R
@@ -6,7 +6,7 @@
 #' @field studyDesignFile name of study design csv file
 #' @field plotReferenceObsData logical for plotting reference observed data in Pediatric and Ratio Comparison workflows
 #' @export
-#' @importFrom ospsuite.utils %||%
+#' @import ospsuite.utils
 PopulationSimulationSet <- R6::R6Class(
   "PopulationSimulationSet",
   inherit = SimulationSet,
@@ -36,12 +36,12 @@ PopulationSimulationSet <- R6::R6Class(
                           studyDesignFile = NULL,
                           plotReferenceObsData = FALSE,
                           ...) {
-      ospsuite.utils::validateIsLogical(referencePopulation)
-      ospsuite.utils::validateIsLogical(plotReferenceObsData)
-      ospsuite.utils::validateIsString(simulationSetName)
-      ospsuite.utils::validateIsString(simulationFile)
-      ospsuite.utils::validateIsString(populationFile)
-      ospsuite.utils::validateIsString(c(populationName, studyDesignFile), nullAllowed = TRUE)
+      validateIsLogical(referencePopulation)
+      validateIsLogical(plotReferenceObsData)
+      validateIsString(simulationSetName)
+      validateIsString(simulationFile)
+      validateIsString(populationFile)
+      validateIsString(c(populationName, studyDesignFile), nullAllowed = TRUE)
       validateIsFileExtension(populationFile, "csv")
 
       super$initialize(

diff --git a/R/simulation-set.R b/R/simulation-set.R
@@ -8,9 +8,10 @@
 #' @field timeUnit display unit for time variable
 #' @field applicationRanges named list of logicals defining which Application ranges are included in
 #' @field minimumSimulationEndTime is the minimum length of time for which a simulation must be run
+#' @field timeOffset shift of display time in time profile plots
 #' reported time profiles and residual plots when applicable
 #' @export
-#' @importFrom ospsuite.utils %||%
+#' @import ospsuite.utils
 SimulationSet <- R6::R6Class(
   "SimulationSet",
   public = list(
@@ -22,6 +23,7 @@ SimulationSet <- R6::R6Class(
     timeUnit = NULL,
     applicationRanges = NULL,
     minimumSimulationEndTime = NULL,
+    timeOffset = NULL,
 
     #' @description
     #' Create a new `SimulationSet` object.
@@ -33,38 +35,41 @@ SimulationSet <- R6::R6Class(
     #' @param timeUnit display unit for time variable. Default is "h"
     #' @param applicationRanges names of application ranges to include in the report. Names are available in enum `ApplicationRanges`.
     #' @param minimumSimulationEndTime is the minimum length of time for which a simulation must be run
+    #' @param timeOffset shift of display time in time profile plots
     #' @return A new `SimulationSet` object
     initialize = function(simulationSetName,
-                          simulationFile,
-                          outputs = NULL,
-                          observedDataFile = NULL,
-                          observedMetaDataFile = NULL,
-                          timeUnit = "h",
-                          applicationRanges = ApplicationRanges,
-                          minimumSimulationEndTime = NULL) {
-      # Test and validate the simulation object
-      ospsuite.utils::validateIsString(simulationSetName)
-      ospsuite.utils::validateIsString(simulationFile)
+                              simulationFile,
+                              outputs = NULL,
+                              observedDataFile = NULL,
+                              observedMetaDataFile = NULL,
+                              timeUnit = "h",
+                              applicationRanges = ApplicationRanges,
+                              minimumSimulationEndTime = NULL,
+                              timeOffset = 0) {
+      # Test and validate the simulation objects
+      validateIsString(simulationSetName)
+      validateIsString(simulationFile)
+      validateIsFileExtension(simulationFile, "pkml")
+      validateIsString(c(observedDataFile, observedMetaDataFile, timeUnit), nullAllowed = TRUE)
+      validateIsPositive(object = minimumSimulationEndTime, nullAllowed = TRUE)
+      validateIsNumeric(timeOffset)
       # For optional input, usually null is allowed
       # but not here as it would mean that nothing would be reported
-      ospsuite.utils::validateIsIncluded(c(applicationRanges), ApplicationRanges)
+      validateIsIncluded(c(applicationRanges), ApplicationRanges)
 
-      validateIsFileExtension(simulationFile, "pkml")
       simulation <- ospsuite::loadSimulation(simulationFile)
+
       # Test and validate outputs and their paths
       validateOutputObject(c(outputs), simulation, nullAllowed = TRUE)
 
-      validateIsPositive(object = minimumSimulationEndTime, nullAllowed = TRUE)
-      self$minimumSimulationEndTime <- minimumSimulationEndTime
-
-      # Test and validate observed data
-      ospsuite.utils::validateIsString(c(observedDataFile, observedMetaDataFile, timeUnit), nullAllowed = TRUE)
       if (!is.null(observedDataFile)) {
         validateObservedMetaDataFile(observedMetaDataFile, observedDataFile, c(outputs))
       }
 
       self$simulationSetName <- simulationSetName
       self$simulationFile <- simulationFile
+      self$minimumSimulationEndTime <- minimumSimulationEndTime
+      self$timeOffset <- timeOffset
 
       self$outputs <- c(outputs)
 
@@ -74,9 +79,9 @@ SimulationSet <- R6::R6Class(
       self$timeUnit <- timeUnit %||% "h"
 
       self$applicationRanges <- list(
-        total = ospsuite.utils::isIncluded(ApplicationRanges$total, applicationRanges),
-        firstApplication = ospsuite.utils::isIncluded(ApplicationRanges$firstApplication, applicationRanges),
-        lastApplication = ospsuite.utils::isIncluded(ApplicationRanges$lastApplication, applicationRanges)
+        total = isIncluded(ApplicationRanges$total, applicationRanges),
+        firstApplication = isIncluded(ApplicationRanges$firstApplication, applicationRanges),
+        lastApplication = isIncluded(ApplicationRanges$lastApplication, applicationRanges)
       )
     }
   )