Merge pull request #1196 from Open-Systems-Pharmacology/develop

Version 11.1

.Rbuildignore

@@ -1,6 +1,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^appveyor\.yml$
+(^appveyor)(.*)(.yml$)
 ^README\.md$
 ^tests/dev
 ^tools
@@ -20,7 +20,6 @@
 ^doc$
 ^docs$
 ^_pkgdown\.yml$
-^appveyor\.yml$
 ^.gitlab-ci\.yml$
 ^data-raw$
 ^pkgdown$

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: ospsuite
 Title: R package to manipulate OSPSuite Models
-Version: 11.0.0
+Version: 11.1.0
 Authors@R: 
     c(person("Open-Systems-Pharmacology Community", role = "cph"),
       person("Michael", "Sevestre", role = c("aut", "cre"), email = "michael@design2code.ca"),
@@ -12,29 +12,34 @@ Authors@R:
 Description: The ospsuite-R package provides the functionality of loading, manipulating, and simulating the simulations 
   created in the Open Systems Pharmacology Software tools PK-Sim and MoBi.
 License: GPL-2 | file LICENSE
-URL: https://github.com/open-systems-pharmacology/ospsuite-r
+URL: https://github.com/open-systems-pharmacology/ospsuite-r, 
+    https://www.open-systems-pharmacology.org/OSPSuite-R/ (release),
+    https://www.open-systems-pharmacology.org/OSPSuite-R/dev (development)
 BugReports: 
     https://github.com/open-systems-pharmacology/ospsuite-r/issues
 Depends: 
     R (>= 3.6),
     rClr (>= 0.9.1)
 Imports: 
     dplyr (>= 1.0.0),
-    ospsuite.utils (>= 1.3.0),
+    ospsuite.utils (>= 1.4.0),
     purrr,
-    R6,
     readr,
     stringr,
     tidyr,
-    tlf (>= 1.3.0)
+    ggplot2,
+    rlang,
+    tlf (>= 1.4.0)
 Suggests:
     knitr,
     rmarkdown,
     testthat (>= 3.0.3),
-    vdiffr (>= 1.0.0)
+    vdiffr (>= 1.0.0),
+    withr
+Language: en-US
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
 Collate: 
@@ -66,12 +71,14 @@ Collate:
     'output-selections.R'
     'parameter-range.R'
     'parameter.R'
-    'path-explorer.R'
     'pk-parameter-sensitivity.R'
     'pk-parameter.R'
     'pk-sim.R'
     'plot-individual-time-profile.R'
+    'plot-observed-vs-simulated.R'
     'plot-population-time-profile.R'
+    'plot-residuals-vs-simulated.R'
+    'plot-residuals-vs-time.R'
     'population-characteristics.R'
     'population.R'
     'quantity-pk-parameter.R'

NAMESPACE

@@ -34,9 +34,11 @@ export(addUserDefinedPKParameter)
 export(allAvailableDimensions)
 export(allPKParameterNames)
 export(calculatePKAnalyses)
+export(calculateResiduals)
 export(clearMemory)
 export(clearOutputIntervals)
 export(clearOutputs)
+export(convertUnits)
 export(createDistributions)
 export(createImporterConfigurationForFile)
 export(createIndividual)
@@ -69,6 +71,7 @@ export(getAllParametersForSensitivityAnalysisMatching)
 export(getAllParametersMatching)
 export(getAllQuantitiesMatching)
 export(getAllQuantityPathsIn)
+export(getAllStateVariableParametersPaths)
 export(getAllStateVariablesPaths)
 export(getBaseUnit)
 export(getContainer)
@@ -80,6 +83,7 @@ export(getOutputValues)
 export(getParameter)
 export(getParameterDisplayPaths)
 export(getQuantity)
+export(getQuantityValuesByPath)
 export(getSimulationTree)
 export(getStandardMoleculeParameters)
 export(getUnitsForDimension)
@@ -89,6 +93,7 @@ export(importPKAnalysesFromCSV)
 export(importResultsFromCSV)
 export(importSensitivityAnalysisResultsFromCSV)
 export(initPKSim)
+export(isExplicitFormulaByPath)
 export(loadAgingDataFromCSV)
 export(loadDataImporterConfiguration)
 export(loadDataSetFromPKML)
@@ -104,7 +109,10 @@ export(pkAnalysesToTibble)
 export(pkParameterByName)
 export(plotGrid)
 export(plotIndividualTimeProfile)
+export(plotObservedVsSimulated)
 export(plotPopulationTimeProfile)
+export(plotResidualsVsSimulated)
+export(plotResidualsVsTime)
 export(populationAsDataFrame)
 export(populationToDataFrame)
 export(populationToTibble)

NEWS.md

@@ -1,4 +1,39 @@
-# ospsuite 11.0 (development version)
+# ospsuite 11.1.197
+
+## New features
+
+* Adds new visualization functions:
+
+    - `plotObservedVsSimulated()` for observed versus simulated data scatter plot.
+    - `plotResidualsVsTime()` for time versus residuals data scatter plot.
+    - `plotResidualsVsSimulated()` for simulated versus residuals data scatter plot.
+
+* Adds new helper functions to work with `DataCombined` objects:
+
+    - `convertUnits()` to convert datasets in `DataCombined` to common units.
+    - `calculateResiduals()` to calculate residuals for datasets in `DataCombined`.
+
+## Major Changes
+
+* The class `SimulationBatch` gets a new property `id`.
+
+* The output of `runSimulationBatches()` is now a named list with names being 
+  the ids of `SimulationBatch`.
+
+* `calculateResiduals()` now uses `log(base = 10)` for calculation of residuals 
+in logarithmic scale instead if `log(base = exp(1))`
+* `calculateResiduals()` does also return residuals for entries where simulated 
+or observed value is 0 in logarithmic scale. These values were ignored in previous 
+versions. If the observed or simulated value is zero or negative, it is replaced 
+by an arbitrary small value `getOSPSuiteSetting("LOG_SAFE_EPSILON")` (1e-20 by default).
+
+## Minor Changes
+
+* `SimulationBatch$addRunValues()` will throw an error when any start value is `NaN`
+* `SimulatioBatch` gets methods `getVariableParameters()` and `getVariableMolecules()`
+that return list of parameter resp. molecule paths that are defined variable.
+
+# ospsuite 11.0.123
 
 ## New features
 

R/cache.R

@@ -94,7 +94,7 @@ Cache <- R6::R6Class(
       if (missing(value)) {
         ls(private$cachedObjects)
       } else {
-        stop(messages$errorPropertyReadOnly("keys"), call. = FALSE)
+        stop(messages$errorPropertyReadOnly("keys"))
       }
     }
   ),

R/container.R

@@ -2,6 +2,7 @@
 #' @docType class
 #' @description  Contains other entities such as Parameter or containers
 #' @format NULL
+#' @keywords internal
 Container <- R6::R6Class(
   "Container",
   cloneable = FALSE,