Project-based Workflow

.gitignore

@@ -57,3 +57,4 @@ tests/testthat/Rplots.pdf
 *.code-workspace
 docs
 pkgdown
+**/~\$*\.xlsx

DESCRIPTION

@@ -22,13 +22,14 @@ Depends:
     ospsuite (>= 12.1.0),
     R (>= 4.1)
 Imports:
+    cli,
     colorspace,
     dplyr,
     fs,
     ggplot2,
     grDevices,
     labeling,
-    ospsuite.parameteridentification (>= 1.3.0),
+    lifecycle,
     ospsuite.utils (>= 1.5.0),
     parallel,
     patchwork,
@@ -69,5 +70,4 @@ RoxygenNote: 7.3.2
 Remotes: 
     ospsuite.utils=Open-Systems-Pharmacology/OSPSuite.RUtils,
     tlf=Open-Systems-Pharmacology/TLF-Library,
-    ospsuite=Open-Systems-Pharmacology/OSPSuite-R,
-    Open-Systems-Pharmacology/ospsuite.parameteridentification
+    ospsuite=Open-Systems-Pharmacology/OSPSuite-R

NAMESPACE

@@ -6,10 +6,9 @@ export(ExportConfiguration)
 export(GenderInt)
 export(LLOQMode)
 export(ProjectConfiguration)
-export(Scenario)
-export(ScenarioConfiguration)
+export(ScenarioConfigurationLegacy)
+export(ScenarioLegacy)
 export(ULOQMode)
-export(applyIndividualParameters)
 export(calculateMeanDataSet)
 export(col2hsv)
 export(compareSimulations)
@@ -20,12 +19,14 @@ export(createEsqlabsExportConfiguration)
 export(createEsqlabsPlotConfiguration)
 export(createEsqlabsPlotGridConfiguration)
 export(createPlotsFromExcel)
-export(createScenarios)
+export(createProjectConfiguration)
 export(enumPutList)
 export(escapeForRegex)
 export(esqLABS_colors)
 export(esqlabsRSettingNames)
-export(example_ProjectConfiguration)
+export(exampleProject)
+export(exampleProjectConfiguration)
+export(exampleProjectConfigurationFile)
 export(executeInParallel)
 export(exportParametersToXLS)
 export(extendParameterStructure)
@@ -40,40 +41,30 @@ export(getIndexClosestToValue)
 export(getMoleculeNameFromQuantity)
 export(hillFunction)
 export(init_project)
-export(initializeSimulation)
 export(isParametersEqual)
 export(isTableFormulasEqual)
 export(loadObservedData)
 export(loadObservedDataFromPKML)
 export(loadScenarioResults)
 export(pathFromClipboard)
 export(readExcel)
-export(readIndividualCharacteristicsFromXLS)
-export(readParametersFromXLS)
-export(readPopulationCharacteristicsFromXLS)
-export(readScenarioConfigurationFromExcel)
 export(removeFromList)
-export(runScenarios)
 export(sampleRandomValue)
 export(saveScenarioResults)
 export(sensitivityCalculation)
 export(sensitivitySpiderPlot)
 export(sensitivityTimeProfiles)
 export(sensitivityTornadoPlot)
-export(setApplications)
 export(setParameterValuesByPathWithCondition)
 export(sineFunction)
 export(sourceAll)
-export(startFunctionVisualizer)
-export(startUnitConverter)
 export(stringToNum)
 export(writeIndividualToXLS)
-export(writeParameterStructureToXLS)
+import(cli)
 import(fs)
 import(ggplot2)
 import(grDevices)
 import(ospsuite)
-import(ospsuite.parameteridentification)
 import(ospsuite.utils)
 import(parallel)
 import(readxl)

NEWS.md

@@ -2,20 +2,39 @@
 
 ## Breaking changes
 
-  - Function `sensitivityCalculation()` with renamed parameter `pkDataFilePath` 
-    to `saOutputFilePath` and updated output files to include PK parameter units (\#696).
+  - Function `sensitivityCalculation()` with renamed parameter `pkDataFilePath`
+    to `saOutputFilePath` and updated output files to include PK parameter units
+    (\#696).
 
 ## Major Changes
 
+  - `createDefaultProjectConfiguration` is now soft-deprecated in favor of
+    `createProjectConfiguration`. (\#692)
+
+  - `ProjectConfiguration` fields have been renamed to be more consistant and
+    easier to understand. (\#692)
+
+  - Files and folders names in project directory have been harmonized and
+    improved (\#692)
+      - `Parameters` folder is now `Configurations`
+      - `Populations` folder is now `PopulationsCSV`
+      - `ApplicationParameters.xslx` file is now `Applications.xlsx`
+      - `PopulationParameters.xslx` file is now `Populations.xlsx`
+      - Previous directory structure is still supported but deprecated.
+
+  - `{ospsuite.parameteridentification}` is not longer a dependency of
+    `{esqlabsR}`.
+
 ## Minor improvements and bug fixes
 
   - Handle simulation failures in `sensitivityCalculation` (\#694).
 
-  - Function `sensitivityCalculation()` supports new parameter `customOutputFunctions`, 
-    allowing user-defined functions for PK parameter calculation (\#685).
-
-  - Function `sensitivitySpiderPlot` now supports `xAxisType` and `yAxisType` options 
-    for switching between percent and absolute values (\#695).
+  - Function `sensitivityCalculation()` supports new parameter
+    `customOutputFunctions`, allowing user-defined functions for PK parameter
+    calculation (\#685).
+
+  - Function `sensitivitySpiderPlot` now supports `xAxisType` and `yAxisType`
+    options for switching between percent and absolute values (\#695).
 
   - Function `sensitivityCalculation()` will throw more informative messages when
     `outputPaths` or `parameterPaths` is not a character vector or NULL (\#712).
@@ -24,8 +43,8 @@
 
 ## Breaking changes
 
-  - `{esqlabsR}` now requires `{ospsuite}` version 12.1.0 or higher to benefit from
-    embedded PK-Sim core files.
+  - `{esqlabsR}` now requires `{ospsuite}` version 12.1.0 or higher to benefit
+    from embedded PK-Sim core files.
 
   - Function `exportSteadyStateToXLS` has been removed in favor of
     `ospsuite::exportSteadyStateToXLS` (\#598)
@@ -37,12 +56,13 @@
     customization options through `defaultPlotConfiguration` (\#632).
 
   - Function `sensitivityTimeProfiles` with new signature and enhanced visuals:
-    - `xAxisScale` and `yAxisScale` to set axis scales to `log` or `lin` (\#669).
-    - `xUnits` and `yUnits` to change units in the plot (\#688).
-    - Enhanced plot customization options through `defaultPlotConfiguration` as
-      described in the documentation (\#669).
-    - Support for adding `observedData` (single or multiple `DataSet` objects) 
-      to the plots (\#674).
+      - `xAxisScale` and `yAxisScale` to set axis scales to `log` or `lin`
+        (\#669).
+      - `xUnits` and `yUnits` to change units in the plot (\#688).
+      - Enhanced plot customization options through `defaultPlotConfiguration`
+        as described in the documentation (\#669).
+      - Support for adding `observedData` (single or multiple `DataSet` objects)
+        to the plots (\#674).
 
   - Function `writeExcel()` is no longer exported. (\#672)
 
@@ -73,8 +93,8 @@
   - More explicit error is shown if x/yOffsetsUnit is not set when x/yOffset is
     defined.
 
-  - Plotting functions have improved dynamic axis breaks, limits calculation, and 
-    labeling (\#691).
+  - Plotting functions have improved dynamic axis breaks, limits calculation,
+    and labeling (\#691).
 
 # esqlabsR 5.1.3