Dev to main for Release V4. (#328)

* Create V4  (#255)

* - Update data-handling vignette
- Function `loadObservedData()` requires a `ProjectConfiguration` instead of a
`ScenarioConfiguration`.

* Remove unused vignettes

* Update AppVeyor to R4.2.0

* Increment version to v4.0.0

* Cleanup for v4

* Update website

* Update reference index

* Removed steady-state function and using ospsuite.parameteridentification (#261)

* Removed steady-state function and using ospsuite.parameteridentification

* Update NEWS.md

Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>

* Removed unused message

* Update documentation

* Update appveyor.yml

* Fix examples

Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>

* Add functions to create plotting-related configs (#265)

- [x] Closes #262
- [x] Closes #263
- [x] Closes #264
- [x] Closes #225
- [x] docs and NEWS
- [x] tests

* Following guidelines for internal function names (#266)

* Added simulationRunOptions parameter (#268)

* Added simulationRunOptions parameter

* Remove `hash` from imports
Adds `stringr` and `labeling` to imports
Remove "return" from an empty switch statement
Missing documented arguments

* Update to roxygen2 7.2.1 (#273)

* Update to roxygen2 7.2.1

* .rd files

* Update exportSteadyStateToXLS.Rd

* Don't write to sheets when there is no data (#274)

Closes #272

* SensitivityAnalysis - use "by path" methods (#271)

* Use unlist

* Assign condition to a variable

* Skipping tests that rely on PK-Sim

* fix `createEsqlabsPlotConfiguration()`

Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>

* Follow coding convention for source code filenames (#275)

* remove empty section from reference page

* Fix failing sensitivity-calculation after ospsuite update (#278)

* Fix failing sensitivity-calculation after ospsuite update

* Update rd

* Add tests for utilities (#280)

* Add tests for file utilities

* snapshot paths have changed?

* skip for now

* try

* problematic test?

* Update test-utilities-file.R

* Update test-utilities-file.R

* Update test-utilities-file.R

* Test for `compareWithNA()`

* rudimentary test for `ScenarioConfiguration`

* Don't skip tests on CI anymore (#283)

* Update README (#282)

* Update README

Closes #281

* Update README.md

* Tests for color utilities and global settings (#285)

* Tests for color utilities

* tests for global settings

* Use functions for error messages

* Additional tests for utilities (#287)

* Additional tests for utilities

* test for `compareSimulationParameters()`

* tweak tests for settings

* Test for `sampleRandomValue()`

* Address review comments

* remove `expect_s3_class()` for R6

* Extract applications (#288)

* - Add a function `getAllApplicationParameters` that returns all parameters of applications in a simulation
- Add a function `exportParametersToXLS` to write parameter information into an excel file that can be loaded in MoBi or R
- Add a function `writeExcel` that is a wrapper for creating a directory (if not present) and writing to excel file

* Update documentation

* Update R/utilities-simulation.R

Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>

* Update R/utilities-parameters.R

Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>

* Address review comments

* Update required R version

* Update NEWS

Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>

* Tests for shiny apps (#290)

* Get rid of a few lints (#291)

* also not used

* - Add default project configuration file (#293)

- Fix documentation for the simulationTime argument of ScenarioConfiguration
- Fix example for setParameterValuesByPathWithCondition
- If simulation time is not defined in the ScenarioConfiguration, use output time schema from the simulation

* More tests for utilities (#294)

* More tests for utilities

* use github version

* skip for now

* Test for `executeInParallel()`

* Try shipping binary

* Revert "Try shipping binary"

This reverts commit 72dda5d.

* Update documentation (#298)

* More tests for scenario config (#296)

* more tests for scenario config

* to shut up codecov

* Get rid of `.getNetHashCode()`

Closes #297

* Added example project

* Add logo for the package (#299)

Stickers are big in the R community, and a good way to market ourselves at conferences and meetings. Print them, and distribute them, so that people can put them on their laptops.

cc @StephanSchaller

* - Remove unused test files
- Styler

* Delete modeling_environment.R

unneeded for the esqlabsR purposes

* Documenting data handling and running simulations (#301)

* Updated the introduction part of the vignette

* Data handling vignette

* Vignette on running simulations

* Propagated vignette updates to the /docs folder

* Updated links to the scenario file to avoid duplicated files

* style

* style changes to vignettes/data-handling.Rmd

Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>

* Restored _snaps files that were mistakenly removed

* wording in introduction

Co-authored-by: Pavel Balazki <pavel.balazki@gmail.com>

* link to aciclovir model

Co-authored-by: Pavel Balazki <pavel.balazki@gmail.com>

* Removed function reference, moved installation and contribution to README.md only

* style changes README.md

Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>

* Removed auto-generated testthat file

* Update vignettes/introduction-esqlabsr.Rmd

* Changes to data-handling.Rmd

Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>
Co-authored-by: Pavel Balazki <pavel.balazki@gmail.com>

* Better explanation of the configuration Excel files

* Restructuring of existing documentation, a clear description of no-code approach

* Run tests for Shiny apps (#303)

* Simulations vignette with references to all configuration files and first lines of output

* Fixed link to the Scenarios.xlsx file

* Visualization vignette

* Sensitivity vignette

* Add getMoleculeNameFromQuantity() (#307)

* Add getMoleculeNameFromQuantity()

* Apply suggestions from code review

Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>

Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>

* Changed plot sizes

* Added troubleshooting sections

* Apply suggestions from code review

style changes

Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>

* Apply suggestions from code review

style changes

Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>

* Renamed chunks to follow style guide

* Added time profiles to sensitivity analysis

* Update vignettes/sensitivity-analysis.Rmd

* Added link to time profiles

* Updated the HTML docs to match the RMD docs (#309)

* Updated the HTML docs to match the RMD docs

* correct typos

Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>

* Suggestions for vignettes (#315)

Co-authored-by: Johanna Eitel <johanna.eitel@esqlabs.com>

* Fixes initializeSimulation() when additionalParams is empty but not NULL #313 (#314)

* Added script for installation

* - List for packages that will be installed from CRAN
- Add "purr" explicitly to be installed from CRAN

* - Add jsonlite to be installed

* - Change defaults for `updatePackages` argument to `FALSE`
- Change defaults for `developerVersion` to `TRUE`
- Remove redundant test for PK-Sim connection

* Add vignette for shiny apps (#316)

* Add vignette for shiny apps

* Added header, minor style changes

* Add ShinyApp link to the introduction
Some minor changes to the vignette

Co-authored-by: Johanna Eitel <johanna.eitel@esqlabs.com>
Co-authored-by: Sergei Vavilov <svavil@gmail.com>
Co-authored-by: Pavel Balazki <pavel.balazki@gmail.com>

* Update website (#327)

* - Remove RData
- Update readme

* Update docs

Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>
Co-authored-by: Johanna Eitel <47447533+hannaei@users.noreply.github.com>
Co-authored-by: Sergei Vavilov <svavil@gmail.com>
Co-authored-by: Johanna Eitel <johanna.eitel@esqlabs.com>

.Rbuildignore

@@ -47,3 +47,4 @@ references.bib
 ^scripts$
 .tgitconfig
 ^rakefile\.rb$
+_\.new\.png$

.gitignore

@@ -52,3 +52,5 @@ revdep/data.sqlite
 /Meta/
 .tgitconfig
 tests/testthat/Rplots.pdf
+# {shinytest2}: Ignore new debug snapshots for `$expect_values()`
+*_.new.png

DESCRIPTION

@@ -1,11 +1,13 @@
 Type: Package
 Package: esqlabsR
 Title: esqLABS utilities package
-Version: 3.0.0
+Version: 4.0.0
 Authors@R: 
     c(person("esqLABS GmbH", role = c("cph", "fnd")),
-      person("Pavel", "Balazki", role = c("cre", "aut"), email = "pavel.balazki@esqlabs.com"),
-      person("Johanna", "Eitel", role = "aut"),
+      person("Pavel", "Balazki", , "https://github.com/PavelBal", role = c("cre", "aut"), 
+      email = "pavel.balazki@esqlabs.com"),
+      person("Johanna", "Eitel", , "https://github.com/hannaei", role = "aut"),
+      person("Sergei", "Vavilov", , "https://github.com/svavil", role = "aut"),
       person("Indrajeet", "Patil", , "patilindrajeet.science@gmail.com", role = "aut",
            comment = c(ORCID = "0000-0003-1995-6531", Twitter = "@patilindrajeets")))
 Maintainer: Pavel Balazki <pavel.balazki@esqlabs.com>
@@ -15,31 +17,37 @@ License: GPL-2
 URL: https://github.com/esqLABS/esqlabsR
 BugReports: https://github.com/esqLABS/esqlabsR/issues
 Depends:
-    ospsuite (>= 11.0)
+    R (>= 4.1),
+    ospsuite (>= 11.0),
+    ospsuite.parameteridentification
 Imports:
     colorspace,
     dplyr,
     ggplot2,
-    hash,
     ospsuite.utils (>= 1.3.0),
     purrr,
-    rClr,
     readxl,
     shiny,
     shinyjs,
     tidyr,
     tools,
+    tlf (>= 1.4.0),
     vctrs,
-    writexl
+    writexl,
+    stringr,
+    labeling
 Suggests: 
+    clipr,
     knitr,
     rmarkdown,
+    shinytest2,
     testthat (>= 3.0.0),
-    vdiffr (>= 1.0.0)
+    vdiffr (>= 1.0.0),
+    withr
 VignetteBuilder: 
     knitr
 Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.1

NAMESPACE

@@ -1,56 +1,47 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%||%")
-export(DataConfiguration)
-export(DataMapping)
-export(DataMappingConfiguration)
 export(Distributions)
 export(GenderInt)
 export(GraphicsDevices)
 export(LLOQMode)
-export(PlotConfiguration)
-export(PlotTypes)
 export(ProjectConfiguration)
 export(ScenarioConfiguration)
-export(XYData)
-export(XYDataTypes)
 export(applyIndividualParameters)
 export(calculateMeanDataSet)
-export(calculateRMSE)
 export(col2hsv)
 export(compareSimulationParameters)
 export(compareWithNA)
 export(createDefaultProjectConfiguration)
+export(createEsqlabsExportConfiguration)
+export(createEsqlabsPlotConfiguration)
+export(createEsqlabsPlotGridConfiguration)
 export(enumPutList)
 export(escapeForRegex)
 export(esqLABS_colors)
+export(esqlabsRSettingNames)
 export(executeInParallel)
+export(exportParametersToXLS)
 export(exportSteadyStateToXLS)
 export(extendParameterStructure)
 export(extendPopulationByUserDefinedParams)
 export(extendPopulationFromXLS)
 export(foldChangeFunction)
 export(geomean)
 export(geosd)
+export(getAllApplicationParameters)
 export(getEsqlabsRSetting)
 export(getIndexClosestToValue)
-export(getQuantilesYData)
-export(getSteadyState)
+export(getMoleculeNameFromQuantity)
 export(hillFunction)
 export(initializeScenario)
 export(initializeSimulation)
-export(isCharInString)
 export(isParametersEqual)
 export(isTableFormulasEqual)
 export(loadObservedData)
 export(pathFromClipboard)
-export(plotBoxPlot)
-export(plotMultiPanel)
-export(plotPredictedVsObserved)
-export(plotXYDataAggregated)
 export(readExcel)
 export(readIndividualCharacteristicsFromXLS)
-export(readOSPSTimeValues)
 export(readParametersFromXLS)
 export(readPopulationCharacteristicsFromXLS)
 export(readScenarioConfigurationFromExcel)
@@ -67,14 +58,14 @@ export(sourceAll)
 export(startFunctionVisualizer)
 export(startUnitConverter)
 export(stringToNum)
+export(writeExcel)
 export(writeIndividualToXLS)
 import(colorspace)
 import(dplyr)
 import(ggplot2)
-import(hash)
 import(ospsuite)
+import(ospsuite.parameteridentification)
 import(ospsuite.utils)
 import(parallel)
-import(rClr)
 import(readxl)
 importFrom(ospsuite.utils,"%||%")

NEWS.md

@@ -1,24 +1,58 @@
-# esqlabsR 3.0.0
+# esqlabsR 4.0.0
+
+MAJOR CHANGES
+
+- Three new functions to create configuration objects needed for data visualization workflows:
+
+  * `createEsqlabsPlotConfiguration()`
+  * `createEsqlabsPlotGridConfiguration()`
+  * `createEsqlabsExportConfiguration()`
+
+- New function `getAllApplicationParameters()` that returns all parameters of 
+applications in a simulation
+- New function `exportParametersToXLS()` to write parameter information into an 
+excel file that can be loaded in MoBi or R using the `readParametersFromXLS()`
+function.
+- New function `writeExcel()` that is a wrapper for creating a directory 
+(if not present) and writing to excel file using `writexl::write_xlsx()`.
+
+BREAKING CHANGES
+
+- The package requires R version >=4.1.
 
+- The package gains new dependencies:
 
+  * [`{ospsuite.parameteridentification}`](https://github.com/Open-Systems-Pharmacology/OSPSuite.ParameterIdentification/) 
+  * [`{tlf}`](https://www.open-systems-pharmacology.org/TLF-Library/).
+
+- Function `getSteadyState()` has been moved to package `{ospsuite.parameteridentification}`.
+
+- Function `loadObservedData()` requires a `ProjectConfiguration` instead of a 
+`ScenarioConfiguration`.
+
+- `DataMapping`, `DataMappingConfiguration`, `XYData`, `DataConfiguration` and 
+associated functions for creating standard figures are moved to `esqlabsRLegacy` 
+[package](https://esqlabs.github.io/esqlabsRLegacy/).
+
+# esqlabsR 3.0.0
 
 NEW FUNCTIONS
 
 - To carry out and visualize sensitivity analysis:
 
-* `sensitivityCalculation()`
-* `sensitivitySpiderPlot()`
-* `sensivitityTimeProfiles()`
+ * `sensitivityCalculation()`
+ * `sensitivitySpiderPlot()`
+ * `sensitivityTimeProfiles()`
 
 - Classes and functions for standard esqLABS simulation workflow:
 
-* `ProjectConfiguration`
-* `ScenarioConfiguration`
-* `createDefaultProjectConfiguration()`
-* `readScenarioConfigurationFromExcel()`
-* `setApplications()`
-* `initializeScenario()`
-* `initializeScenario()`
+ * `ProjectConfiguration`
+ * `ScenarioConfiguration`
+ * `createDefaultProjectConfiguration()`
+ * `readScenarioConfigurationFromExcel()`
+ * `setApplications()`
+ * `initializeScenario()`
+ * `initializeScenario()`
 
 - Maintenance and bug fixes.