Merge pull request #1009 from Open-Systems-Pharmacology/develop

Version 2.1.244

.Rbuildignore

@@ -5,3 +5,12 @@
 ^tests/dev
 ^tools
 ^\.covrignore$
+^\.github$
+^docs$
+^scripts$
+^LICENSE\.md$
+^_pkgdown\.yml$
+^rakefile\.rb
+^inst/extdata/RaltegravirSim\.pkml$
+^tests/data/input-data/RaltegravirSim\.pkml$
+^tests/data/input-data/individualPksimSim\.pkml$

.github/workflows/LinuxImages.yml

@@ -8,8 +8,8 @@ jobs:
     strategy:
         fail-fast: false
         matrix:
-            r_version: [3.6.3, 4.1.0]
-            os_version: [centos7, bionic]
+            r_version: [4.1.0] #[3.6.3, 4.1.0]
+            os_version: [bionic] #[centos7, bionic]
     runs-on: ubuntu-latest
     steps:
       - name: Checkout

.github/workflows/install_packages_cran.sh

@@ -1,6 +1,6 @@
 #!/bin/sh
 
 # Install packages
-R --no-save -e "install.packages(c('remotes', 'dplyr', 'tidyr', 'purrr', 'patchwork'), repos='http://cran.rstudio.com/')"
+R --no-save -e "install.packages(c('remotes', 'dplyr', 'tidyr', 'purrr', 'patchwork', 'readxl'), repos='http://cran.rstudio.com/')"
 R --no-save -e "remotes::install_github('Open-Systems-Pharmacology/OSPSuite.RUtils', ref ='develop')"
 R --no-save -e "remotes::install_github('Open-Systems-Pharmacology/TLF-Library', ref ='develop')"

.github/workflows/testRE.R

@@ -1,3 +1,4 @@
+# spelling::spell_check_package()
 library('ospsuite')
 setwd('tests')
 library(testthat)

DESCRIPTION

@@ -1,51 +1,55 @@
-Type: Package
-Package: ospsuite.reportingengine
-Title: R package to create reports for the Open Systems Pharmacology models
-Version: 2.0.0
-Authors@R: 
-    c(person(given = "Open-Systems-Pharmacology Community",
-             role = "cph"),
-      person(given = "Michael",
-             family = "Sevestre",
-             role = c("aut", "cre"),
-             email = "[email protected]",
-             comment = c(ORCID = "0000-0002-3054-8160")),
-      person(given = "Juri",
-             family = "Solodenko",
-             role = "aut",
-             email = "[email protected]",
-             comment = c(ORCID = "0000-0001-6922-588X")),
-      person(given = "Pierre",
-             family = "Chelle",
-             role = "aut",
-             email = "[email protected]"),
-      person(given = "Abdullah",
-             family = "Hamadeh",
-             role = "aut",
-             email = "[email protected]"))
-Description: Creates tables and figures and combines them into (Markdown and MS-Word) reports.
-License: GPL-2 | file LICENSE
-URL: https://github.com/open-systems-pharmacology/ospsuite.reportingengine
-BugReports: 
-    https://github.com/open-systems-pharmacology/ospsuite.reportingengine/issues
-Depends: 
-    R (>= 3.5),
-    ospsuite (>= 11.0),
-    tlf (>= 1.4.0)
-Imports: 
-    R6,
-    ggplot2,
-    jsonlite,
-    ospsuite.utils (>= 1.3.0)
-Suggests: 
-    testthat (>= 2.1.0),
-    knitr,
-    rmarkdown,
-    Rmpi,
-    readxl,
-    tracelib,
-    styler
-Encoding: UTF-8
-LazyData: true
-RoxygenNote: 7.1.1
-VignetteBuilder: knitr
+Type: Package
+Package: ospsuite.reportingengine
+Title: R package to create reports for the Open Systems Pharmacology models
+Version: 2.1.0
+Authors@R: 
+    c(person(given = "Open-Systems-Pharmacology Community",
+             role = "cph"),
+      person(given = "Michael",
+             family = "Sevestre",
+             role = c("aut", "cre"),
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0002-3054-8160")),
+      person(given = "Juri",
+             family = "Solodenko",
+             role = "aut",
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0001-6922-588X")),
+      person(given = "Pierre",
+             family = "Chelle",
+             role = "aut",
+             email = "[email protected]"),
+      person(given = "Abdullah",
+             family = "Hamadeh",
+             role = "aut",
+             email = "[email protected]"))
+Description: Creates tables and figures and combines them into (Markdown and MS-Word) reports.
+License: GPL-2 | file LICENSE
+URL: https://github.com/open-systems-pharmacology/ospsuite.reportingengine
+BugReports: 
+    https://github.com/open-systems-pharmacology/ospsuite.reportingengine/issues
+Depends: 
+    R (>= 3.5),
+    ospsuite (>= 11.1),
+    tlf (>= 1.5.0)
+Imports: 
+    R6,
+    ggplot2,
+    jsonlite,
+    ospsuite.utils (>= 1.4.0),
+    dplyr
+Suggests: 
+    testthat (>= 2.1.0),
+    knitr,
+    rmarkdown,
+    Rmpi,
+    readxl,
+    tracelib,
+    styler,
+    rClr,
+    crayon,
+    webshot
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.2.1
+VignetteBuilder: knitr

NAMESPACE

@@ -5,6 +5,7 @@ export(AllAvailableTasks)
 export(ApplicationRanges)
 export(ConfigurationPlan)
 export(DataSelectionKeys)
+export(DataSource)
 export(GofPlotTask)
 export(LogTypes)
 export(MeanModelWorkflow)
@@ -23,6 +24,7 @@ export(SensitivityPlotSettings)
 export(SimulationSet)
 export(StandardPlotTasks)
 export(StandardSimulationTasks)
+export(StatisticsTypes)
 export(Task)
 export(activateWorkflowTasks)
 export(addFigureChunk)
@@ -44,7 +46,6 @@ export(anchor)
 export(calculateArithmeticErrorRange)
 export(calculateGMFE)
 export(calculateGeometricErrorRange)
-export(calculateResiduals)
 export(checkLibraryLoaded)
 export(checkPopulationLoaded)
 export(checkSimulationLoaded)
@@ -55,27 +56,40 @@ export(defaultQuantileVec)
 export(defaultSensitivityAnalysisNumberOfCores)
 export(defaultSimulationNumberOfCores)
 export(defaultVariationRange)
+export(displayConfigurationPlanPlotInfo)
 export(evalDataFilter)
 export(generateResultFileNames)
+export(geomean)
+export(geomeanDividedBySD)
+export(geomeanMultipliedBySD)
 export(getAnchorName)
 export(getDefaultDemographyXParameters)
+export(getDefaultMCRandomSeed)
+export(getDefaultMCRepetitions)
 export(getDefaultPKParametersXParameters)
 export(getDefaultPkParametersXParameters)
 export(getMeanSensitivityAnalysisResultsFileNames)
 export(getMolWeightForCompound)
 export(getOutputPathsInSimulationSet)
 export(getPKAnalysisResultsFileNames)
+export(getPKParameterGroupsInOutput)
 export(getPKParametersInOutput)
 export(getPKParametersInSimulationSet)
 export(getPkAnalysisResultsFileNames)
+export(getPopulationPKData)
+export(getPopulationPKMetaData)
 export(getPopulationSensitivityAnalysisResultsFileNames)
 export(getReportingEngineInfo)
 export(getResiduals)
+export(getSelectedData)
+export(getSelectedRows)
 export(getSimulationDescriptor)
 export(getSimulationParameterDisplayPaths)
 export(getSimulationResultFileNames)
+export(getStatisticsFromType)
 export(getTaskInputs)
 export(getWorkflowParameterDisplayPaths)
+export(getWorkflowReferencePopulationName)
 export(getXParametersForDemogrpahyPlot)
 export(getXParametersForPKParametersPlot)
 export(getXParametersForPkParametersPlot)
@@ -84,7 +98,6 @@ export(getYParametersForPKParametersPlot)
 export(getYParametersForPkParametersPlot)
 export(hasAnchor)
 export(inactivateWorkflowTasks)
-export(isBetween)
 export(lastPathElement)
 export(loadCalculatePKParametersTask)
 export(loadCalculateSensitivityTask)
@@ -105,39 +118,41 @@ export(loadSimulateTask)
 export(loadSimulationWithUpdatedPaths)
 export(loadStudyDesign)
 export(loadWorkflowPopulation)
+export(logCatch)
 export(logDebug)
 export(logError)
 export(logInfo)
-export(logWorkflow)
 export(measureValuesBetween)
 export(mergeMarkdownFiles)
 export(plotAbsorptionTimeProfile)
 export(plotDemographyHistogram)
 export(plotMassBalanceCumulativeTimeProfile)
 export(plotMassBalancePieChart)
 export(plotMassBalanceTimeProfile)
-export(plotMeanObsVsPred)
-export(plotMeanResVsPred)
-export(plotMeanResVsTime)
 export(plotMeanTimeProfile)
-export(plotPopulationTimeProfile)
-export(plotResidualsHistogram)
-export(plotResidualsQQPlot)
+export(plotMeanTimeProfileLog)
+export(plotPopTimeProfile)
+export(plotPopTimeProfileLog)
 export(prettyCaption)
 export(ratioBoxplot)
 export(readObservedDataFile)
 export(removeForbiddenLetters)
 export(renderReport)
 export(renderWordReport)
 export(resetReport)
+export(saveLogs)
+export(saveLogsToJson)
 export(saveTaskResults)
 export(setDefaultAutoAxisLimitMargin)
 export(setDefaultBins)
+export(setDefaultMCRandomSeed)
+export(setDefaultMCRepetitions)
 export(setDefaultNumericFormat)
 export(setDefaultPlotFormat)
 export(setDefaultStairstep)
 export(setDefaultTheme)
 export(setDefaultThemeFromJson)
+export(setDefaultTimeProfileStatistics)
 export(setPlotFormat)
 export(setSimulationDescriptor)
 export(setWatermarkConfiguration)
@@ -149,16 +164,17 @@ export(setXParametersForPkParametersPlot)
 export(setYParametersForDemogrpahyPlot)
 export(setYParametersForPKParametersPlot)
 export(setYParametersForPkParametersPlot)
+export(showLogMessages)
 export(simulateModelOnCore)
 export(startQualificationRunner)
 export(trimFileName)
 export(updateSimulationIndividualParameters)
 export(vpcParameterPlot)
+import(dplyr)
 import(ggplot2)
 import(jsonlite)
 import(ospsuite)
 import(ospsuite.utils)
-import(stats)
 import(tlf)
 import(utils)
 importFrom(ospsuite.utils,"%||%")

NEWS.md

@@ -1,16 +1,48 @@
-# ospsuite.reportingengine 2.0.189
+# ospsuite.reportingengine 2.1.244
+
+## New features
+
+- Population workflows can use Monte Carlo sampling to handle ratio comparison (#536) as documented in the article [PK Parameters in Population Workflows](../articles/pop-pk-parameters.html#ratio-comparison).
+- [`Output`](../reference/Output.html) objects can now include `color` and `fill` properties that will be displayed in the corresponding plots (#418, #883)
+- `dataSelection` is now available at both `SimulationSet` and `Output` levels (#881)
+- Excel template is up-to-date with the new features (#882) and documented in the article [Excel Template](../articles/excel-template.html)
+- Mean and Population workflows can display a title/cover page at the beginning of the report (#854) as documented in article [Add a title page to your workflow report](../articles/add-title-page.html)
+- Qualification Time Profiles handle dual axis plots (#934, #985)
+
+## Minor improvements and bug fixes
+
+- In qualification workflows, logging now includes information regarding the configuration plan location (#930)
+- By default, plot dimensions are now quadratic (#877)
+- Statistics in population workflow time profiles now use geometric mean and sd as default and can be easily updated with enum helper [`StatisticsTypes `](../reference/StatisticsTypes.html) and function `setDefaultTimeProfileStatistics()` (#862)
+- Goodness of fit plots and captions were improved (#418, #863, #865, #867, #871, #874, #875, #878, #884, #886, #887, #888)
+- Displayed qualification plots now includes following updates:
+   - better scaled watermark (#849)
+   - margin added to prevent truncated ticklabels (#951)
+   - gof and time profile use correct colors (#952)
+   - residual label match calculation method (#953)
+   - legend does not shrink the plot size (#861)
+- Creation of word reports now includes following updates:
+   - page breaks at appropriate places (#971)
+   - figure/table numbering (#967) are now fixed
+   - default reference word document has been updated (#748, #749, #750 and #754)
+   - tags for subscript (wrapped by `<sub>...</sub>`) and superscript (wrapped by `<sup>...</sup>`) are converted to word (#968)
+   - equations wrapped by `$$...$$` and written in LaTeX format are converted to word
+   - bookmarks are now created from markdown anchors (#923)
+- Qualification time profiles use base unit if unit is not defined by user (#867, #991)
+
+# ospsuite.reportingengine 2.0.191
 
 ## New features
 
 - Qualification workflows are now available ! (#2)
-  - Qualification Workflows have their own [vignette](https://www.open-systems-pharmacology.org/OSPSuite.ReportingEngine/articles/qualification-workflow.html) to help you start (#566)
-  - A template qualification workflow R script is available on Github orat `system.file("extdata", "qualification-workflow-template.R", package = "ospsuite.reportingengine")` and can also be downloaded from [Github](https://github.com/Open-Systems-Pharmacology/OSPSuite.ReportingEngine/blob/develop/inst/extdata/qualification-workflow-template.R) (#572)
+  - Qualification Workflows have their own [vignette](../articles/qualification-workflow.html) to help you start (#566)
+  - A template qualification workflow R script is available on GitHub at `system.file("extdata", "qualification-workflow-template.R", package = "ospsuite.reportingengine")` and can also be downloaded from [GitHub](https://github.com/Open-Systems-Pharmacology/OSPSuite.ReportingEngine/blob/develop/inst/extdata/qualification-workflow-template.R) (#572)
   - Function `adjustTitlePage` can be used to personalize the report title page (#755)
   - Configuration plans can be re-loaded on `QualificationWorkflow` objects to update the report display (#567)
   - DDI subunits option is available (#642)
 - With `ospsuite` version 10, simulations can be run in parallel (#526)
 - Workflows account for time offset in simulation sets using option `timeOffset` for time profile plots (#313) or through user defined PK parameters for PK parameter plots (#578).
-- User can define their own word report template to tune the styles of their report by providing a reference word document to the `wordConversionTemplate` of their Workflow object. A word reference template is available on [Github](https://github.com/Open-Systems-Pharmacology/OSPSuite.ReportingEngine/blob/develop/inst/extdata/reference.docx) (#756)
+- User can define their own word report template to tune the styles of their report by providing a reference word document to the `wordConversionTemplate` of their Workflow object. A word reference template is available on [GitHub](https://github.com/Open-Systems-Pharmacology/OSPSuite.ReportingEngine/blob/develop/inst/extdata/reference.docx) (#756)
 - The function `copyReport` can be used to copy markdown/word reports (#814)
 
 ## Minor improvements and bug fixes
@@ -27,7 +59,7 @@
 
 * Descriptor of simulation sets is now available and can be defined in Excel template (#445) as well as using the function `setSimulationDescriptor` (#423).
 * Each task property `settings` is now an R6 object (#396). This allows users to have an easy and direct access to setting properties.
-* Posibility to read time and measurement units from nonmem columns (#414)
+* Possibility to read time and measurement units from nonmem columns (#414)
 
 ## Minor improvements and bug fixes