From 524d7a21563cab2820c6da3c6663dbcd923873bb Mon Sep 17 00:00:00 2001
From: pchelle <chelle.pierre@gmail.com>
Date: Thu, 30 Nov 2023 11:30:35 -0500
Subject: [PATCH] Fixes #1097 update demography caption

New populations such as disease states will be included in later versions
---
 R/captions.R             | 10 ++---
 inst/extdata/obsPop.csv  | 84 ++++++++++++++++++++--------------------
 vignettes/demography.Rmd | 43 ++++++++++++++++++++
 3 files changed, 89 insertions(+), 48 deletions(-)

diff --git a/R/captions.R b/R/captions.R
index aa90a4ea..0de4a978 100644
--- a/R/captions.R
+++ b/R/captions.R
@@ -80,12 +80,10 @@ captions <- list(
         referenceSetText,
         ". ",
         dataSource,
-        getPlotScaleCaption("Profiles", plotScale),
         switch(parameterClass,
-          "character" = paste0(" and ", getBoxplotDescriptor()),
-          ""
-        ),
-        "."
+          "character" = paste0("Data is ", getBoxplotDescriptor(), "."),
+          getPlotScaleCaption("Profiles", plotScale)
+        )
       ))
     }
   ),
@@ -228,7 +226,7 @@ getDataSourceCaption <- function(structureSet) {
     return("")
   }
   dataSourceCaption <- structureSet$simulationSet$dataSource$getCaption(structureSet$workflowFolder)
-  return(paste0(dataSourceCaption, ". "))
+  return(dataSourceCaption)
 }
 
 getGoodnessOfFitCaptions <- function(structureSet, plotType, plotScale = "linear", settings = NULL) {
diff --git a/inst/extdata/obsPop.csv b/inst/extdata/obsPop.csv
index b1c13793..8dc50f67 100644
--- a/inst/extdata/obsPop.csv
+++ b/inst/extdata/obsPop.csv
@@ -1,43 +1,43 @@
 ID,GENDER,POP,WEIGHT,AGE
-0,MALE,Adults,52,20
-1,MALE,Adults,48,13
-2,MALE,Adults,56,14
-3,MALE,Children,33,10
-4,MALE,Adults,87,37
-5,MALE,Adults,52,16
-6,MALE,Adults,64,25
-7,MALE,Adults,65,21
-8,MALE,Adults,66,27
-9,MALE,Adults,43,12
-10,MALE,Adults,51,14
-11,MALE,Adults,60,35
-12,MALE,Adults,66,14
-13,MALE,Adults,43,12
-14,MALE,Children,25,7
-15,MALE,Adults,80,40
-16,MALE,Adults,66,33
-17,FEMALE,Adults,50,20
-18,FEMALE,Adults,41,19
-19,FEMALE,Adults,58,34
-20,FEMALE,Adults,50,16
-21,FEMALE,Children,21,8
-22,FEMALE,Adults,86,23
-23,FEMALE,Adults,76,23
-24,FEMALE,Adults,68,27
-25,FEMALE,Adults,64,19
-26,FEMALE,Adults,40,16
-27,FEMALE,Adults,64,19
-28,FEMALE,Adults,72,40
-29,FEMALE,Adults,65,40
-30,FEMALE,Adults,46,19
-31,FEMALE,Adults,45,13
-32,FEMALE,Adults,64,38
-33,FEMALE,Adults,34,12
-34,FEMALE,Adults,48,14
-35,FEMALE,Adults,64,37
-36,FEMALE,Adults,58,38
-37,FEMALE,Adults,43,13
-38,FEMALE,Adults,63,15
-39,FEMALE,Adults,47,15
-40,FEMALE,Adults,61,34
-41,FEMALE,Adults,52,37
+0,MALE,Adults,52,16
+1,MALE,Children,48,9
+2,MALE,Children,56,10
+3,MALE,Children,33,6
+4,MALE,Adults,87,33
+5,MALE,Children,52,12
+6,MALE,Adults,64,21
+7,MALE,Adults,65,17
+8,MALE,Adults,66,23
+9,MALE,Children,43,8
+10,MALE,Children,51,10
+11,MALE,Adults,60,31
+12,MALE,Children,66,10
+13,MALE,Children,43,8
+14,MALE,Children,25,3
+15,MALE,Adults,80,36
+16,MALE,Adults,66,29
+17,FEMALE,Adults,50,16
+18,FEMALE,Adults,41,15
+19,FEMALE,Adults,58,30
+20,FEMALE,Children,50,12
+21,FEMALE,Children,21,4
+22,FEMALE,Adults,86,19
+23,FEMALE,Adults,76,19
+24,FEMALE,Adults,68,23
+25,FEMALE,Adults,64,15
+26,FEMALE,Children,40,12
+27,FEMALE,Adults,64,15
+28,FEMALE,Adults,72,36
+29,FEMALE,Adults,65,36
+30,FEMALE,Adults,46,15
+31,FEMALE,Children,45,9
+32,FEMALE,Adults,64,34
+33,FEMALE,Children,34,8
+34,FEMALE,Children,48,10
+35,FEMALE,Adults,64,33
+36,FEMALE,Adults,58,34
+37,FEMALE,Children,43,9
+38,FEMALE,Children,63,11
+39,FEMALE,Children,47,11
+40,FEMALE,Adults,61,30
+41,FEMALE,Adults,52,33
diff --git a/vignettes/demography.Rmd b/vignettes/demography.Rmd
index 71ce26ff..07b9b996 100644
--- a/vignettes/demography.Rmd
+++ b/vignettes/demography.Rmd
@@ -621,6 +621,49 @@ It is however possible to remove this settings in case the bars do not overlap b
 workflow$plotDemography$settings$dodge <- FALSE
 ```
 
+In the example below, dodging is removed within a parallel comparison workflow:
+
+<details>
+<summary> __Code__ </summary>
+
+```{r}
+parallelWorkflow <- PopulationWorkflow$new(
+  workflowType = PopulationWorkflowTypes$parallelComparison,
+  simulationSets = c(adultSet, childrenSet),
+  workflowFolder = "Parallel-Histograms",
+  createWordReport = FALSE
+)
+
+inactivateWorkflowTasks(parallelWorkflow)
+activateWorkflowTasks(parallelWorkflow, tasks = AllAvailableTasks$plotDemography)
+
+displayedParameters  <- list(
+  Age = "Organism|Age", 
+  Weight = "Organism|Weight", 
+  Gender = "Gender"
+  )
+setYParametersForDemogrpahyPlot(workflow = parallelWorkflow, parameters = displayedParameters)
+
+# Turn off dodging of histogram bars
+parallelWorkflow$plotDemography$settings$dodge <- FALSE
+
+parallelWorkflow$runWorkflow()
+
+```
+
+</details>
+
+
+```{r example parallel report dodge, echo=FALSE, results='asis'}
+cat(includeReportFromWorkflow(parallelWorkflow))
+```
+
+```{r delete parallel report dodge, include = FALSE, echo=FALSE}
+# Remove the workflow folders
+unlink(parallelWorkflow$workflowFolder, recursive = TRUE)
+```
+
+
 ## Display reference population global range <a id="ref-global-range"></a>
 
 Pediatric workflow range plots compare simulation sets to the **reference** simulation set ([#17](https://github.com/Open-Systems-Pharmacology/OSPSuite.ReportingEngine/issues/17)).