final revs to shiny interface

README.md

 # Overview
 
-This package provides the core computations used in [Serostatus Testing & Dengue Vaccine Cost-Benefit Thresholds](doi:10.1098/rsif.2019.0234).
+This package provides the core computations used in [Serostatus Testing & Dengue Vaccine Cost-Benefit Thresholds](https://doi.org/10.1098/rsif.2019.0234).
 
 If `ggplot2` is present, the package also provides some convenient `scale_...` elements. If not, these functions issue a warning when used.
 

inst/shiny/demo/app.R

@@ -36,7 +36,9 @@ geom_heatcontour <- function(
 thm <- theme_minimal()
 
 ui <- navbarPage(
-  title = div(img(src="cmmid_newlogo.svg", height="45px"), span("Dengvaxia Maximum ROI"), height="50px"),
+  title = div(
+    a(img(src="cmmid_newlogo.svg", height="45px"), href="https://cmmid.github.io/"), span("Dengvaxia Maximum ROI", style="line-height:45px")
+  ),
   windowTitle = "Dengvaxia Maximum ROI",
   theme = "styling.css",
   tabPanel("Serosurvey Input", fluidPage(
@@ -69,7 +71,7 @@ ui <- navbarPage(
                     p("High Risk Fraction:", textOutput("p_H", inline = T))
                   ),
                   mainPanel( # display panel for inputs
-                    plotOutput("seroPlot", width = "auto")
+                    plotOutput("seroPlot", height = "auto")
                   )
     ))),
   tabPanel("ROI by Testing Strategy", fluidPage(
@@ -105,7 +107,7 @@ ui <- navbarPage(
                                                            min = 10, max = 10000, step = 10, value = 5000))
                   ),
                   mainPanel(
-                    plotOutput("strategyROI")
+                    plotOutput("strategyROI", height="auto")
                   )
     )
   )),
@@ -125,10 +127,11 @@ ui <- navbarPage(
                   ),
                   mainPanel(
                     #tableOutput("testROI"),
-                    plotOutput("scanROI")
+                    plotOutput("scanROI", height="auto")
                   )
     )
   )),
+  tabPanel("Notes", fluidPage(includeMarkdown("notes.md"))),
   position="fixed-top", collapsible = TRUE
 )
 
@@ -269,6 +272,9 @@ server <- function(input, output, session) {
       scale_linetype_ROIlvl() + scale_color_ROIsign() + scale_fill_ROI() +
       scale_x_startAge() + scale_y_endAge() +
       thm + theme(panel.grid.minor = element_blank())
+  },
+  height = function() {
+    session$clientData$output_strategyROI_width
   })
 
   output$testROI <- renderTable({
@@ -283,6 +289,9 @@ server <- function(input, output, session) {
       scale_linetype_ROIlvl() + scale_color_ROIsign() + scale_fill_ROI() +
       rescale_y_Vcost(input$S) + rescale_x_Tcost(input$S) +
       thm
+  },
+  height = function() {
+    session$clientData$output_scanROI_width
   })
 
 }

inst/shiny/demo/notes.md

+### Notes
+
+This application provides an interactive version of the analysis in [Serostatus Testing & Dengue Vaccine Cost-Benefit Thresholds](https://doi.org/10.1098/rsif.2019.0234).
+
+It is included as part of the [`denvax`](https://cran.r-project.org/package=denvax) package, and the source can be found as part of the [package source](https://gitlab.com/cabp_LSHTM/denvax/-/tree/master/inst/shiny/demo).
+
+### Authors
+
+This application was developed during a hack-a-thon hosted by the [Centre for Mathematical Modelling of Infectious Disease](https://cmmid.lshtm.ac.uk). The following people contributed: A. Richards, Y. Jafari, T. Sumner, B. Savagar, L. Yakob, N. Waterlow, Y. Liu, B. Quilty, J. Villabona Arenas, and D. Simons.
+
+The current version of the application was refined by Sam Clifford and Carl Pearson.

inst/shiny/demo/www/styling.css

@@ -34,6 +34,10 @@ hr { margin:5px; border-top: 1px solid grey; }
   background-color: #00BF6F !important;
 }
 
+.navbar-default .navbar-nav > li > a:hover {
+  color: #00BF6F;
+}
+
 .navbar-default .navbar-nav > li > a {
   color: white;
 }
@@ -42,6 +46,12 @@ hr { margin:5px; border-top: 1px solid grey; }
   background-color: white;
 }
 
+.navbar-default .navbar-brand:hover {
+  color: white !important;
+}
+
 .navbar-default .navbar-brand {
   color: white;
+  padding: 2.5px;
+  padding-right: 15px;
 }