update documentation and fix details in graphics

R/mod_tabItemDamage.R

@@ -94,8 +94,13 @@ mod_tabItemDamage_ui <- function(id){
             box(title = iconed("Damage", "cogs"),
                 solidHeader = TRUE,
                 width = 8, status = "success",
+                p("The graphic on the left is the histogram showing the probability distribution of Damage
+                 (default example is survival probability) along the period cover by source exposure."),
+                p("Damage unit is the survival probability of larvae as provided by the histogram.
+                   So here, damage is the daily probability of survival at each laying site."),
                 column(width = 6,
                        plotOutput(ns("profileDAMAGE")),
+                       p("You can download the data just generated through the CSV and the KML files."),
                        downloadButton(ns("download_DAMAGE"),
                                       "Download Damage CSV",
                                       style="color: #fff; background-color: #33595f; border-color: #052327"),
@@ -113,8 +118,6 @@ mod_tabItemDamage_ui <- function(id){
                                         onInitialize = I('function() { this.setValue(""); }')
                                       )
                        ),
-                       p("Legend of damage units is the survival probability of larvae as provided by the histogram.
-                       So here, damage is the daily probability of survival at each laying site."),
                        plotOutput(ns("mapDAMAGE"))
                 )
             )
@@ -342,6 +345,8 @@ mod_tabItemDamage_server <- function(input, output, session, r){
     ggplot() +
       theme_minimal() +
       scale_color_gradient(low = "green", high = "red", name = "Damage") +
+      geom_sf(data = r$landscapeSOURCE, alpha = 0.2, fill = "red", color = "red") +
+      geom_sf(data = r$landscapeHOST,  alpha = 0.2, fill = "blue", color = "blue") +
       geom_sf(data = r$individualSITE_dev) + 
       geom_sf(data = DFdamage(),
               aes(color = tryCatch(DAMAGE, error = function(cond){"black"})), size = 4, alpha = 0.5)

R/mod_tabItemDevelopment.R

@@ -94,6 +94,12 @@ mod_tabItemDevelopment_ui <- function(id){
                 solidHeader = TRUE,
                 width = 8,
                 status = "success",
+                p("The graphic on the left is the histogram showing the number of
+                emerging individuals (in brown) and the period of living (in green).
+                Of course, it should cover the period you defined for emergence, but also it extends this period.
+                The plot on the right is the map of the laying site (in black), additional
+                brown points are provide to highlight the date of emergence and green points represent period of living.
+                  You vertical red line on the left graphic correspond to the date you selected."),
                 column(width = 6,
                        plotOutput(ns("histIndDEV"))
                 ),
@@ -312,7 +318,7 @@ mod_tabItemDevelopment_server <- function(input, output, session, r){
     req(input$ctrlDATEMapIND) # need to avoid error
     ggplot() +
       theme_minimal() +
-      geom_sf(data = r$landscapeHOST) +
+      geom_sf(data = r$landscapeHOST,  alpha = 0.5, fill = "blue", color = "blue") +
       geom_sf(data = r$individualSITE, color = "black", size = 2) +
       geom_sf(data = DFmapINDIVIDUAL(), color = "#8ab600", size = 4, alpha = 0.5) +
       geom_sf(data = DFmapEMERGENCE(), color = "#a95e26", size = 4, alpha = 0.5)

R/mod_tabItemDispersal.R

@@ -53,6 +53,10 @@ mod_tabItemDispersal_ui <- function(id){
                 solidHeader = TRUE,
                 width = 6, status = "warning",
                 #
+                p("The shapefile provide previously needs to be convert into a raster.
+                Increasing this value can dramatically increase the computing time. So we fix maximum at 1024.
+               However, you have to keep in mind that resolution is the length of landscape border (previously defined by the square frame)
+               devided by the number of pixel (max 1024). For better resolution, you can upload the shiny App on your own machine."),
                 shinyWidgets::sliderTextInput(inputId = ns("kernelSizeRaster"),
                                 "Number of pixels along one side:",
                                 choices=2^(2:10),
@@ -299,9 +303,9 @@ mod_tabItemDispersal_server <- function(input, output, session, r){
         tags$br(),
         "Default value is 2^8.",
         tags$br(),
-        tags$b("Increasing this value can dramatically increase the computing time. So we fix maximum at 1024.
-               However, you have to keep in mind that resolution is the length of landscape border (previously defined by the square frame)
-               devided by the number of pixel (max 1024). For better resolution, you can upload the shiny app on your own machine.")
+        p("Increasing this value can dramatically increase the computing time. So we fix maximum at 1024.
+           However, you have to keep in mind that resolution is the length of landscape border (previously defined by the square frame)
+           devided by the number of pixel (max 1024). For better resolution, you can upload the shiny app on your own machine.")
       ),
       html = TRUE
     )

R/mod_tabItemExposure.R

@@ -62,11 +62,14 @@ mod_tabItemExposure_ui <- function(id){
             box(title = iconed("Exposure", "cogs"),
                 solidHeader = TRUE,
                 width = 8, status = "success",
+                p("The graphic on the left is the histogram of the distribution of Exposure 
+                in each laying site of the landscape along the period cover by source exposure."),
+                p("Exposure unit are the same as emission units."),
                 column(
                   width = 6,
                   plotOutput(ns("profileEXPOSURE")),
                   hr(),
-                  p("Dowload the exposure data set which has been generated."),
+                  p("Download the exposure data set which has been generated."),
                   downloadButton(ns("download_EXPOSURE"),
                                  "Download Exposure CSV",
                                  style="color: #fff; background-color: #33595f; border-color: #052327")#,
@@ -195,7 +198,7 @@ mod_tabItemExposure_server <- function(input, output, session, r){
       
       ggplot() +
         theme_minimal() +
-        labs(x = "Time", y = "Probability Distribution of Exposure") +
+        labs(x = "Time", y = "Distribution of Exposure") +
         geom_line(data = DFsumEXPOSURE,
                   aes(x = Date, y = mean_EXPOSURE), color = "red") +
         geom_ribbon(data = DFsumEXPOSURE,
@@ -230,6 +233,8 @@ mod_tabItemExposure_server <- function(input, output, session, r){
       ggplot() +
         theme_minimal() +
         scale_color_gradient(low = "green", high = "red", name = "Exposure") +
+        geom_sf(data = r$landscapeSOURCE, alpha = 0.2, fill = "red", color = "red") +
+        geom_sf(data = r$landscapeHOST,  alpha = 0.2, fill = "blue", color = "blue") +
         geom_sf(data = r$individualSITE_dev) +
         geom_sf(data = DFexposureINDIVIDUAL(),
                 aes(color = tryCatch(EXPOSURE, error = function(cond){"black"})), size = 4, alpha = 0.5)

R/mod_tabItemInteractiveMap.R

@@ -68,6 +68,8 @@ mod_tabItemInteractiveMap_ui <- function(id){
                 width = 12,
                 status = "success",
                 solidHeader = TRUE,
+                p("The Date you select here is the date of representation of the map hereafter,
+                  and correspond to the vertical red bars on the two histograms. "),
                 selectizeInput(ns("ctrlDATEMapRISK"),
                                label = "Choose Column Date",
                                choices = NULL,
@@ -75,10 +77,13 @@ mod_tabItemInteractiveMap_ui <- function(id){
                                  placeholder = 'Please select column below',
                                  onInitialize = I('function() { this.setValue(""); }')
                                )),
+                p("Histograms: (left) exposure, (right) damage."),
                 column(width = 6,
+                       p("Exposure distribution in landscape as a function of time."),
                        plotOutput(ns("profileRISKexposure"))
                 ),
                 column(width = 6,
+                       p("Damage distribution in landscape as a function of time."),
                        plotOutput(ns("profileRISKdamage"))
                 ),
                 column(width = 2,
@@ -88,6 +93,14 @@ mod_tabItemInteractiveMap_ui <- function(id){
                                    min = 0, max = 1000,
                                    value = 50)
                 ),
+                p("Risk map at the time provided. Legend of the risk map:"),
+                tags$ul(
+                  tags$li(strong("large rounded square"), "landscape frame - tick 'Frame' to add/remove"), 
+                  tags$li(strong("red area"), "source area - tick 'Source' to add/remove"),
+                  tags$li(strong("blue area"), "host area - tick 'Host' to add/remove"), 
+                  tags$li(strong("black points"), "laying site - tick 'Site' to add/remove"), 
+                  tags$li(strong("colored points"), "damage value - tick 'Damage point' to add/remove")
+                ),
                 column(width = 10,
                        leafletOutput(ns("mapRISK"), height = 500)
                        )
@@ -143,7 +156,7 @@ mod_tabItemInteractiveMap_server <- function(input, output, session, r){
     req(input$ctrlDATEMapRISK)
     ggplot() +
       theme_minimal() +
-      labs(x = "Time", y = "Probability Distribution of Exposure") +
+      labs(x = "Time", y = "Distribution of Exposure") +
       geom_line(data = DFhistogramEXPOSURE,
                 aes(x = Date, y = mean_EXPOSURE), color = "red") +
       geom_ribbon(data = DFhistogramEXPOSURE,