documentation of all items

R/mod_tabItemDamage.R

@@ -28,15 +28,14 @@ mod_tabItemDamage_ui <- function(id){
               collapsible = TRUE,
               closable = FALSE,
               footer_padding = FALSE,
-                p("Information about damage ..."),
-                hr(),
-                h4("Check list of previous items:"),
-                verbatimTextOutput(ns("CheckDamage")),
+              h4("Check list of previous items"),
+              verbatimTextOutput(ns("CheckDamage")),
               hr(),
-              h4("Once all elements in Check list is OK, this part allows to compute dispersal probability."),
-              br(),
-              h3("Computing damage:"),
-              tags$video(id = ns("videoDispersal"),
+              h4("Computing damage"),
+              p("Once all elements in Check list is OK, this part allows to compute damage probability.
+                There are two options, either a classical dose response model based on LC50 and the Slope,
+                or through the GUTS modelling approach were the user has to upload the parameters."),
+                tags$video(id = ns("videoDamage"),
                          type = "video/mp4",
                          src = "www/damage_capture2.mp4",
                          controls = "controls",
@@ -47,11 +46,6 @@ mod_tabItemDamage_ui <- function(id){
             box(title = iconed("Model", "sliders-h"),
                 solidHeader = TRUE,
                 width = 4, status = "warning",
-                  # actionButton(ns("Xple_DAMAGE"),
-                  #              "CLICK HERE FOR EXAMPLE DATA",
-                  #              icon("paper-plane"), 
-                  #              style="color: #fff; background-color: #33595f; border-color: #052327"),
-                  # hr(),
                   tabsetPanel(id = ns("tabsetDAMAGEsurv"),
                               tabPanel(title = "Dose Response",
                                        value = "DRsurvDAMAGE",

R/mod_tabItemDevelopment.R

@@ -28,15 +28,13 @@ mod_tabItemDevelopment_ui <- function(id){
               collapsible = TRUE,
               closable = FALSE,
               footer_padding = FALSE,
-                p("Information about development ..."),
-                hr(),
-                h4("Check list of previous items:"),
-                verbatimTextOutput(ns("CheckDevelopment")),
+              h4("Check list of previous items"),
+              verbatimTextOutput(ns("CheckDevelopment")),
               hr(),
-              h4("Once all elements in Check list is OK, this part allows to compute dispersal probability."),
-              br(),
-              h3("Computing site and date of emergences:"),
-              tags$video(id = ns("videoDispersal"),
+              h4("Computing development of the organisms."),
+              p("Once all elements in Check list is OK, this part allows to compute the development of the organisms.
+                Either by fixing a lifespan, or by uploading a Degree Day model. For the Degree Day model, the user must upload a time serie with temperature"),
+              tags$video(id = ns("videoDevelopment"),
                          type = "video/mp4",
                          src = "www/phenology_capture2.mp4",
                          controls = "controls",

R/mod_tabItemDispersal.R

@@ -28,22 +28,17 @@ mod_tabItemDispersal_ui <- function(id){
               collapsible = TRUE,
               closable = FALSE,
               footer_padding = FALSE,
-              # img(src = 'www/modelScheme_item_2.jpg', title = "item1",  width = "800px"),
-              hr(),
-              h4("Check list of previous items:"),
+              h4("Check list of previous items"),
+              p("Please, for each step of the app, check that all items of this kind of list is ok."),
               verbatimTextOutput(ns("CheckDispersal")),
               hr(),
-              h4("Once all elements in Check list is OK, this part allows to compute dispersal probability."),
-              br(),
-              # column(width = 6,
-                     # align="center",
-                     h3("Tutorial on running dispersal kernel:"),
-                     tags$video(id = ns("videoDispersal"),
-                                type = "video/mp4",
-                                src = "www/dispersal_capture2.mp4",
-                                controls = "controls",
-                                height = "300px")
-              # ),
+              h4("How to run a dispersal kernel"),
+              p("Once all elements in Check list is OK, this part allows to compute dispersal probability."),
+               tags$video(id = ns("videoDispersal"),
+                          type = "video/mp4",
+                          src = "www/dispersal_capture2.mp4",
+                          controls = "controls",
+                          height = "300px")
             )
           ),
           fluidRow( # width of fluidrow is 12

R/mod_tabItemEmission.R

@@ -31,14 +31,12 @@ mod_tabItemEmission_ui <- function(id){
               collapsible = TRUE,
               closable = FALSE,
               footer_padding = FALSE,
-              hr(),
-              h4("Check list of previous items:"),
+              h4("Check list of previous items"),
               verbatimTextOutput(ns("CheckEmission")),
               hr(),
-              h4("Once all elements in Check list is OK, this part allows to compute dispersal probability."),
-              br(),
-              h3("Computing convolution dispersal and emission:"),
-              tags$video(id = ns("videoDispersal"),
+              h4("Computing convolution dispersal and emission"),
+              p("Once all elements in Check list is OK, this part allows to compute dispersal probability."),
+              tags$video(id = ns("videoEmission"),
                          type = "video/mp4",
                          src = "www/emission_capture2.mp4",
                          controls = "controls",

R/mod_tabItemExposure.R

@@ -28,22 +28,20 @@ mod_tabItemExposure_ui <- function(id){
               collapsible = TRUE,
               closable = FALSE,
               footer_padding = FALSE,
-              p("Information about exposure ..."),
-              hr(),
-              h4("Check list of previous items:"),
+              h4("Check list of previous items"),
               verbatimTextOutput(ns("CheckExposure")),
               hr(),
-              h4("Once all elements in Check list is OK, this part allows to compute dispersal probability."),
-              br(),
-              h3("Computing exposure:"),
-              tags$video(id = ns("videoDispersal"),
+              h4("Computing exposure"),
+              p("Once all elements in Check list is OK, this part allows to compute exposure probability.
+                Nothing has to be upload or parameterized by the user, just click on the run button if emission and organisms overlap."),
+              tags$video(id = ns("videoExposure"),
                          type = "video/mp4",
                          src = "www/exposure_capture2.mp4",
                          controls = "controls",
                          height = "300px")
             )
           ),
-          fluidRow( # width of fluidrow is 12
+          fluidRow( # width of fluid-row is 12
             box(title = iconed("Overlapping", "calendar-check"),
                 solidHeader = TRUE,
                 width = 4, status = "warning",

R/mod_tabItemHost.R

@@ -28,15 +28,12 @@ mod_tabItemHost_ui <- function(id){
               collapsible = TRUE,
               closable = FALSE,
               footer_padding = FALSE,
-                p("Location of host plants."),
-                hr(),
-                h4("Check list of previous items:"),
-                verbatimTextOutput(ns("CheckHost")),
+              h4("Check list of previous items"),
+              verbatimTextOutput(ns("CheckHost")),
               hr(),
-              h4("Once all elements in Check list is OK, this part allows to compute dispersal probability."),
-              br(),
-              h3("Computing site and date of emergences:"),
-              tags$video(id = ns("videoDispersal"),
+              h4("Computing site and date of emergences"),
+              p("Once all elements in Check list is OK, this part allows to compute location of habitat (i.e., laying site)."),
+              tags$video(id = ns("videoHabitat"),
                          type = "video/mp4",
                          src = "www/habitat_capture2.mp4",
                          controls = "controls",

R/mod_tabItemInteractiveMap.R

@@ -47,12 +47,9 @@ mod_tabItemInteractiveMap_ui <- function(id){
                 collapsible = TRUE,
                 closable = FALSE,
                 footer_padding = FALSE,
-                  p("Information on Interactive Map ..."),
-                hr(),
-                h4("Once all elements in Check list is OK, this part allows to compute dispersal probability."),
-                br(),
-                h3("Computing site and date of emergences:"),
-                tags$video(id = ns("videoDispersal"),
+                h4("Explore the Interactive Map"),
+                p("The final risk map is given in the item."),
+                tags$video(id = ns("videoInteractiveMap"),
                            type = "video/mp4",
                            src = "www/interactiveMap_capture2.mp4",
                            controls = "controls",
@@ -284,26 +281,7 @@ mod_tabItemInteractiveMap_server <- function(input, output, session, r){
 
   })
 
-  # Use a separate observer to recreate the legend as needed.
-  # observe({
-  # 
-  #   req(r$damageINDIVIDUAL)
-  #   DFdamageUNNEST <-  r$damageINDIVIDUAL %>%
-  #         tidyr::unnest( c(Date, DAMAGE))
-  #   # req(DFdamageUNNEST())
-  # 
-  #   proxy <- leafletProxy("mapRISK")
-  # 
-  #   proxy %>% clearControls()
-  #   if (input$legend) {
-  #     pal <- colorpalDAMAGE()
-  #     proxy %>% addLegend(data = DFdamageUNNEST,
-  #                         position = "bottomright",
-  #                         pal = pal, values = ~DAMAGE
-  #     )
-  #   }
-  # })
-  
+
 
 }
     

R/mod_tabItemLandscape.R

@@ -32,27 +32,31 @@ mod_tabItemLandscape_ui <- function(id){
                 collapsible = TRUE,
                 closable = FALSE,
                 footer_padding = FALSE,
-                h4("In this part, you have to download the source file, the host file and to compute 
-                    or load a square frame including host and sources in the same spatial square."),
-                column(width = 6,
-                       align="center",
-                       h4("Tutorial on building KML landscape files."),
-                       tags$video(id = ns("videoLandscape_makeKML"),
-                                  type = "video/mp4",
-                                  src = "www/maizeFieldMap_VIDEO_medium2.mp4",
-                                  controls = "controls",
-                                  height = "300px")
-                       ),
-                column(width = 6,
-                       align="center",
-                       h4("Tutorial on Uploading landscape elements."),
-                       tags$video(id = ns("videoLandscape_load"),
-                                  type = "video/mp4",
-                                  src = "www/load_landscape_medium3.mp4",
-                                  controls = "controls",
-                                  height = "300px")
-                       )
-              )
+                p("In this part, you have to: (1) download the source file, (2) download the host file and (3) compute 
+                    or load a square frame to gather host and source within the same spatial square."),
+                hr(),
+                  h4("Tutorial on building KML landscape files."),
+                 p("The following video shows how to create a KML filr with umap,",
+                   a(href="umap", "https://umap.openstreetmap.fr/fr/"),
+                   ". But you can also use Google Earth to create a KML file."
+                   ),
+                 tags$video(id = ns("videoLandscape_makeKML"),
+                            type = "video/mp4",
+                            src = "www/maizeFieldMap_VIDEO_medium2.mp4",
+                            controls = "controls",
+                            height = "300px"),
+                hr(),
+                 h4("Tutorial on Uploading landscape elements."),
+                 p("Once you created a KML file, the following video presents the way to upload it in the
+                   app. While you can change it with the app, make sure 'source' and 'host' jml files
+                   have the same geographic coordinate system."
+                 ),
+                 tags$video(id = ns("videoLandscape_load"),
+                            type = "video/mp4",
+                            src = "www/load_landscape_medium3.mp4",
+                            controls = "controls",
+                            height = "300px")
+                )
             ),
             fluidRow( # width of fluidrow is 12
               box(title = iconed("Source and Host", "database"),
@@ -204,7 +208,7 @@ mod_tabItemLandscape_ui <- function(id){
                     solidHeader = FALSE,
                     p("Red: Source"),
                     p("Blue: Host"),
-                    plotly::plotlyOutput(ns("plotLANDSCAPE"))
+                    plotOutput(ns("plotLANDSCAPE"))
                   ),
                   box(
                     width = 6, status = "success",
@@ -378,14 +382,12 @@ mod_tabItemLandscape_server <- function(input, output, session, r){
     paste("EPSG initial:", sf::st_crs(r$landscapeSQUAREFRAME$epsg))
   })
   
-  output$plotLANDSCAPE <- plotly::renderPlotly({
-    plotly::ggplotly(
-      p = ggplot() +
+  output$plotLANDSCAPE <- renderPlot({
+      ggplot() +
         theme_minimal() +
         geom_sf(data = r$landscapeSQUAREFRAME, fill = NA) +
         geom_sf(data = r$landscapeSOURCE, alpha = 0.5, fill = "red", color = "red") +
         geom_sf(data = r$landscapeHOST, alpha = 0.5, fill = "blue", color = "blue")
-    )
   })
 
   output$mapLANDSCAPE <- renderLeaflet({

R/mod_tabItemStart.R

@@ -64,24 +64,14 @@ of the", strong("dynamics of toxin ingestion on lethal and sublethal effects at
               footer_padding = FALSE,
               solidHeader = TRUE,
                 align="center",
-                # solidHeader = TRUE,
-                # title = iconed("Start", "rocket"),
-                # status = "success",
                 actionButton('switchLandscapeTab',
                              label = h4("Click Here to Start Modelling"),
-                             # icon = icon("forward"),
                              style="color: #fff; background-color: #00a65a; border-color: #00a65a")
-                # hr(),
-                # actionButton('switchLandscapeTab',
-                #              label = h5("Wait, you may need some", strong("information"), "about how the", strong("application"), "work... what is just the object of the next", strong("blue box.")),
-                #              icon = icon("pause"),
-                #              style="color: #fff; background-color: #00c0ef; border-color: #00c0ef")
             )
           ),
           fluidRow(
-            hr(),
             shinydashboardPlus::gradientBox(
-              title = iconed(" - How to Run and Explore a Simulation", "info"),
+              title = iconed(" - Information", "info"),
               width = 12,
               gradientColor = "purple",
               boxToolSize = "xs",
@@ -89,33 +79,34 @@ of the", strong("dynamics of toxin ingestion on lethal and sublethal effects at
               closable = FALSE,
               footer_padding = FALSE,
               solidHeader = TRUE,
-              column(
-                width = 6,
-                # align="center",
-                p(strong("Getting Started"), "in the current home page, and follow the", strong("7 steps:"), 
-                  strong("1. Landscape"), "you define a landscape with sources and host plant location,",
-                  strong("2. Dispersal"), ": apply a dispersal kernel on sources,",
-                  strong("3. Emission"), ": apply emission function on sources,",
-                  strong("4. Host"), ": define location and phenology,",
-                  strong("5. Development"), ": define development model of organisms,",
-                  strong("6. Exposure"), ": compute exposure of organisms,",
-                  strong("7. Damage"), ": compute lethal and eventually sublethal damages,",
-                  strong("Interactive Map"), ": explore results on maps,",
-                  strong("Report"), ": compose a report of simulation."),
-                tags$img(src = 'www/modelScheme.jpg',
-                         title = "EFSA Home", 
-                         height = "350px")
+              # ---
+              hr(),
+              h4("General structure of the application"),
+              p("The application is made of 7 steps of computing and an Interactive Map:"),
+              tags$ul(
+                tags$li(strong("Getting Started"), "in the current home page, and follow the", strong("7 steps:")), 
+                tags$li(strong("1. Landscape"), "you define a landscape with sources and host plant location,"),
+                tags$li(strong("2. Dispersal"), ": apply a dispersal kernel on sources,"),
+                tags$li(strong("3. Emission"), ": apply emission function on sources,"),
+                tags$li(strong("4. Host"), ": define location and phenology,"),
+                tags$li(strong("5. Development"), ": define development model of organisms,"),
+                tags$li(strong("6. Exposure"), ": compute exposure of organisms,"),
+                tags$li(strong("7. Damage"), ": compute lethal and eventually sublethal damages,"),
+                tags$li(strong("Interactive Map"), ": explore results on maps,")
               ),
-              column(width = 6,
-                     align="center",
-                     h4("Video taking a quick look at all simulation steps:"),
-                     br(),
-                     tags$video(id = ns("videoStart_all"),
-                                type = "video/mp4",
-                                src = "www/video_allStart2.mp4",
-                                controls = "controls",
-                                height = "350px")
-              )
+              tags$img(src = 'www/modelScheme.jpg',
+                       title = "EFSA Home", 
+                       height = "350px"),
+              hr(),
+              h4("Quick look at all simulation steps"),
+              p("The following video shows the use of all 7 steps of the application. 
+                In each item, additional video detail its use."),
+              br(),
+              tags$video(id = ns("videoStart_all"),
+                         type = "video/mp4",
+                         src = "www/video_allStart2.mp4",
+                         controls = "controls",
+                         height = "350px")
             )
           ),
           briskaRshinyApp::footerPage()

R/zz_fun.R

@@ -41,6 +41,9 @@ headerNavigationPage <- function(backNavKey, nextNavKey){
       collapsible = FALSE,
       closable = FALSE,
       footer_padding = FALSE,
+      p("While you can move between items using the sidebar, we recommand you the use this navigation box with blue and green button.
+        The reason is that some computing requires previous items to be completed: for instance, dispersal computing in the second item
+        requires to have a source file downloaded in the first item."),
       column(width = 6,
              h4("Come back to the previous page," ),
              actionButton(backNavKey,