Multiple smaller fixes and addition of threats

iiasa · Apr 2, 2024 · 6305cf9 · 6305cf9
1 parent 0fac477
commit 6305cf9
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Showing 9 changed files with 177 additions and 19 deletions.
diff --git a/R/app_ui.R b/R/app_ui.R
@@ -203,6 +203,7 @@ golem_add_external_resources <- function() {
     sever::useSever(),
     waiter::use_waiter(),
     shinyFeedback::useShinyFeedback(),
+    shinyWidgets::useSweetAlert(),
     shinyjs::useShinyjs()
   )
 }
diff --git a/R/mod_Design.R b/R/mod_Design.R
@@ -189,7 +189,12 @@ mod_Design_ui <- function(id){
                       parameters or input data. Examples include planning approaches
                       that account for various climate scenarios or assumptions regarding
                       constraints. Please record whether there multiple scenarios
-                      or variants have been explored."),
+                      or variants have been explored and how"),
+                    shiny::br(),
+                    shiny::helpText("What does not qualify here: 'Scenarios' that
+                                    are essentially sensitivity checks or parameter
+                                    calibrations. Only select Yes if multiple outputs are
+                                    presented in the work."),
                     shinyWidgets::awesomeRadio(
                       inputId = ns("checkscenarios"),
                       label = "Are there multiple variants or scenarios explored in the planning?",
@@ -254,7 +259,7 @@ mod_Design_ui <- function(id){
                         shinyWidgets::pickerInput(
                           inputId = ns("stakeholderint"),
                           label = "Types of stakeholder interactions:",
-                          choices = c("Informed","Consulted","Involved",
+                          choices = c("Informed","Consulted","Dialogue","Involved",
                                       "Collaborated","Co-design"),
                           multiple = TRUE,
                           options = list(

diff --git a/R/mod_Export.R b/R/mod_Export.R
@@ -139,8 +139,15 @@ mod_Export_server <- function(id, results){
     mand <- get_protocol_mandatory()
 
     # Check for mandatory outputs and highlight them in text
-    output$missingtext <- shiny::renderText("Highlight here all entries not yet filled!")
-    # observeEvent()
+    shiny::observeEvent(input$downloadData, {
+        # # Check the value of all mandatory fields
+        # output$missingtext <- shiny::renderText({
+        #   # validate(
+        #   #   need(input$sldr > 5,"Require > 5")
+        #   # )
+        #   test
+        # })
+    })
 
     # Get output format
     oftype <- shiny::reactive({input$downloadFormat})

diff --git a/R/mod_Home.R b/R/mod_Home.R
@@ -59,7 +59,7 @@ mod_Home_ui <- function(id){
                label = "In order for a planning study to be eligible for the protocol they should:",
                choices = c("Make use of decision theoretic or multiple-criteria-based approaches!",
                            "Are spatial, spatial-temporal or at least use spatial input!",
-                           "Have a biodiversity and/or conservation focus or angle! *",
+                           "Have a biodiversity and/or conservation objective! *",
                            "Use an algorithic prioritization to identify best areas or actions! **"),
                icon = shiny::icon("thumbs-up"),
                status = "primary",

diff --git a/R/mod_Overview.R b/R/mod_Overview.R
@@ -247,7 +247,7 @@ mod_Overview_ui <- function(id){
             collapsed = FALSE,
             collapsible = TRUE,
             # icon = icon("magnifying-glass-chart"),
-            shiny::imageOutput(ns("peng2011"),inline = TRUE,fill = TRUE),
+            shiny::imageOutput(ns("peng2011"),inline = TRUE,fill = FALSE),
             shiny::br(),
             shiny::helpText("Source: Peng, R. D. (2011). Reproducible research in computational science. Science, 334(6060), 1226-1227."),
             shiny::br(),
@@ -484,8 +484,8 @@ mod_Overview_server <- function(id, results, parentsession){
       )
       # Return a list containing the filename and alt text
       list(src = path_figure,
-           width = "80%",
-           height = "50%",
+           width = "300px",
+           height = "120px",
            alt = paste("Peng 2011, Reproducible Research in Computational Science, Science"))
 
     }, deleteFile = FALSE)

diff --git a/R/mod_Prioritization.R b/R/mod_Prioritization.R
@@ -169,7 +169,8 @@ mod_Prioritization_ui <- function(id){
                          chosen representative indicators or values.",
                          "An example would be for example summarizing the average amount of
                          a threatened species range covered, or overlap with other spatial layers."),
-                       DT::DTOutput(outputId = ns("perfidenticators")),
+                       shiny::br(),
+                       DT::DTOutput(outputId = ns("evalperformance")),
                        shiny::actionButton(inputId = ns("add_indicator"), label = "Add a new indicator",
                                            icon = shiny::icon("plus")),
                        shiny::actionButton(inputId = ns("remove_indicator"), label = "Remove last indicator",
@@ -239,7 +240,7 @@ mod_Prioritization_server <- function(id, results, parentsession){
     ids <- get_protocol_ids(group = "prioritization")
     shiny::observe({
       for(id in ids){
-        if(id == "perfidenticators"){
+        if(id == "evalperformance"){
           results[[id]] <- data.frame(indicators()) |> asplit(MARGIN = 1)
         } else {
           results[[id]] <- input[[id]]
@@ -293,15 +294,15 @@ mod_Prioritization_server <- function(id, results, parentsession){
     })
 
     #output the datatable based on the dataframe (and make it editable)
-    output$perfidenticators <- DT::renderDT({
+    output$evalperformance <- DT::renderDT({
       DT::datatable(indicators(),rownames = FALSE,
                     filter = "none", selection = "none",
                     style = "auto",
                     editable = TRUE)
     })
 
-    shiny::observeEvent(input$perfidenticators_cell_edit, {
-      info <- input$perfidenticators_cell_edit
+    shiny::observeEvent(input$evalperformance_cell_edit, {
+      info <- input$evalperformance_cell_edit
       modified_data <- indicators()
       modified_data[info$row, info$col+1] <- info$value
       indicators(modified_data)

diff --git a/R/mod_Specification.R b/R/mod_Specification.R
@@ -176,7 +176,7 @@ mod_Specification_ui <- function(id){
                          shiny::p("Planning can be conducted on all land or sea within a given
                            region, but it can also be specific to certain ecosystems
                            or land-use types, such as for example forests.",
-                           shiny::strong("Check No if all available land or sea was considered.")),
+                           shiny::strong("Check No if all available land or sea within the study region was considered.")),
                           shinyWidgets::awesomeRadio(
                             inputId = ns("checkecosystem"),
                             label = "Was there any ecosystem specificity?",
@@ -263,6 +263,98 @@ mod_Specification_ui <- function(id){
                      )
                ) # Column end
              ), # Fluid row end
+            shiny::br(),
+            # Entries #
+            shiny::fluidRow(
+              shiny::column(width = 2),
+              shiny::column(width = 12,
+                            # Threats
+                            bs4Dash::box(
+                              title = 'Threats and pressures',
+                              closable = FALSE,
+                              width = 12,
+                              solidHeader = TRUE,
+                              status = "primary",
+                              collapsible = TRUE,
+                              shiny::p("Select any threats or pressures that were targeted in the planning
+                                       or that, directly or indirectly, shape the planning outcome.
+                                       The threat description broadly follows the IUCN Threat categorization system."),
+                              shiny::br(),
+                              shiny::helpText("IUCN Threat classification: https://www.iucnredlist.org/resources/threat-classification-scheme"),
+                            # Threat types
+                            bs4Dash::box(
+                              title = "Threat or pressure types",
+                              closable = FALSE,
+                              width = 12,
+                              solidHeader = TRUE,
+                              status = "secondary",
+                              collapsible = FALSE,
+                              shinyWidgets::pickerInput(
+                                inputId = ns("threattypes"),
+                                label = "Select/deselect all options",
+                                choices = c(
+                                  "None",
+                                  "Residential & commercial development",
+                                  "Agriculture & Aquaculture",
+                                  "Energy production & Mining",
+                                  "Transportation & Traffic",
+                                  "Biological Resource Use (fishing, harvesting, logging)",
+                                  "Human Intrusions & Disturbance (recreation, war)",
+                                  "Natural system modification (Fire, Dams)",
+                                  "Invasive species, genes or diseases",
+                                  "Pollution (Waste water, pollutants)",
+                                  "Climate Change and severe weather (droughts, flooding)",
+                                  "Geological events (Earthquakes)",
+                                  "Other"
+                                ),
+                                options = list(`actions-box` = TRUE),
+                                multiple = TRUE
+                              ),
+                              shiny::br(),
+                              # Any other types?
+                              shiny::conditionalPanel(
+                                condition = "input.threattypes == 'Other'",
+                                ns = ns,
+                                shiny::textAreaInput(inputId = ns("otherthreattype"), label = "Other types",
+                                                     placeholder = 'Any other type of threat or pressure not considered? Describe',
+                                                     height = "45px", width = "100%", resize = "none")
+                                )
+                          ), # Threat type box end
+                          shiny::br(),
+                          # How were Threats considered/included?
+                          bs4Dash::box(
+                            title = "How were threats considered in the planning?",
+                            closable = FALSE,
+                            width = 12,
+                            solidHeader = TRUE,
+                            status = "secondary",
+                            collapsible = FALSE,
+                            shiny::p('There are multiple ways of including threats and pressures, for example
+                                     by considering them as risk factor in the prioritization,
+                                     as cost or penalty in selecting a solution.
+                                     Here we record these various options.'),
+                            shinyWidgets::pickerInput(
+                              inputId = ns("threatinclusion"),
+                              label = "Select/deselect all options",
+                              choices = c(
+                                "Feature (aggregated risk)",
+                                "Feature (individual)",
+                                "Cost layer",
+                                "Selection penalty",
+                                "Exclusion area",
+                                "Management zone or feature contribution",
+                                "Other"
+                              ),
+                              options = list(`actions-box` = TRUE),
+                              multiple = TRUE
+                            ),
+                            shiny::textAreaInput(inputId = ns("threatdetail"), label = "Threat details",
+                                                 placeholder = 'Elaborate on other ways of including threats in the planning',
+                                                 height = "60px", width = "100%", resize = "vertical")
+                          )
+                  ) # Threats and pressures box end
+              ) # Fluid column end
+             ), # Fluidrow end
              shiny::br(),
              # Entries #
              shiny::fluidRow(

diff --git a/R/utils_format_protocol.R b/R/utils_format_protocol.R
@@ -66,7 +66,8 @@ format_protocol <- function(results, format = "data.frame",path_protocol = NULL)
 #' List to table
 #'
 #' @description
-#' A helper function that converted
+#' A helper function that converts a list to a table. Used internally
+#' by format_protocol.
 #'
 #' @param protocol A filled out protocol in [`list`] format.
 #' @return The return value, if any, from executing the utility.

diff --git a/inst/01_protocol.yaml b/inst/01_protocol.yaml
@@ -258,6 +258,7 @@ design:
     conditional_options:
       - Informed
       - Consulted
+      - Dialogue
       - Involved
       - Collaborated
       - Co-design
@@ -338,8 +339,8 @@ specification:
       - m2
       - km2
       - ha
-      - ft2,
-      - yd2,
+      - ft2
+      - yd2
       - mi2
       - acre
     mandatory: false
@@ -408,6 +409,54 @@ specification:
     mandatory: true
     popexample: "Existing protected areas were considered to be part of every solution (included)."
 
+  threattypes:
+    render-nr: 1
+    render-id: 'threattypes'
+    render-group: 'threatpressures'
+    question: 'What types of threats or pressures are included in the planning?'
+    description: 'Select any threats or pressures that were targeted in the planning or that, directly or indirectly, shape the planning outcome. The threat description broadly follows the IUCN Threat categorization system.'
+    fieldtype: 'multiplechoice'
+    options:
+      - None
+      - Residential & commercial development
+      - Agriculture & Aquaculture
+      - Energy production & Mining
+      - Transportation & Traffic
+      - Biological Resource Use (fishing, harvesting, logging)
+      - Human Intrusions & Disturbance (recreation, war)
+      - Natural system modification (Fire, Dams)
+      - Invasive species, genes or diseases
+      - Pollution (Waste water, pollutants)
+      - Climate Change and severe weather (droughts, flooding)
+      - Geological events (Earthquakes)
+      - Other
+    fieldtype_conditional_render-id: 'otherthreattype'
+    fieldtype_conditional: 'textbox'
+    mandatory: true
+    popexample: "Select any type of pressure or threat considered in this work."
+
+  threatinclusion:
+    render-nr: 2
+    render-id: 'threatinclusion'
+    render-group: 'threatpressures'
+    question: 'How were threats considered in the planning?'
+    description: 'There are multiple ways of including threats and pressures, for example
+    by considering them as risk factor in the prioritization, as cost or penalty in selecting
+    a solution. Here we record these various options.'
+    fieldtype: 'multiplechoice'
+    options:
+      - Feature (aggregated risk)
+      - Feature (individual)
+      - Cost layer
+      - Selection penalty
+      - Exclusion area
+      - Management zone or feature contribution
+      - Other
+    fieldtype_conditional_render-id: 'threatdetail'
+    fieldtype_conditional: 'textbox'
+    mandatory: false
+    popexample: "Anthropogenic land-use pressures were considered as a selection penalty"
+
   featuretypes:
     render-nr: 1
     render-id: 'featuretypes'
@@ -465,6 +514,8 @@ specification:
     popexample: "A description where or how the feature layers came about, if they are
     the result of some modelling process or similar."
 
+
+
 #### Context ####
 context:
   decisionvariable:
@@ -545,8 +596,8 @@ context:
     fieldtype: 'selectizedropdown'
     options:
       - None
-      - Flat (e.g. 30 percent),
-      - Log-linear,
+      - Flat (e.g. 30 percent)
+      - Log-linear
       - Minimum Area of Suitable Habitat
       - Other
     fieldtype_conditional_render-id: 'targetdetail'