Multiple updates to ui elements, started with study region implementa…

…tion #2

DESCRIPTION

@@ -21,16 +21,19 @@ Imports:
     DT,
     waiter,
     dplyr,
-    readr,
+    leaflet,
+    sf,
+    terra,
+    readr
+Suggests:
     markdown,
-    rmarkdown
+    rmarkdown,
+    spelling,
+    testthat (>= 3.0.0)
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 RoxygenNote: 7.3.1
 URL: https://github.com/iiasa/ODPSCP
 BugReports: https://github.com/iiasa/ODPSCP/issues
-Suggests: 
-    spelling,
-    testthat (>= 3.0.0)
 Config/testthat/edition: 3

NEWS.md

@@ -3,6 +3,8 @@
 * Incorporated Expert-Feedback and updated the protocol with additional fields and explanations.
 * Added glossary, to be further expanded in future versions #4
 * Added tooltip to the protocol for each fields (can be toggled off) #6
+* Added option for enabling study region delineation #2
+* Added option to export a word or pdf summary of the protocol #5
 * Added a bookmark option to store the current setting of the protocol as server id (experimental)
 
 ## Version 0.2

R/ODPSCP-package.R

@@ -0,0 +1,14 @@
+#' @title ODPSCP
+#'
+#' @description
+#' The ODPSCP shiny interface comes in a series of UI and server plus helper functions
+#' that support the standardized reporting of prioritization results.
+#'
+#' @name ODPSCP
+#' @docType package
+#' @keywords internal
+"_PACKAGE"
+
+globalVariables(c(
+  "element"
+))

R/app_ui.R

@@ -28,13 +28,14 @@ app_ui <- function(request) {
           color = "primary",
           opacity = 0,
           href = NULL,
-          image = shiny::img(src = "www/logo.png", height = "20px")
+          image = shiny::img(src = base::normalizePath(system.file("app/www/logo.png", package = "ODPSCP")),
+                             height = "20px")
         ),
         status = "white",
         border = TRUE,
         compact = FALSE,
         leftUi = NULL, rightUi = NULL,
-        shiny::div(style="position:relative; left:calc(65%);",
+        shiny::div(style="position:relative; left:calc(5%);",
                    shinyWidgets::actionBttn(
                      inputId = "bookmark",
                      label = "Save settings",

R/mod_Design.R

@@ -29,7 +29,7 @@ mod_Design_ui <- function(id){
                    design elements of the study. These elements usually do not
                    consider methodological specifications of the planning, but
                    rather the conceptual understanding of the aims, purpose, and
-                   framework underlying a study."
+                   any framework underlying a study."
                  ),
                  shiny::hr()
           )
@@ -74,10 +74,11 @@ mod_Design_ui <- function(id){
                      # Study framework
                      shiny::p("Does the study follow an analytical framework, either explicitly
                        defined within the study or through a reference to previous
-                       work? This could for example also be a specific planning protocol."),
+                       work? This could for example also be a specific planning protocol or established
+                       approaches such as structure decision making or adapative management."),
                      shiny::p("Example framework references:"),
                      shiny::p("Pressey, R. L., & Bottrill, M. C. (2009). Approaches to landscape-and seascape-scale conservation planning: convergence, contrasts and challenges. Oryx, 43(4), 464-475."),
-                     shiny::p("Álvarez-Romero, J. G., Adams, V. M., Pressey, R. L., Douglas, M., Dale, A. P., Augé, A. A., ... & Perdrisat, I. (2015). Integrated cross-realm planning: A decision-makers' perspective. Biological Conservation, 191, 799-808."),
+                     shiny::p("Alvarez-Romero, J. G., Adams, V. M., Pressey, R. L., Douglas, M., Dale, A. P., Auge, A. A., ... & Perdrisat, I. (2015). Integrated cross-realm planning: A decision-makers' perspective. Biological Conservation, 191, 799-808."),
                      shiny::p("Niemiec, R. M., Gruby, R., Quartuch, M., Cavaliere, C. T., Teel, T. L., Crooks, K., ... & Manfredo, M. (2021). Integrating social science into conservation planning. Biological Conservation, 262, 109298."),
                      shinyWidgets::pickerInput(
                        inputId = ns("studyframework"),
@@ -134,11 +135,14 @@ mod_Design_ui <- function(id){
                       such as the identification of areas to be placed under
                       conservation management (e.g. Protected areas)"),
                     shiny::selectizeInput(inputId = ns("studypurpose"),
-                                          label = "Identify or add a primary purpose",
-                                          choices = c("","Area-based allocation", "Management improvement",
-                                                      "Action-based planning", "Monitoring and evaluation",
-                                                      "Land-use allocation"),
-                                          multiple = FALSE,
+                                          label = "Identify or add primary purpose(s)",
+                                          choices = c("","Area-based allocation",
+                                                      "Management evaluation",
+                                                      "Management improvement",
+                                                      "Action-based planning",
+                                                      "Monitoring and evaluation"
+                                                      ),
+                                          multiple = TRUE,
                                           options = list(create = TRUE,
                                                          placeholder = "Choose from list, or type and click to add a new option."))
                   ),
@@ -265,6 +269,10 @@ mod_Design_ui <- function(id){
                         solidHeader = TRUE,
                         status = "secondary",
                         collapsible = FALSE,
+                        shiny::p("Select or add broad groups of who was engaged.
+                                 Note that co-authors are generally not considered stakeholders
+                                 unless co-authorship is given due to co-design of the
+                                 whole planning study."),
                         shiny::selectizeInput(inputId = ns("stakeholdertype"),
                                               label = "Who was engaged?",
                                               choices = c("Policy makers (International)",

R/mod_Export.R

@@ -27,21 +27,45 @@ mod_Export_ui <- function(id){
             width = 12,
             solidHeader = TRUE,
             collapsible = FALSE,
-            "All protocol entries can be exported in a Range of different formats
-            for further use. Currently supported are the compressed 'rData', 'csv' and
-            'yaml' format.
-            ",
+            shiny::p(
+              "All protocol entries can be exported in a range of different formats
+              for further use such as appending them to a manuscript.
+              It should be noted that only 'rData', 'csv' and 'yaml' are
+              machine-readable formats and be imported again by ODPSCP.
+              "
+            ),
+            shiny::br(),
             # Output format
             shinyWidgets::radioGroupButtons(
               inputId = ns("downloadFormat"),
               label = "Output Format",
               individual = TRUE,
+              justified = TRUE,
+              size = "lg",
               status = "info",
-              choices = c('rData', 'csv', 'yaml'),
-              selected = 'rData'
+              choices = c('docx', 'pdf', 'rData', 'csv', 'yaml'),
+              selected = 'rData',
+              checkIcon = list(
+                yes = shiny::icon("circle-down"),
+                no = NULL
+              )
             ),
             shiny::br(),
             # Conditional info
+            shiny::conditionalPanel(
+              condition = "input.downloadFormat == 'docx'",
+              ns = ns,
+              shiny::p("Protocol will be rendered as docx Word document, which
+                       can be easily modified as well. Suitabile for manuscript
+                       appendices or personal records.")
+            ),
+            shiny::conditionalPanel(
+              condition = "input.downloadFormat == 'pdf'",
+              ns = ns,
+              shiny::p("Protocol will be rendered as document and then converted
+                       to a PDF format. This is the most convenient format for
+                       appending the protocol to any publications for example.")
+            ),
             shiny::conditionalPanel(
               condition = "input.downloadFormat == 'rData'",
               ns = ns,
@@ -66,12 +90,16 @@ mod_Export_ui <- function(id){
               any text editor and loaded as lists into R via yaml::read_yaml(file).")
             ),
             shiny::br(),
+            shiny::hr(),
+            shiny::div(id = ns("missing"), class = 'missing',
+                       shiny::textOutput(outputId = ns("missingtext"))),
+            shiny::br(),
             # Button
             shiny::downloadButton(ns("downloadData"), "Download the protocol")
           )
         ),
         shiny::tabPanel(
-          title = "Render protocol",
+          title = "Render protocol table",
           icon = shiny::icon("list-alt",lib = "glyphicon"),
           bs4Dash::box(
             title = "Protocol",
@@ -107,6 +135,13 @@ mod_Export_server <- function(id, results){
                     editable = FALSE)
     })
 
+    # Get mandatory protocol entries
+    mand <- get_protocol_mandatory()
+
+    # Check for mandatory outputs and highlight them in text
+    output$missingtext <- shiny::renderText("Highlight here all entries not yet filled!")
+    # observeEvent()
+
     # Get output format
     oftype <- shiny::reactive({input$downloadFormat})
 
@@ -136,6 +171,12 @@ mod_Export_server <- function(id, results){
           protocol <- format_protocol(results, format = "list")
           yaml::write_yaml(protocol, file = file)
           # yaml::read_yaml("../../../Downloads/test.yaml")
+        } else if(oftype() == "docx"){
+          # Create document from results
+          message("Not yet implemented...")
+        } else if(oftype() == "pdf"){
+          # Create document from results
+          message("Not yet implemented...")
         }
       }
     )

R/mod_Glossary.R

@@ -44,7 +44,7 @@ mod_Glossary_server <- function(id){
                          package = "ODPSCP",
                          mustWork = TRUE)
     output$glossary_table <- DT::renderDataTable(
-      read.csv(ppath, sep = ",",header = TRUE) |>
+      utils::read.csv(ppath, sep = ",",header = TRUE) |>
         DT::datatable(filter = "none", rownames = FALSE,
                       editable = FALSE)
     )

R/mod_Home.R

@@ -31,17 +31,15 @@ mod_Home_ui <- function(id){
                  from a range of scientific disciplines.",
              style= "font-size: 18px;"),
 
-              shiny::p("Area-based and action-based conservation planning are critical scientific
-                tools in reaching conservation policy objectives across scales.
-                Yet despite decades of research and numerous scientific advances
-                in Europe ",shiny::a(href = 'https://osf.io/8x2ug/', '(Jung et al. 2023)',
+              shiny::p("Area-based and action-based conservation planning are critical
+                       in reaching conservation policy objectives across scales. Yet
+                       despite decades of research and numerous scientific advances
+                       in Europe ",shiny::a(href = 'https://osf.io/8x2ug/', '(Jung et al. 2023)',
                                                     target = "_blank", .noWS = "outside"),".",
-                " and globally ",shiny::a(href = 'https://www.annualreviews.org/doi/10.1146/annurev-environ-102016-060902',
-                                   '(McIntosh et al. 2017)',
-                                   target = "_blank", .noWS = "outside"),
-                ", it often remains incomprehensible for those unfamiliar with the
-                planning how decisions where reached or what factors were considered
-                influential in determining the identified outcomes.",
+                       " and globally ",shiny::a(href = 'https://www.annualreviews.org/doi/10.1146/annurev-environ-102016-060902', '(McIntosh et al. 2017)', target = "_blank", .noWS = "outside"),
+                       ", it often remains incomprehensible for those unfamiliar with the
+                       planning how decisions where reached or what factors were considered
+                       influential in determining the identified outcomes.",
                style= "font-size: 18px;"),
 
              # img(src = "", width = "60%", style="display: block; margin-left: auto; margin-right: auto;
@@ -54,7 +52,26 @@ mod_Home_ui <- function(id){
                expert evaluation of the conducted planning. Third, it helps study
                authors and decision makers to identify key strength, but also
                weaknesses of a systematic planning exercise. ", style= "font-size: 18px;"),
-
+             # --- #
+             shiny::hr(),
+             shinyWidgets::prettyCheckboxGroup(
+               inputId = ns("eligibility"),
+               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! *",
+                           "Use an algorithic prioritization to identify best areas or actions! **"),
+               icon = shiny::icon("thumbs-up"),
+               status = "primary",
+               outline = TRUE,
+               inline = TRUE,
+               plain = TRUE,
+               animation = "jelly"
+             ),
+             shiny::helpText("* This is not say that non-biodiversity focussed planning studies (such as optimal cropland management allocation) can not be entered per se."),shiny::br(),
+             shiny::helpText("** Studies presenting methodological advances are not suitable for the protocol,
+                             unless they are demonstrated in an applied scenario."),
+             shiny::hr(),
              shiny::p("This Shiny web application helps to implement the protocol through
                an easy understandable user interface and allows export the created
                protocols in a range of formats for further usages. We encourage the