Merge pull request bcgov#35 from poissonconsulting/dev

Updates to app

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: shinywqbench
 Title: R Shiny App to Calculates Aquatic Life Benchmarks
-Version: 0.1.0
+Version: 0.1.0.9000
 Authors@R: c(
     person("Ayla", "Pearson", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0001-7388-1222")),
@@ -23,6 +23,7 @@ Imports:
     ggplot2,
     knitr,
     markdown,
+    pkgload,
     readr,
     rlang,
     rmarkdown,

NAMESPACE

@@ -4,4 +4,5 @@ export(run_wqbench_app)
 import(shiny)
 importFrom(knitr,kable)
 importFrom(markdown,markdownToHTML)
+importFrom(pkgload,load_all)
 importFrom(rlang,.data)

NEWS.md

@@ -1,9 +1,12 @@
 <!-- NEWS.md is maintained by https://cynkra.github.io/fledge, do not edit -->
 
-# shinywqbench 1.0.0
+# shinywqbench (development version)
 
-- App is fully functional
+- Updating title, adding instructions to data tab, updating user and about tabs
+
+# shinywqbench 0.1.0
 
+- App is fully functional
 
 # shinywqbench 0.0.0.9000
 

R/app-ui.R

@@ -20,7 +20,7 @@ app_ui <- function() {
     shinyjs::useShinyjs(),
     waiter::useWaiter(),
     navbarPage(
-      title = "Aquatic Life Water Quality Benchmark Generator - DRAFT",
+      title = "Emergent Contaminant Aquatic Life Benchmarks - DRAFT",
       selected = "tab1",
       id = "navbarID",
       tabPanel(

R/mod-data.R

@@ -15,41 +15,61 @@
 mod_data_ui <- function(id, label = "data") {
   ns <- NS(id)
 
-  sidebarLayout(
-    sidebarPanel(
-      tagList(
-        radioButtons(
-          ns("chem_type"),
-          label = "Select chemical by",
-          choices = c("Name", "CAS Registry Number (without dashes)"),
-          selected = "Name",
-          inline = TRUE
-        ),
-        shinyjs::hidden(
-          div(
-            id = ns("div_name"),
-            selectizeInput(
-              ns("select_chem_name"),
-              label = "",
-              choices = NULL
-            ),
-          )
-        ),
-        shinyjs::hidden(
-          div(
-            id = ns("div_cas"),
-            selectizeInput(
-              ns("select_cas_num"),
-              label = "",
-              choices = NULL,
-              selected = NULL
+  fluidRow(
+    column(
+      4,
+      wellPanel(
+        tagList(
+          radioButtons(
+            ns("chem_type"),
+            label = "Select chemical by",
+            choices = c("Name", "CAS Registry Number (without dashes)"),
+            selected = "Name",
+            inline = TRUE
+          ),
+          shinyjs::hidden(
+            div(
+              id = ns("div_name"),
+              selectizeInput(
+                ns("select_chem_name"),
+                label = "",
+                choices = NULL
+              ),
+            )
+          ),
+          shinyjs::hidden(
+            div(
+              id = ns("div_cas"),
+              selectizeInput(
+                ns("select_cas_num"),
+                label = "",
+                choices = NULL,
+                selected = NULL
+              )
             )
           )
-        )
+        ),
+        actionButton(ns("run"), "Run"),
       ),
-      actionButton(ns("run"), "Run"),
+      wellPanel(
+        p("Select a chemical by name or with the CAS registry number (without dashes) by using the radio buttons."),
+        p("1. To clear a selection, hit the backspace button in the input field."),
+        p("2. If you are unable to find the chemical by name try the CAS number."),
+        p(
+          "3. You can use the", 
+          a("CompTox Chemicals Dashboard", href = "https://comptox.epa.gov/dashboard/"), 
+          "maintained by the US EPA to look up a CAS number."
+        ),
+        p(
+          "4. The", 
+          a("CompTox Chemicals Dashboard", href = "https://comptox.epa.gov/dashboard/"), 
+          "is also helpful to look up synonyms. Many chemicals have multiple names."
+        ),
+        p("Once a chemical has been selected, hit the Run button."),
+      )
     ),
-    mainPanel(
+    column(
+      8,
       tabsetPanel(
         tabPanel(
           title = "1.1 Data Review",
@@ -86,7 +106,92 @@ mod_data_ui <- function(id, label = "data") {
           )
         )
       )
-    )
+
+  )
+
+
+  # sidebarLayout(
+  #   sidebarPanel(
+  #     
+  #     fluidRow(
+  #       column(
+  #         width = 1
+  #         tagList(
+  #           radioButtons(
+  #             ns("chem_type"),
+  #             label = "Select chemical by",
+  #             choices = c("Name", "CAS Registry Number (without dashes)"),
+  #             selected = "Name",
+  #             inline = TRUE
+  #           ),
+  #           shinyjs::hidden(
+  #             div(
+  #               id = ns("div_name"),
+  #               selectizeInput(
+  #                 ns("select_chem_name"),
+  #                 label = "",
+  #                 choices = NULL
+  #               ),
+  #             )
+  #           ),
+  #           shinyjs::hidden(
+  #             div(
+  #               id = ns("div_cas"),
+  #               selectizeInput(
+  #                 ns("select_cas_num"),
+  #                 label = "",
+  #                 choices = NULL,
+  #                 selected = NULL
+  #               )
+  #             )
+  #           )
+  #         ),
+  #         actionButton(ns("run"), "Run"),
+  #       ),
+  #       column(
+  #         tabPanel("Instructions here"),
+  #       ),
+  #     ),
+  #   ),
+  #   
+    #mainPanel(
+      # tabsetPanel(
+      #   tabPanel(
+      #     title = "1.1 Data Review",
+      #     well_panel(
+      #       inline(uiOutput(ns("download_raw"))),
+      #       inline(uiOutput(ns("button_select"))),
+      #       br(),
+      #       h3(uiOutput(ns("ui_text_1"))),
+      #       br(),
+      #       br(),
+      #       uiOutput(ns("ui_table_selected"))
+      #     )
+      #   ),
+      #   tabPanel(
+      #     title = "1.2 View Plot",
+      #     well_panel(
+      #       uiOutput(ns("download_plot")),
+      #       br(),
+      #       h3(uiOutput(ns("ui_text_2"))),
+      #       br(),
+      #       br(),
+      #       uiOutput(ns("ui_plot"))
+      #     )
+      #   ),
+      #   tabPanel(
+      #     title = "1.3 Aggregated Data",
+      #     well_panel(
+      #       uiOutput(ns("download_aggregated")),
+      #       br(),
+      #       h3(uiOutput(ns("ui_text_3"))),
+      #       br(),
+      #       br(),
+      #       uiOutput(ns("ui_table_aggregated"))
+      #     )
+      #   )
+      # )
+   # )
   )
 }
 

R/namespace.R

@@ -16,4 +16,5 @@
 #' @importFrom rlang .data
 #' @importFrom knitr kable
 #' @importFrom markdown markdownToHTML
+#' @importFrom pkgload load_all
 NULL

inst/extdata/about.md

@@ -14,9 +14,15 @@
 # limitations under the License.
 -->
 
-**This app is under development and is being shared for testing purposes only.**
+The purpose of this app is to allow the user to calculate aquatic life benchmarks for emergent contaminants when no water quality guidelines are available.
+Although these benchmarks follow methods similar to those outlined in the [BC WQG derivation protocol](https://www2.gov.bc.ca/assets/gov/environment/air-land-water/water/waterquality/water-quality-guidelines/derivation-protocol/bc_wqg_aquatic_life_derivation_protocol.pdf), many steps have been omitted including data quality screening and expert review and therefore these benchmarks are not equivalent to water quality guidelines.
+Rather the purpose of the benchmarks is to support the assessment of monitoring data and the potential for a chemical to impact the aquatic environment.
 
-This app calculates aquatic life benchmarks for use when interpreting monitoring results when no water quality guidelines is available.  The app requires the user to first screen the data and then follow the necessary steps to calculate a benchmark.  
+If you have any feedback or comments on this app, please email them to [email protected]  For further information on this app, please see the draft overview: 
+Tillmanns, A.R. and Pearson, A.  2023.  DRAFT wqbench: A Tool for Calculating Emergent Contaminant Aquatic Life Benchmarks.  Ministry of Water, Land and Resource Stewardship. Province of British Columbia, Victoria.
+
+
+
 
 The app automatically completes the following steps:
 

inst/extdata/user.md

@@ -14,8 +14,6 @@
 # limitations under the License.
 -->
 
-
-This app **generates aquatic life water quality benchmarks**. 
 The app is built from the R package [wqbench](https://github.com/bcgov/wqbench), and shares the same functionality.
 
 ## How to Use the shinywqbench App