Merge pull request bcgov#37 from poissonconsulting/updates

Updates

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -8,8 +8,6 @@
 .RProfile
 .httr-oauth
 
-*.html
-
 docs/
 inst/docs/
 

DESCRIPTION

@@ -26,6 +26,7 @@ Imports:
     markdown,
     pkgload,
     readr,
+    readxl,
     rlang,
     rmarkdown,
     shiny,

R/app-ui.R

@@ -22,7 +22,7 @@ app_ui <- function() {
     navbarPage(
       title = div(
         img(src = "../images/gov3_bc_logo.png", style = "padding-right: 20px;"),
-        "Emerging Contaminant Aquatic Life Benchmarks - DRAFT"
+        "Emerging Contaminant Aquatic Life Benchmarks"
       ),
       selected = "tab1",
       id = "navbarID",

R/mod-data.R

@@ -76,7 +76,7 @@ mod_data_ui <- function(id, label = "data") {
         p("Once a chemical has been selected, hit the Run button."),
       ),
       wellPanel(
-        p("To add your own data."),
+        p("To append your data to the existing set."),
         p("1. Download and fill in template. Check the User Guide tab for descriptions of each column."),
         uiOutput(ns("download_add")),
         br(),
@@ -85,7 +85,7 @@ mod_data_ui <- function(id, label = "data") {
           ns("file_add"), 
           "",
           multiple = FALSE,
-          accept = c(".csv")
+          accept = c(".xlsx")
         ),
         p("3. Click the Add button to add the uploaded data."),
         actionButton(ns("add_button"), "Add"),
@@ -281,13 +281,19 @@ mod_data_server <- function(id) {
       })
 
       output$dl_add <- downloadHandler(
-        filename = function() paste0("template-wqbench.csv"),
+        filename = function() paste0("template-wqbench.xlsx"),
         content = function(file) {
-          readr::write_csv(wqbench::template[0, -1], file)
+          file.copy(
+            from = system.file(
+              package = "wqbench",
+              "template/template-data.xlsx"
+            ),
+            to = file
+          )
         }
       )
 
-      # Add data
+      # Add uploaded data
       observeEvent(input$add_button, {
         # Check that data already present
         if (is.null(rv$data)) {
@@ -303,16 +309,16 @@ mod_data_server <- function(id) {
         }
 
         check_uploaded_1 <- try(
-          check_upload(input$file_add$datapath, ext = "csv"), 
+          check_upload(input$file_add$datapath, ext = "xlsx"), 
           silent = TRUE
         )
         if (is_try_error(check_uploaded_1)) {
           return(showModal(check_modal(check_uploaded_1)))
         }
 
-        add_tbl_1 <- readr::read_csv(
+        add_tbl_1 <- readxl::read_excel(
           input$file_add$datapath,
-          show_col_types = FALSE
+          sheet = "data"
         )
 
         if (nrow(add_tbl_1) == 0) {
@@ -359,10 +365,12 @@ mod_data_server <- function(id) {
             ecological_group = factor(
               .data$ecological_group, 
               levels = levels(rv$data$ecological_group)
-            ), 
-            remove_row = FALSE
+            )
           )
-
+
+        add_tbl_1 <- wqbench::wqb_classify_duration(add_tbl_1, quiet = TRUE)
+        add_tbl_1 <- wqbench::wqb_standardize_effect(add_tbl_1, quiet = TRUE)
+        add_tbl_1$remove_row <- FALSE
         # 3. Add to data set
         rv$data <-
           rv$data |>

README.Rmd

@@ -5,7 +5,7 @@ output: github_document
 # shinywqbench
 
 <!-- badges: start -->
-[![img](https://img.shields.io/badge/Lifecycle-Experimental-339999)](https://github.com/bcgov/repomountie/blob/master/doc/lifecycle-badges.md)
+[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 <!-- badges: end -->
 
 This package is a shiny app that makes using the functions of the `wqbench` package accessible to non-R users. 

README.md

@@ -3,7 +3,8 @@
 
 <!-- badges: start -->
 
-[![img](https://img.shields.io/badge/Lifecycle-Experimental-339999)](https://github.com/bcgov/repomountie/blob/master/doc/lifecycle-badges.md)
+[![Lifecycle:
+stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 <!-- badges: end -->
 
 This package is a shiny app that makes using the functions of the

app.R

@@ -1,2 +1,16 @@
+# Copyright 2023 Province of British Columbia
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 pkgload::load_all(".")
 shinywqbench::run_wqbench_app()

inst/app/www/footer.html

@@ -0,0 +1,24 @@
+<div id="footer">
+  <div id="footerWrapper">
+    <div id="footerAdminSection">
+      <div id="footerAdminLinksContainer" class="container">
+        <div id="footerAdminLinks" class="row">
+          <ul class="inline">
+            <li data-order="0">
+              <a href="//www2.gov.bc.ca/gov/content/home/disclaimer" target="_self">Disclaimer</a>
+            </li>
+            <li data-order="1">
+              <a href="//www2.gov.bc.ca/gov/content/home/privacy" target="_self">Privacy</a>
+            </li>
+            <li data-order="2">
+              <a href="//www2.gov.bc.ca/gov/content/home/accessibility" target="_self">Accessibility</a>
+            </li>
+            <li data-order="3">
+              <a href="//www2.gov.bc.ca/gov/content/home/copyright" target="_self">Copyright</a>
+            </li>
+          </ul>
+        </div>
+      </div>
+    </div>
+  </div>
+</div>

inst/extdata/about.md

@@ -19,7 +19,7 @@ Although these benchmarks follow methods similar to those outlined in the [BC WQ
 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.
 
 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 Emerging Contaminant Aquatic Life Benchmarks.  Ministry of Water, Land and Resource Stewardship. Province of British Columbia, Victoria.](https://www2.gov.bc.ca/assets/gov/environment/air-land-water/water/waterquality/water-quality-guidelines/approved-wqgs/benchmarks_for_emerging_contaminants_overview_draft_august_2023.pdf)
+[Tillmanns, A.R. and Pearson, A.  2023. wqbench: A Tool for Calculating Emerging Contaminant Aquatic Life Benchmarks.  Ministry of Water, Land and Resource Stewardship. Province of British Columbia, Victoria.](https://www2.gov.bc.ca/assets/gov/environment/air-land-water/water/waterquality/water-quality-guidelines/approved-wqgs/benchmarks_for_emerging_contaminants_overview_draft_august_2023.pdf)
 
 
 
@@ -35,6 +35,4 @@ The app automatically completes the following steps:
 
 A full description of the steps can be found in the accompanying document, "An overview of the aquatic life water quality benchmark generator" which will eventually be published.
 
-Please do not cite this app at this point.
-
 The code is released under the [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0).

rsconnect/shinyapps.io/poissonconsulting/shinywqbench.dcf

@@ -0,0 +1,10 @@
+name: shinywqbench
+title:
+username: poissonconsulting
+account: poissonconsulting
+server: shinyapps.io
+hostUrl: https://api.shinyapps.io/v1
+appId: 8452407
+bundleId: 8416442
+url: https://poissonconsulting.shinyapps.io/shinywqbench/
+version: 1