From 9fd931aeeba4ab7bdede1a625f64e7024c2b55aa Mon Sep 17 00:00:00 2001
From: Naeem Model <me@nmode.ca>
Date: Sun, 9 Jun 2024 16:01:51 +0000
Subject: Update Shiny app

- Remove template/logic for single data entry
- Change 'Add estimators' to 'About estimators'; adding estimators and viewing estimates are now done in the same tab
- Swap rows and columns in estimates table (estimators as row names, datasets as column names)
- Add a separate column for the serial interval to the estimates table
- Add plots for daily and weekly data using the Plotly library
- Remove italics from the subscript in all occurences of 'R_0'
- Fix code/text formatting
---
 inst/app/templates/content/data/enter-data.html    | 17 ++++----
 .../content/data/enter-data/bulk-entry.html        | 48 ----------------------
 .../templates/content/data/enter-data/entry.html   | 48 ----------------------
 .../content/data/enter-data/load-samples.html      |  2 +
 .../content/data/enter-data/manual-entry.html      | 11 +++++
 .../content/data/enter-data/required-format.html   | 25 +++++++++++
 .../content/data/enter-data/single-entry.html      | 39 ------------------
 .../content/data/enter-data/upload-data.html       | 12 ++++++
 inst/app/templates/content/data/view-data.html     | 22 ++--------
 .../content/data/view-data/data-plots.html         |  7 ++++
 .../content/data/view-data/data-table.html         | 18 ++++++++
 11 files changed, 87 insertions(+), 162 deletions(-)
 delete mode 100644 inst/app/templates/content/data/enter-data/bulk-entry.html
 delete mode 100644 inst/app/templates/content/data/enter-data/entry.html
 create mode 100644 inst/app/templates/content/data/enter-data/manual-entry.html
 create mode 100644 inst/app/templates/content/data/enter-data/required-format.html
 delete mode 100644 inst/app/templates/content/data/enter-data/single-entry.html
 create mode 100644 inst/app/templates/content/data/enter-data/upload-data.html
 create mode 100644 inst/app/templates/content/data/view-data/data-plots.html
 create mode 100644 inst/app/templates/content/data/view-data/data-table.html

(limited to 'inst/app/templates/content/data')

diff --git a/inst/app/templates/content/data/enter-data.html b/inst/app/templates/content/data/enter-data.html
index 77846fa..254f1d7 100644
--- a/inst/app/templates/content/data/enter-data.html
+++ b/inst/app/templates/content/data/enter-data.html
@@ -1,8 +1,9 @@
-
-<form class="mb-5">
-  {{ htmlTemplate("templates/content/data/enter-data/entry.html") }}
-</form>
-<hr>
-<form>
-  {{ htmlTemplate("templates/content/data/enter-data/load-samples.html") }}
-</form>
+<form class="mb-5">
+  {{ htmlTemplate("templates/content/data/enter-data/required-format.html") }}
+  {{ htmlTemplate("templates/content/data/enter-data/manual-entry.html") }}
+  {{ htmlTemplate("templates/content/data/enter-data/upload-data.html") }}
+</form>
+<hr>
+<form>
+  {{ htmlTemplate("templates/content/data/enter-data/load-samples.html") }}
+</form>
diff --git a/inst/app/templates/content/data/enter-data/bulk-entry.html b/inst/app/templates/content/data/enter-data/bulk-entry.html
deleted file mode 100644
index 30fab06..0000000
--- a/inst/app/templates/content/data/enter-data/bulk-entry.html
+++ /dev/null
@@ -1,48 +0,0 @@
-<h4 class="mb-3">Bulk entry</h4>
-<!-- Button to toggle help text. -->
-<button type="button" class="btn btn-outline-primary btn-sm" id="bulk-help-toggle"
-        data-bs-toggle="collapse" data-bs-target="#bulk-help">Show required format</button>
-<!-- Help text for bulk input format. -->
-<div class="collapse mt-2" id="bulk-help">
-  <div class="card card-body border-primary">
-    <p>Manually enter rows or upload a CSV file in the following format:</p>
-    <p class="overflow-x-scroll text-nowrap font-monospace">
-      <u>Dataset name</u>,<u>Time units</u>,<u>Case counts</u>
-    </p>
-    <p>
-      <u class="font-monospace">Time units</u> must be one of
-      <u class="font-monospace">Days</u> or 
-      <u class="font-monospace">Weeks</u>, and
-      <u class="font-monospace">Case counts</u>
-      must be a comma-separated list of one or more non-negative integers.
-    </p>
-    <p>Example:</p>
-    <p class="overflow-x-scroll text-nowrap font-monospace lh-sm">
-      Montreal,Days,1,2,3,4,5,6,7,8,9,19<br>
-      Ottawa,Weeks,1,2,3,4,5,6,7,8,9,19<br>
-      Toronto,Days,1,2,3,4,5,6,7,8,9,19
-    </p>
-  </div>
-</div>
-<!-- Data input area. -->
-<div class="my-4">
-  <label class="form-label" for="data_area">Enter manually</label>
-  <textarea id="data_area" class="form-control" rows="3" wrap="off"></textarea>
-  <div>
-    <small id="data_area_warn" class="form-text text-primary shiny-html-output"></small>
-  </div>
-  <button id="data_bulk" type="button" class="btn btn-outline-primary btn-sm action-button mt-3">
-    <span class="glyphicon glyphicon-plus"></span> Add
-  </button>
-</div>
-<!-- File input for data upload (hidden). -->
-<input class="form-control" type="file" id="data_upload" accept="text/csv,text/comma-separated-values,text/plain,.csv">
-<!-- Custom button to trigger file selector for data upload (visible). -->
-<label class="form-label" for="data-upload-select">Upload a CSV file</label>
-<div class="input-group">
-  <button id="data-upload-select" type="button" class="btn btn-outline-primary btn-sm">
-    <span class="glyphicon glyphicon-file"></span> Select file
-  </button>
-  <input type="text" id="data-upload-name" class="form-control" placeholder="No file selected" disabled>
-</div>
-<small id="data_upload_warn" class="form-text text-primary shiny-html-output"></small>
diff --git a/inst/app/templates/content/data/enter-data/entry.html b/inst/app/templates/content/data/enter-data/entry.html
deleted file mode 100644
index be43625..0000000
--- a/inst/app/templates/content/data/enter-data/entry.html
+++ /dev/null
@@ -1,48 +0,0 @@
-
-<!-- Button to toggle help text. -->
-<button type="button" class="btn btn-outline-primary btn-sm" id="bulk-help-toggle"
-        data-bs-toggle="collapse" data-bs-target="#bulk-help">Show required format</button>
-<!-- Help text for bulk input format. -->
-<div class="collapse mt-2" id="bulk-help">
-  <div class="card card-body border-primary">
-    <p>Manually enter rows or upload a CSV file in the following format:</p>
-    <p class="overflow-x-scroll text-nowrap font-monospace">
-      <u>Dataset name</u>,<u>Time units</u>,<u>Case counts</u>
-    </p>
-    <p>
-      <u class="font-monospace">Time units</u> must be one of
-      <u class="font-monospace">Days</u> or 
-      <u class="font-monospace">Weeks</u>, and
-      <u class="font-monospace">Case counts</u>
-      must be a comma-separated list of one or more non-negative integers.
-    </p>
-    <p>Example:</p>
-    <p class="overflow-x-scroll text-nowrap font-monospace lh-sm">
-      Montreal,Days,1,2,3,4,5,6,7,8,9,19<br>
-      Ottawa,Weeks,1,2,3,4,5,6,7,8,9,19<br>
-      Toronto,Days,1,2,3,4,5,6,7,8,9,19
-    </p>
-  </div>
-</div>
-<!-- Data input area. -->
-<div class="my-4">
-  <label class="form-label" for="data_area">Enter manually</label>
-  <textarea id="data_area" class="form-control" rows="3" wrap="off"></textarea>
-  <div>
-    <small id="data_area_warn" class="form-text text-primary shiny-html-output"></small>
-  </div>
-  <button id="data_bulk" type="button" class="btn btn-outline-primary btn-sm action-button mt-3">
-    <span class="glyphicon glyphicon-plus"></span> Add
-  </button>
-</div>
-<!-- File input for data upload (hidden). -->
-<input class="form-control" type="file" id="data_upload" accept="text/csv,text/comma-separated-values,text/plain,.csv">
-<!-- Custom button to trigger file selector for data upload (visible). -->
-<label class="form-label" for="data-upload-select">Upload a CSV file</label>
-<div class="input-group">
-  <button id="data-upload-select" type="button" class="btn btn-outline-primary btn-sm">
-    <span class="glyphicon glyphicon-file"></span> Select file
-  </button>
-  <input type="text" id="data-upload-name" class="form-control" placeholder="No file selected" disabled>
-</div>
-<small id="data_upload_warn" class="form-text text-primary shiny-html-output"></small>
diff --git a/inst/app/templates/content/data/enter-data/load-samples.html b/inst/app/templates/content/data/enter-data/load-samples.html
index a42a8c8..2a4f013 100644
--- a/inst/app/templates/content/data/enter-data/load-samples.html
+++ b/inst/app/templates/content/data/enter-data/load-samples.html
@@ -1,4 +1,5 @@
 <h4 class="mb-3">Load samples</h4>
+<!-- Checkboxes for sample data. -->
 {{
   checkboxInput(inputId = "covid_canada", label = "COVID-19 Canada, 2020/03/03 - 2020/03/31 (Weekly)",
     value = FALSE, width = "100%"
@@ -9,6 +10,7 @@
     value = FALSE, width = "100%"
   )
 }}
+<!-- Warning text. -->
 <div>
   <small id="data_samples_warn" class="form-text text-primary shiny-text-output"></small>
 </div>
diff --git a/inst/app/templates/content/data/enter-data/manual-entry.html b/inst/app/templates/content/data/enter-data/manual-entry.html
new file mode 100644
index 0000000..a6319d9
--- /dev/null
+++ b/inst/app/templates/content/data/enter-data/manual-entry.html
@@ -0,0 +1,11 @@
+<!-- Data input area (manual entry). -->
+<div class="my-4">
+  <label class="form-label" for="data_area">Enter manually</label>
+  <textarea id="data_area" class="form-control" rows="3" wrap="off"></textarea>
+  <div>
+    <small id="data_area_warn" class="form-text text-primary shiny-html-output"></small>
+  </div>
+  <button id="data_bulk" type="button" class="btn btn-outline-primary btn-sm action-button mt-3">
+    <span class="glyphicon glyphicon-plus"></span> Add
+  </button>
+</div>
diff --git a/inst/app/templates/content/data/enter-data/required-format.html b/inst/app/templates/content/data/enter-data/required-format.html
new file mode 100644
index 0000000..724dd83
--- /dev/null
+++ b/inst/app/templates/content/data/enter-data/required-format.html
@@ -0,0 +1,25 @@
+<!-- Button to toggle help text. -->
+<button type="button" class="btn btn-outline-primary btn-sm" id="data-format-toggle"
+        data-bs-toggle="collapse" data-bs-target="#data-format">Show required format</button>
+<!-- Help text for data input format. -->
+<div class="collapse mt-2" id="data-format">
+  <div class="card card-body border-primary">
+    <p>Manually enter rows or upload a CSV file in the following format:</p>
+    <p class="overflow-x-scroll text-nowrap font-monospace">
+      <u>Dataset name</u>,<u>Time units</u>,<u>Case counts</u>
+    </p>
+    <p>
+      <u class="font-monospace">Time units</u> must be one of
+      <u class="font-monospace">Days</u> or 
+      <u class="font-monospace">Weeks</u>, and
+      <u class="font-monospace">Case counts</u>
+      must be a comma-separated list of one or more non-negative integers.
+    </p>
+    <p>Example:</p>
+    <p class="overflow-x-scroll text-nowrap font-monospace lh-sm">
+      Disease A,Days,1,2,3,4,5,6,7,8,9<br>
+      Disease B,Weeks,3,1,4,1,5,2,9<br>
+      Disease C,Days,2,3,5,7,11,13,17,19
+    </p>
+  </div>
+</div>
diff --git a/inst/app/templates/content/data/enter-data/single-entry.html b/inst/app/templates/content/data/enter-data/single-entry.html
deleted file mode 100644
index 9f249d9..0000000
--- a/inst/app/templates/content/data/enter-data/single-entry.html
+++ /dev/null
@@ -1,39 +0,0 @@
-<h4>Single entry</h4>
-<!-- Dataset name. -->
-<div class="my-3">
-  <label class="form-label" for="data_name">Dataset name</label>
-  <input name="data_name" class="form-control" type="text">
-  <small id="data_name_warn" class="form-text text-primary shiny-text-output"></small>
-</div>
-<!-- Case counts. -->
-<div class="mb-3">
-  <label class="form-label" for="data_counts">
-    Case counts
-    <sup data-bs-toggle="tooltip" data-bs-placement="right"
-         data-bs-title="Enter as a comma-separated list of non-negative integers (example: 0,1,1,2,3,5,8,13).">
-      [?]
-    </sup>
-  </label>
-  <input name="data_counts" class="form-control" type="text">
-  <small id="data_counts_warn" class="form-text text-primary shiny-text-output"></small>
-</div>
-<!-- Time units. -->
-<div class="mb-3">
-  <label class="form-label" for="data_units">Time units</label>
-  <div class="shiny-input-radiogroup" id="data_units">
-    <div class="form-check form-check-inline">
-      <label class="form-check-label">
-        <input type="radio" class="form-check-input me-2" name="data_units" value="Days">Days
-      </label>
-    </div>
-    <div class="form-check form-check-inline">
-      <label class="form-check-label">
-        <input type="radio" class="form-check-input me-2" name="data_units" value="Weeks" checked>Weeks
-      </label>
-    </div>
-  </div>
-</div>
-<!-- Submit data. -->
-<button id="data_single" type="button" class="btn btn-outline-primary btn-sm action-button">
-  <span class="glyphicon glyphicon-plus"></span> Add
-</button>
diff --git a/inst/app/templates/content/data/enter-data/upload-data.html b/inst/app/templates/content/data/enter-data/upload-data.html
new file mode 100644
index 0000000..740047b
--- /dev/null
+++ b/inst/app/templates/content/data/enter-data/upload-data.html
@@ -0,0 +1,12 @@
+<!-- File input for data upload (hidden). -->
+<input class="form-control" type="file" id="data_upload" accept="text/csv,text/comma-separated-values,text/plain,.csv">
+<!-- Custom button to trigger file selector for data upload (visible). -->
+<label class="form-label" for="data-upload-select">Upload a CSV file</label>
+<div class="input-group">
+  <button id="data-upload-select" type="button" class="btn btn-outline-primary btn-sm">
+    <span class="glyphicon glyphicon-file"></span> Select file
+  </button>
+  <input type="text" id="data-upload-name" class="form-control" placeholder="No file selected" disabled>
+</div>
+<!-- Warning text. -->
+<small id="data_upload_warn" class="form-text text-primary shiny-html-output"></small>
diff --git a/inst/app/templates/content/data/view-data.html b/inst/app/templates/content/data/view-data.html
index 52f1e85..880cf7f 100644
--- a/inst/app/templates/content/data/view-data.html
+++ b/inst/app/templates/content/data/view-data.html
@@ -1,19 +1,3 @@
-<h4>Data table</h4>
-<!-- Data table. -->
-<div class="my-3">
-  {{ DT::dataTableOutput(outputId = "data_table") }}
-</div>
-<!-- Display inactive delete button when no rows are selected. -->
-<button type="button" class="btn btn-primary btn-sm text-white" disabled
-        data-display-if="'data_table_rows_selected' in input && input.data_table_rows_selected.length == 0">
-  <span class="glyphicon glyphicon-remove"></span> Delete row(s)
-</button>
-<!-- Display active delete button when at least one row is selected. -->
-<button id="data_delete" type="button" class="btn btn-primary btn-sm action-button text-white"
-        data-display-if="'data_table_rows_selected' in input && input.data_table_rows_selected.length != 0">
-  <span class="glyphicon glyphicon-remove"></span> Delete row(s)
-</button>
-<!-- Button to export data table as a CSV file. -->
-<a id="data_export" type="button" class="btn btn-outline-primary btn-sm shiny-download-link">
-  <span class="glyphicon glyphicon-download-alt"></span> Export table
-</a>
+{{ htmlTemplate("templates/content/data/view-data/data-table.html") }}
+<hr>
+{{ htmlTemplate("templates/content/data/view-data/data-plots.html") }}
diff --git a/inst/app/templates/content/data/view-data/data-plots.html b/inst/app/templates/content/data/view-data/data-plots.html
new file mode 100644
index 0000000..5019088
--- /dev/null
+++ b/inst/app/templates/content/data/view-data/data-plots.html
@@ -0,0 +1,7 @@
+<h4>Data plots</h4>
+<div class="container my-5">
+  {{ plotly::plotlyOutput(outputId = "data_plot_days") }}
+</div>
+<div class="container">
+  {{ plotly::plotlyOutput(outputId = "data_plot_weeks") }}
+</div>
diff --git a/inst/app/templates/content/data/view-data/data-table.html b/inst/app/templates/content/data/view-data/data-table.html
new file mode 100644
index 0000000..590a5b9
--- /dev/null
+++ b/inst/app/templates/content/data/view-data/data-table.html
@@ -0,0 +1,18 @@
+<h4>Data table</h4>
+<div class="my-3">
+  {{ DT::dataTableOutput(outputId = "data_table") }}
+</div>
+<!-- Display inactive delete button when no rows are selected. -->
+<button type="button" class="btn btn-primary btn-sm text-white" disabled
+        data-display-if="'data_table_rows_selected' in input && input.data_table_rows_selected.length == 0">
+  <span class="glyphicon glyphicon-remove"></span> Delete row(s)
+</button>
+<!-- Display active delete button when at least one row is selected. -->
+<button id="data_delete" type="button" class="btn btn-primary btn-sm action-button text-white"
+        data-display-if="'data_table_rows_selected' in input && input.data_table_rows_selected.length != 0">
+  <span class="glyphicon glyphicon-remove"></span> Delete row(s)
+</button>
+<!-- Button to export data table as a CSV file. -->
+<a id="data_export" type="button" class="btn btn-outline-primary btn-sm shiny-download-link">
+  <span class="glyphicon glyphicon-download-alt"></span> Export table
+</a>
-- 
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