Revamp Shiny app

23 files changed, 352 insertions, 0 deletions

diff --git a/inst/app/templates/content/about.html b/inst/app/templates/content/about.html
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+<h1>Welcome to the Rnaught web application!</h1>
+<p>
+  Rnaught is an R package and web application for estimating the
+  <a href="https://en.wikipedia.org/wiki/Basic_reproduction_number" target="_blank">basic reproduction number</a>
+  of infectious diseases. For information about using this application, view the
+  <span class="fw-bold text-primary">Help <span class="glyphicon glyphicon-question-sign"></span></span> tab.
+  To learn more about the package, visit the online
+  <a href="https://MI2YorkU.github.io/Rnaught" target="_blank">documentation</a> or
+  <a href="https://github.com/MI2YorkU/Rnaught" target="_blank">GitHub</a> repository.
+  Technical details about the estimators featured in this project can be found in the reference
+  <a href="https://doi.org/10.1371/journal.pone.0269306" target="_blank">article</a>.
+</p>
+
+<h4>What is the basic reproduction number?</h4>
+<p>
+  The basic reproduction number, denoted <em>R<sub>0</sub></em>, describes the expected number of infections caused by a
+  single infectious individual. It assumes that all individuals in a given population are susceptible to the disease,
+  and that no preventive measures (such as lockdowns or vaccinations) have been enforced. As such, it is a useful
+  indicator of the transmissibility of a disease during the early stages of its detection.
+</p>
+<p>
+  If <em>R<sub>0</sub></em> &lt; 1, then the disease will eventually die out. On the other hand, if
+  <em>R<sub>0</sub></em> &gt; 1, the rate at which the disease spreads is exponential. Typically, it is difficult to
+  determine <em>R<sub>0</sub></em> precisely, due to uncertainty in information relating to the spread of the disease.
+  Therefore, many estimation methods exist, each based on their own models and yielding different estimates. It is the
+  responsibility of public health officials to employ the most appropriate estimator given the situation at hand.
+</p>
diff --git a/inst/app/templates/content/data.html b/inst/app/templates/content/data.html
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+++ b/inst/app/templates/content/data.html
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+<nav class="nav nav-tabs">
+  <a class="nav-link active" data-bs-toggle="tab" href="#enter-data">Enter data</a>
+  <a class="nav-link" data-bs-toggle="tab" href="#view-data">View data</a>
+</nav>
+
+<div class="container-fluid tab-content">
+  <div id="enter-data" class="pt-3 tab-pane fade show active">
+    {{ htmlTemplate("templates/content/data/enter-data.html") }}
+  </div>
+  <div id="view-data" class="pt-3 tab-pane fade">
+    {{ htmlTemplate("templates/content/data/view-data.html") }}
+  </div>
+</div>
diff --git a/inst/app/templates/content/data/enter-data.html b/inst/app/templates/content/data/enter-data.html
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+++ b/inst/app/templates/content/data/enter-data.html
@@ -0,0 +1,13 @@
+<div class="row mb-5">
+  <form class="col-md">
+    {{ htmlTemplate("templates/content/data/enter-data/single-entry.html") }}
+  </form>
+  <div class="col-md mt-5 mt-md-0 d-flex flex-column align-items-center">
+    <h5>Data plot</h5>
+    {{ plotOutput(outputId = "data_plot") }}
+  </div>
+</div>
+<hr>
+<form>
+  {{ htmlTemplate("templates/content/data/enter-data/bulk-entry.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
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index 0000000..82a3ccf
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+++ b/inst/app/templates/content/data/enter-data/bulk-entry.html
@@ -0,0 +1,37 @@
+<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>Enter one or more rows 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>
+  <textarea id="data_area" class="form-control shiny-input-textarea my-3" rows="3" wrap="off"></textarea>
+  <small id="data_area_warn" class="form-text text-primary shiny-html-output"></small>
+</div>
+<!-- Submit data. -->
+<button id="data_bulk" 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/single-entry.html b/inst/app/templates/content/data/enter-data/single-entry.html
new file mode 100644
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+++ b/inst/app/templates/content/data/enter-data/single-entry.html
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+<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/view-data.html b/inst/app/templates/content/data/view-data.html
new file mode 100644
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+++ b/inst/app/templates/content/data/view-data.html
@@ -0,0 +1,19 @@
+<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>
diff --git a/inst/app/templates/content/estimators.html b/inst/app/templates/content/estimators.html
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+++ b/inst/app/templates/content/estimators.html
@@ -0,0 +1,13 @@
+<nav class="nav nav-tabs">
+  <a class="nav-link active" data-bs-toggle="tab" href="#add-estimators">Add estimators</a>
+  <a class="nav-link" data-bs-toggle="tab" href="#view-estimates">View estimates</a>
+</nav>
+
+<div class="container-fluid tab-content">
+  <div id="add-estimators" class="pt-3 tab-pane fade show active">
+    {{ htmlTemplate("templates/content/estimators/add-estimators.html") }}
+  </div>
+  <div id="view-estimates" class="pt-3 tab-pane fade">
+    {{ htmlTemplate("templates/content/estimators/view-estimates.html") }}
+  </div>
+</div>
diff --git a/inst/app/templates/content/estimators/add-estimators.html b/inst/app/templates/content/estimators/add-estimators.html
new file mode 100644
index 0000000..dce2dae
--- /dev/null
+++ b/inst/app/templates/content/estimators/add-estimators.html
@@ -0,0 +1,34 @@
+<div class="accordion accordion-flush" id="estimators-accordion">
+  {{ 
+    htmlTemplate("templates/content/estimators/add-estimators/components/panel.html",
+      id = "id",
+      header = "Incidence Decay (ID)",
+      reference_label = "Fisman et al. (PloS One, 2013)",
+      reference_url = "https://doi.org/10.1371/journal.pone.0083622"
+    )
+  }}
+  {{
+    htmlTemplate("templates/content/estimators/add-estimators/components/panel.html",
+      id = "idea",
+      header = "Incidence Decay and Exponential Adjustment (IDEA)",
+      reference_label = "Fisman et al. (PloS One, 2013)",
+      reference_url = "https://doi.org/10.1371/journal.pone.0083622"
+    )
+  }}
+  {{
+    htmlTemplate("templates/content/estimators/add-estimators/components/panel.html",
+      id = "seq_bayes",
+      header = "Sequential Bayes (seqB)",
+      reference_label = "Bettencourt and Riberio (PloS One, 2008)",
+      reference_url = "https://doi.org/10.1371/journal.pone.0002185"
+    )
+  }}
+  {{
+    htmlTemplate("templates/content/estimators/add-estimators/components/panel.html",
+      id = "wp",
+      header = "White and Pagano (WP)",
+      reference_label = "White and Pagano (Statistics in Medicine, 2008)",
+      reference_url = "https://doi.org/10.1002/sim.3136"
+    )
+  }}
+</div>
diff --git a/inst/app/templates/content/estimators/add-estimators/components/mu.html b/inst/app/templates/content/estimators/add-estimators/components/mu.html
new file mode 100644
index 0000000..f25a1c8
--- /dev/null
+++ b/inst/app/templates/content/estimators/add-estimators/components/mu.html
@@ -0,0 +1,20 @@
+<!-- Serial interval label and help tooltip. -->
+<label class="form-label" for="mu_{{ id }}">
+  Serial interval (&#956;)
+  <sup data-bs-toggle="tooltip" data-bs-placement="right"
+       data-bs-title="The serial interval is the time between when an infected individual (the infector) becomes
+                      symptomatic, to when another individual (who is infected by the infector) becomes symptomatic.">
+    [?]
+  </sup>
+</label>
+<div class="input-group">
+  <!-- Serial interval input field. -->
+  <input name="mu_{{ id }}" class="form-control" type="text">
+  <!-- Days/weeks dropdown. -->
+  <select name="mu_{{ id }}_units" class="form-select">
+    <option value="Days" selected>Days</option>
+    <option value="Weeks">Weeks</option>
+  </select>
+</div>
+<!-- Warning text for incorrect values. -->
+<small id="mu_{{ id }}_warn" class="form-text text-primary shiny-text-output"></small>
diff --git a/inst/app/templates/content/estimators/add-estimators/components/panel.html b/inst/app/templates/content/estimators/add-estimators/components/panel.html
new file mode 100644
index 0000000..b1e0378
--- /dev/null
+++ b/inst/app/templates/content/estimators/add-estimators/components/panel.html
@@ -0,0 +1,21 @@
+<div class="accordion-item">
+  <h2 class="accordion-header">
+    <button class="accordion-button collapsed" type="button"
+            data-bs-toggle="collapse" data-bs-target="#{{ id }}">
+      <h4>{{ header }}</h4>
+    </button>
+  </h2>
+  <div id="{{ id }}" class="accordion-collapse collapse" data-bs-parent="#estimators-accordion">
+    <div class="accordion-body">
+      <p>Reference: <a href="{{ reference_url }}" target="_blank"><em>{{ reference_label }}</em></a></p>
+      <p>{{ htmlTemplate(paste0("templates/content/estimators/add-estimators/descriptions/", id, ".html")) }}</p>
+      <h5>Parameters</h5>
+      <form class="my-3">
+        {{ htmlTemplate(paste0("templates/content/estimators/add-estimators/parameters/", id, ".html")) }}
+      </form>
+      <button id="add_{{ id }}" type="button" class="btn btn-outline-primary btn-sm action-button">
+        <span class="glyphicon glyphicon-plus"></span> Add
+      </button>
+    </div>
+  </div>
+</div>
diff --git a/inst/app/templates/content/estimators/add-estimators/descriptions/id.html b/inst/app/templates/content/estimators/add-estimators/descriptions/id.html
new file mode 100644
index 0000000..b182ae5
--- /dev/null
+++ b/inst/app/templates/content/estimators/add-estimators/descriptions/id.html
@@ -0,0 +1 @@
+This is a short description of the ID method.
diff --git a/inst/app/templates/content/estimators/add-estimators/descriptions/idea.html b/inst/app/templates/content/estimators/add-estimators/descriptions/idea.html
new file mode 100644
index 0000000..edfbb79
--- /dev/null
+++ b/inst/app/templates/content/estimators/add-estimators/descriptions/idea.html
@@ -0,0 +1 @@
+This is a short description of the IDEA method.
diff --git a/inst/app/templates/content/estimators/add-estimators/descriptions/seq_bayes.html b/inst/app/templates/content/estimators/add-estimators/descriptions/seq_bayes.html
new file mode 100644
index 0000000..f6df3ee
--- /dev/null
+++ b/inst/app/templates/content/estimators/add-estimators/descriptions/seq_bayes.html
@@ -0,0 +1 @@
+This is a short description of the seqB method.
diff --git a/inst/app/templates/content/estimators/add-estimators/descriptions/wp.html b/inst/app/templates/content/estimators/add-estimators/descriptions/wp.html
new file mode 100644
index 0000000..640b44d
--- /dev/null
+++ b/inst/app/templates/content/estimators/add-estimators/descriptions/wp.html
@@ -0,0 +1 @@
+This is a short description of the WP method.
diff --git a/inst/app/templates/content/estimators/add-estimators/parameters/id.html b/inst/app/templates/content/estimators/add-estimators/parameters/id.html
new file mode 100644
index 0000000..a3159ca
--- /dev/null
+++ b/inst/app/templates/content/estimators/add-estimators/parameters/id.html
@@ -0,0 +1 @@
+{{ htmlTemplate("templates/content/estimators/add-estimators/components/mu.html", id = "id") }}
diff --git a/inst/app/templates/content/estimators/add-estimators/parameters/idea.html b/inst/app/templates/content/estimators/add-estimators/parameters/idea.html
new file mode 100644
index 0000000..379be84
--- /dev/null
+++ b/inst/app/templates/content/estimators/add-estimators/parameters/idea.html
@@ -0,0 +1 @@
+{{ htmlTemplate("templates/content/estimators/add-estimators/components/mu.html", id = "idea") }}
diff --git a/inst/app/templates/content/estimators/add-estimators/parameters/seq_bayes.html b/inst/app/templates/content/estimators/add-estimators/parameters/seq_bayes.html
new file mode 100644
index 0000000..bcc82b7
--- /dev/null
+++ b/inst/app/templates/content/estimators/add-estimators/parameters/seq_bayes.html
@@ -0,0 +1,22 @@
+<div class="row">
+  <!-- Serial interval (mu). -->
+  <div class="col-md">
+    {{ htmlTemplate("templates/content/estimators/add-estimators/components/mu.html", id = "seq_bayes") }}
+  </div>
+  <!-- Maximum value of the uniform prior (kappa). -->
+  <div class="col-md mt-2 mt-md-0">
+    <!-- Label and help tooltip. -->
+    <label class="form-label" for="kappa">
+      Maximum prior (&#954;)
+      <sup data-bs-toggle="tooltip" data-bs-placement="right" data-bs-html="true"
+           data-bs-title="The initial maximum belief of <em>R<sub>0</sub></em>. The higher this value, the higher
+                          <em>R<sub>0</sub></em> is believed to be prior to the estimation.">
+        [?]
+      </sup>
+    </label>
+    <!-- Input field. -->
+    <input name="kappa" class="form-control" type="text" placeholder="Default: 20">
+    <!-- Warning text for incorrect values. -->
+    <small id="kappa_warn" class="form-text text-primary shiny-text-output"></small>
+  </div>
+</div>
diff --git a/inst/app/templates/content/estimators/add-estimators/parameters/wp.html b/inst/app/templates/content/estimators/add-estimators/parameters/wp.html
new file mode 100644
index 0000000..b789a23
--- /dev/null
+++ b/inst/app/templates/content/estimators/add-estimators/parameters/wp.html
@@ -0,0 +1,39 @@
+<!-- Radio buttons to specify whether the serial interval is known. -->
+<label class="form-label" for="wp_mu_known">Is the serial interval known?</label>
+<div class="shiny-input-radiogroup" id="wp_mu_known">
+  <div class="form-check form-check-inline">
+    <label class="form-check-label">
+      <input type="radio" class="form-check-input me-2" name="wp_mu_known" value="Yes" checked>Yes
+    </label>
+  </div>
+  <div class="form-check form-check-inline">
+    <label class="form-check-label">
+      <input type="radio" class="form-check-input me-2" name="wp_mu_known" value="No">No
+    </label>
+  </div>
+</div>
+<!-- Show the input field for the serial interval if it is known. -->
+<div data-display-if="input.wp_mu_known == 'Yes'" class="mt-2 mt-md-0">
+    {{ htmlTemplate("templates/content/estimators/add-estimators/components/mu.html", id = "wp") }}
+</div>
+<!-- Show the input fields for the grid search parameters if the serial interval is unknown. -->
+<div data-display-if="input.wp_mu_known == 'No'" class="row">
+  <!-- Grid length. -->
+  <div class="col-md mt-2 mt-md-0">
+    <label class="form-label" for="grid_length">Grid length</label>
+    <input name="grid_length" class="form-control" type="text" placeholder="Default: 100">
+    <small id="grid_length_warn" class="form-text text-primary shiny-text-output"></small>
+  </div>
+  <!-- Maximum shape. -->
+  <div class="col-md mt-2 mt-md-0">
+    <label class="form-label" for="max_shape">Maximum shape</label>
+    <input name="max_shape" class="form-control" type="text" placeholder="Default: 10">
+    <small id="max_shape_warn" class="form-text text-primary shiny-text-output"></small>
+  </div>
+  <!-- Grid length. -->
+  <div class="col-md mt-2 mt-md-0">
+    <label class="form-label" for="max_scale">Maximum scale</label>
+    <input name="max_scale" class="form-control" type="text" placeholder="Default: 10">
+    <small id="max_scale_warn" class="form-text text-primary shiny-text-output"></small>
+  </div>
+</div>
diff --git a/inst/app/templates/content/estimators/view-estimates.html b/inst/app/templates/content/estimators/view-estimates.html
new file mode 100644
index 0000000..e81fff6
--- /dev/null
+++ b/inst/app/templates/content/estimators/view-estimates.html
@@ -0,0 +1,21 @@
+<h4>Estimates table</h4>
+<!-- Estimates table. -->
+<div class="my-3">
+  {{ DT::dataTableOutput(outputId = "estimates_table") }}
+</div>
+<!-- Display inactive delete button when no columns are selected. -->
+<button type="button" class="btn btn-primary btn-sm text-white" disabled
+        data-display-if="'estimates_table_columns_selected' in input &&
+                         input.estimates_table_columns_selected.length == 0">
+  <span class="glyphicon glyphicon-remove"></span> Delete column(s)
+</button>
+<!-- Display active delete button when at least one column is selected. -->
+<button id="estimators_delete" type="button" class="btn btn-primary btn-sm action-button text-white"
+        data-display-if="'estimates_table_columns_selected' in input &&
+                         input.estimates_table_columns_selected.length != 0">
+  <span class="glyphicon glyphicon-remove"></span> Delete column(s)
+</button>
+<!-- Button to export estimates table as a CSV file. -->
+<a id="estimates_export" type="button" class="btn btn-outline-primary btn-sm shiny-download-link">
+  <span class="glyphicon glyphicon-download-alt"></span> Export table
+</a>
diff --git a/inst/app/templates/content/help.html b/inst/app/templates/content/help.html
new file mode 100644
index 0000000..388afb1
--- /dev/null
+++ b/inst/app/templates/content/help.html
@@ -0,0 +1,14 @@
+<div class="accordion accordion-flush" id="help-accordion">
+  {{
+    htmlTemplate("templates/content/help/panel.html",
+      id = "example-help-1",
+      header = "Example help 1"
+    )
+  }}
+  {{
+    htmlTemplate("templates/content/help/panel.html",
+      id = "example-help-2",
+      header = "Example help 2"
+    )
+  }}
+</div>
diff --git a/inst/app/templates/content/help/example-help-1.html b/inst/app/templates/content/help/example-help-1.html
new file mode 100644
index 0000000..245b9b6
--- /dev/null
+++ b/inst/app/templates/content/help/example-help-1.html
@@ -0,0 +1 @@
+Example help 1
diff --git a/inst/app/templates/content/help/example-help-2.html b/inst/app/templates/content/help/example-help-2.html
new file mode 100644
index 0000000..a4817b5
--- /dev/null
+++ b/inst/app/templates/content/help/example-help-2.html
@@ -0,0 +1 @@
+Example help 2
diff --git a/inst/app/templates/content/help/panel.html b/inst/app/templates/content/help/panel.html
new file mode 100644
index 0000000..9eb6e2e
--- /dev/null
+++ b/inst/app/templates/content/help/panel.html
@@ -0,0 +1,12 @@
+<div class="accordion-item">
+  <h2 class="accordion-header">
+    <button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#{{ id }}">
+      {{ header }}
+    </button>
+  </h2>
+  <div id="{{ id }}" class="accordion-collapse collapse" data-bs-parent="#help-accordion">
+    <div class="accordion-body">
+      {{ htmlTemplate(paste0("templates/content/help/", id, ".html")) }}
+    </div>
+  </div>
+</div>