From e920b3e514e717fc05ed524267d3b53e272fec51 Mon Sep 17 00:00:00 2001
From: Naeem Model <me@nmode.ca>
Date: Mon, 6 Jan 2025 23:55:43 +0000
Subject: Update web app entry point

- Rename 'app' -> 'web'
- Return shiny app object in entry point function
---
 .../content/estimation/about-estimators.html       | 31 +++++++++++++++++
 .../content/estimation/about-estimators/id.html    |  3 ++
 .../content/estimation/about-estimators/idea.html  |  4 +++
 .../content/estimation/about-estimators/panel.html | 14 ++++++++
 .../estimation/about-estimators/seq_bayes.html     |  9 +++++
 .../content/estimation/about-estimators/wp.html    |  6 ++++
 .../templates/content/estimation/estimates.html    |  3 ++
 .../estimation/estimates/add-estimators.html       | 16 +++++++++
 .../estimation/estimates/add-estimators/id.html    |  1 +
 .../estimation/estimates/add-estimators/idea.html  |  1 +
 .../estimation/estimates/add-estimators/mu.html    | 22 ++++++++++++
 .../estimates/add-estimators/parameters.html       |  7 ++++
 .../estimates/add-estimators/seq_bayes.html        | 22 ++++++++++++
 .../estimation/estimates/add-estimators/wp.html    | 39 ++++++++++++++++++++++
 .../estimation/estimates/estimates-table.html      | 19 +++++++++++
 15 files changed, 197 insertions(+)
 create mode 100644 inst/web/templates/content/estimation/about-estimators.html
 create mode 100644 inst/web/templates/content/estimation/about-estimators/id.html
 create mode 100644 inst/web/templates/content/estimation/about-estimators/idea.html
 create mode 100644 inst/web/templates/content/estimation/about-estimators/panel.html
 create mode 100644 inst/web/templates/content/estimation/about-estimators/seq_bayes.html
 create mode 100644 inst/web/templates/content/estimation/about-estimators/wp.html
 create mode 100644 inst/web/templates/content/estimation/estimates.html
 create mode 100644 inst/web/templates/content/estimation/estimates/add-estimators.html
 create mode 100644 inst/web/templates/content/estimation/estimates/add-estimators/id.html
 create mode 100644 inst/web/templates/content/estimation/estimates/add-estimators/idea.html
 create mode 100644 inst/web/templates/content/estimation/estimates/add-estimators/mu.html
 create mode 100644 inst/web/templates/content/estimation/estimates/add-estimators/parameters.html
 create mode 100644 inst/web/templates/content/estimation/estimates/add-estimators/seq_bayes.html
 create mode 100644 inst/web/templates/content/estimation/estimates/add-estimators/wp.html
 create mode 100644 inst/web/templates/content/estimation/estimates/estimates-table.html

(limited to 'inst/web/templates/content/estimation')

diff --git a/inst/web/templates/content/estimation/about-estimators.html b/inst/web/templates/content/estimation/about-estimators.html
new file mode 100644
index 0000000..db2898b
--- /dev/null
+++ b/inst/web/templates/content/estimation/about-estimators.html
@@ -0,0 +1,31 @@
+<div class="accordion accordion-flush" id="estimation-accordion">
+  {{
+    htmlTemplate("templates/content/estimation/about-estimators/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/estimation/about-estimators/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/estimation/about-estimators/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/estimation/about-estimators/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/web/templates/content/estimation/about-estimators/id.html b/inst/web/templates/content/estimation/about-estimators/id.html
new file mode 100644
index 0000000..fc70b1c
--- /dev/null
+++ b/inst/web/templates/content/estimation/about-estimators/id.html
@@ -0,0 +1,3 @@
+The Incidence Decay (ID) estimator uses the method of least squares to estimate <em>R</em><sub>0</sub>.
+This method assumes the serial interval is known, and is built under the SIR assumption.
+We note that the use of this method might result in the underestimation of <em>R</em><sub>0</sub>.
diff --git a/inst/web/templates/content/estimation/about-estimators/idea.html b/inst/web/templates/content/estimation/about-estimators/idea.html
new file mode 100644
index 0000000..67548f8
--- /dev/null
+++ b/inst/web/templates/content/estimation/about-estimators/idea.html
@@ -0,0 +1,4 @@
+The Incidence Decay and Exponential Adjustment (ID) estimator is an alternative formulation of the Incidence Decay (ID) model which includes a decay factor to reflect the often observed outbreak decline.
+This addresses the potential underestimation of the <em>R</em><sub>0</sub> estimate when using the ID method.
+The method of least squares is used to estimate <em>R</em><sub>0</sub>, and similar to the ID model, the serial interval is assumed to be known and this method is developed assuming the SIR model.
+We note that, since we need to obtain a minimizer of the decay factor to solve the optimization problem, we require that the number of cases in the dataset be at least 2.
diff --git a/inst/web/templates/content/estimation/about-estimators/panel.html b/inst/web/templates/content/estimation/about-estimators/panel.html
new file mode 100644
index 0000000..98fe155
--- /dev/null
+++ b/inst/web/templates/content/estimation/about-estimators/panel.html
@@ -0,0 +1,14 @@
+<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/estimation/about-estimators/", id, ".html")) }}</p>
+    </div>
+  </div>
+</div>
diff --git a/inst/web/templates/content/estimation/about-estimators/seq_bayes.html b/inst/web/templates/content/estimation/about-estimators/seq_bayes.html
new file mode 100644
index 0000000..8f66ab4
--- /dev/null
+++ b/inst/web/templates/content/estimation/about-estimators/seq_bayes.html
@@ -0,0 +1,9 @@
+The sequential Bayes (seqB) estimator uses a Bayesian approach to estimate <em>R</em><sub>0</sub> which updates the reproductive number estimate as data accumulates over time.
+This approach is based on the SIR model, and assumes that the mean of the serial distribution (ie. the serial interval (SI)) is known.
+It is assumed that infectious counts are observed at periodic times (ie. daily, weekly).
+This method cannot handle datasets where there are no new infections observed in a time interval, thus, to remedy this, 
+some manipulation may be necessary to make the times at which infectious counts are observed sufficiently course (ie. weeks instead of days).
+Further, this method is also inappropriate in situations where long intervals between cases are observed in the initial stages of the epidemic.
+Finally, the <em>R</em><sub>0</sub> approximation behaves similarly to a branching process, which means that throughout, the population size “available” to be infected remains constant.
+We note that this assumption does not hold for the SIR/SEIR/SEAIR compartmental models.
+As such, seqB estimates should only really be considered early on in an epidemic, ie. before the inflection point of an epidemic, if the dataset being used follows these models. 
diff --git a/inst/web/templates/content/estimation/about-estimators/wp.html b/inst/web/templates/content/estimation/about-estimators/wp.html
new file mode 100644
index 0000000..c6f4580
--- /dev/null
+++ b/inst/web/templates/content/estimation/about-estimators/wp.html
@@ -0,0 +1,6 @@
+The White and Pagano (WP) estimator uses maximum likelihood estimation to estimate <em>R</em><sub>0</sub>.
+In this method, the serial interval (SI) is either known, or can be estimated along with <em>R</em><sub>0</sub>.
+It is assumed that the number of infectious individuals are observable at discrete time points (ie. daily or weekly).
+Further, this method also assumes an underlying branching process, which means that throughout, the population size “available” to be infected remains constant.
+We note that this assumption does not hold for the SIR/SEIR/SEAIR compartmental models.
+As such, WP estimates should only really be considered early on in an epidemic, ie. before the inflection point of an epidemic, if the dataset being used follows these models.
diff --git a/inst/web/templates/content/estimation/estimates.html b/inst/web/templates/content/estimation/estimates.html
new file mode 100644
index 0000000..bc9124e
--- /dev/null
+++ b/inst/web/templates/content/estimation/estimates.html
@@ -0,0 +1,3 @@
+{{ htmlTemplate("templates/content/estimation/estimates/estimates-table.html") }}
+<hr>
+{{ htmlTemplate("templates/content/estimation/estimates/add-estimators.html") }}
diff --git a/inst/web/templates/content/estimation/estimates/add-estimators.html b/inst/web/templates/content/estimation/estimates/add-estimators.html
new file mode 100644
index 0000000..60111c7
--- /dev/null
+++ b/inst/web/templates/content/estimation/estimates/add-estimators.html
@@ -0,0 +1,16 @@
+<h4>Add estimators</h4>
+<form class="my-3">
+  <!-- Dropdown to select estimator. -->
+  <label class="form-label" for="estimator_select">Select estimator:</label>
+  <select name="estimator_select" class="form-select">
+    <option value="id" selected>Incidence Decay (ID)</option>
+    <option value="idea">Incidence Decay and Exponential Adjustment (IDEA)</option>
+    <option value="seq_bayes">Sequential Bayes (seqB)</option>
+    <option value="wp">White and Pagano (WP)</option>
+  </select>
+  <!-- Parameters. -->
+  {{ htmlTemplate("templates/content/estimation/estimates/add-estimators/parameters.html", id = "id") }}
+  {{ htmlTemplate("templates/content/estimation/estimates/add-estimators/parameters.html", id = "idea") }}
+  {{ htmlTemplate("templates/content/estimation/estimates/add-estimators/parameters.html", id = "seq_bayes") }}
+  {{ htmlTemplate("templates/content/estimation/estimates/add-estimators/parameters.html", id = "wp") }}
+</form>
diff --git a/inst/web/templates/content/estimation/estimates/add-estimators/id.html b/inst/web/templates/content/estimation/estimates/add-estimators/id.html
new file mode 100644
index 0000000..7c35e55
--- /dev/null
+++ b/inst/web/templates/content/estimation/estimates/add-estimators/id.html
@@ -0,0 +1 @@
+{{ htmlTemplate("templates/content/estimation/estimates/add-estimators/mu.html", id = "id") }}
diff --git a/inst/web/templates/content/estimation/estimates/add-estimators/idea.html b/inst/web/templates/content/estimation/estimates/add-estimators/idea.html
new file mode 100644
index 0000000..781349f
--- /dev/null
+++ b/inst/web/templates/content/estimation/estimates/add-estimators/idea.html
@@ -0,0 +1 @@
+{{ htmlTemplate("templates/content/estimation/estimates/add-estimators/mu.html", id = "idea") }}
diff --git a/inst/web/templates/content/estimation/estimates/add-estimators/mu.html b/inst/web/templates/content/estimation/estimates/add-estimators/mu.html
new file mode 100644
index 0000000..8781574
--- /dev/null
+++ b/inst/web/templates/content/estimation/estimates/add-estimators/mu.html
@@ -0,0 +1,22 @@
+<!-- Serial interval label and help tooltip. -->
+<label class="form-label" for="mu_{{ id }}">
+  Serial interval
+  <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. -->
+<div>
+  <small id="mu_{{ id }}_warn" class="form-text text-primary shiny-text-output"></small>
+</div>
diff --git a/inst/web/templates/content/estimation/estimates/add-estimators/parameters.html b/inst/web/templates/content/estimation/estimates/add-estimators/parameters.html
new file mode 100644
index 0000000..5250e31
--- /dev/null
+++ b/inst/web/templates/content/estimation/estimates/add-estimators/parameters.html
@@ -0,0 +1,7 @@
+<div class="my-4" data-display-if="input.estimator_select === '{{ id }}'">
+  <h5>Parameters</h5>
+  {{ htmlTemplate(paste0("templates/content/estimation/estimates/add-estimators/", id, ".html")) }}
+  <button id="add_{{ id }}" 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/web/templates/content/estimation/estimates/add-estimators/seq_bayes.html b/inst/web/templates/content/estimation/estimates/add-estimators/seq_bayes.html
new file mode 100644
index 0000000..028fabc
--- /dev/null
+++ b/inst/web/templates/content/estimation/estimates/add-estimators/seq_bayes.html
@@ -0,0 +1,22 @@
+<div class="row">
+  <!-- Serial interval (mu). -->
+  <div class="col-md">
+    {{ htmlTemplate("templates/content/estimation/estimates/add-estimators/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</em><sub>0</sub>. The higher this value, the higher
+                          <em>R</em><sub>0</sub> 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/web/templates/content/estimation/estimates/add-estimators/wp.html b/inst/web/templates/content/estimation/estimates/add-estimators/wp.html
new file mode 100644
index 0000000..511170f
--- /dev/null
+++ b/inst/web/templates/content/estimation/estimates/add-estimators/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/estimation/estimates/add-estimators/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/web/templates/content/estimation/estimates/estimates-table.html b/inst/web/templates/content/estimation/estimates/estimates-table.html
new file mode 100644
index 0000000..4704d03
--- /dev/null
+++ b/inst/web/templates/content/estimation/estimates/estimates-table.html
@@ -0,0 +1,19 @@
+<h4>Estimates table</h4>
+<!-- Estimates table. -->
+<div class="my-3">
+  {{ DT::dataTableOutput(outputId = "estimates_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="'estimates_table_rows_selected' in input && input.estimates_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="estimators_delete" type="button" class="btn btn-primary btn-sm action-button text-white"
+        data-display-if="'estimates_table_rows_selected' in input && input.estimates_table_rows_selected.length != 0">
+  <span class="glyphicon glyphicon-remove"></span> Delete row(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>
-- 
cgit v1.2.3