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
---
 .../content/estimators/add-estimators.html         | 19 -----------
 .../estimators/add-estimators/components/mu.html   | 20 -----------
 .../add-estimators/components/panel.html           | 21 ------------
 .../estimators/add-estimators/descriptions/id.html |  1 -
 .../add-estimators/descriptions/idea.html          |  1 -
 .../estimators/add-estimators/descriptions/mu.html |  7 ----
 .../add-estimators/descriptions/seq_bayes.html     |  1 -
 .../estimators/add-estimators/descriptions/wp.html |  1 -
 .../estimators/add-estimators/parameters/id.html   |  1 -
 .../estimators/add-estimators/parameters/idea.html |  1 -
 .../estimators/add-estimators/parameters/mu.html   |  1 -
 .../add-estimators/parameters/seq_bayes.html       | 22 ------------
 .../estimators/add-estimators/parameters/wp.html   | 39 ----------------------
 .../content/estimators/view-estimates.html         | 21 ------------
 14 files changed, 156 deletions(-)
 delete mode 100644 inst/app/templates/content/estimators/add-estimators.html
 delete mode 100644 inst/app/templates/content/estimators/add-estimators/components/mu.html
 delete mode 100644 inst/app/templates/content/estimators/add-estimators/components/panel.html
 delete mode 100644 inst/app/templates/content/estimators/add-estimators/descriptions/id.html
 delete mode 100644 inst/app/templates/content/estimators/add-estimators/descriptions/idea.html
 delete mode 100644 inst/app/templates/content/estimators/add-estimators/descriptions/mu.html
 delete mode 100644 inst/app/templates/content/estimators/add-estimators/descriptions/seq_bayes.html
 delete mode 100644 inst/app/templates/content/estimators/add-estimators/descriptions/wp.html
 delete mode 100644 inst/app/templates/content/estimators/add-estimators/parameters/id.html
 delete mode 100644 inst/app/templates/content/estimators/add-estimators/parameters/idea.html
 delete mode 100644 inst/app/templates/content/estimators/add-estimators/parameters/mu.html
 delete mode 100644 inst/app/templates/content/estimators/add-estimators/parameters/seq_bayes.html
 delete mode 100644 inst/app/templates/content/estimators/add-estimators/parameters/wp.html
 delete mode 100644 inst/app/templates/content/estimators/view-estimates.html

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

diff --git a/inst/app/templates/content/estimators/add-estimators.html b/inst/app/templates/content/estimators/add-estimators.html
deleted file mode 100644
index 0d7562e..0000000
--- a/inst/app/templates/content/estimators/add-estimators.html
+++ /dev/null
@@ -1,19 +0,0 @@
-<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
deleted file mode 100644
index f25a1c8..0000000
--- a/inst/app/templates/content/estimators/add-estimators/components/mu.html
+++ /dev/null
@@ -1,20 +0,0 @@
-<!-- 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
deleted file mode 100644
index b1e0378..0000000
--- a/inst/app/templates/content/estimators/add-estimators/components/panel.html
+++ /dev/null
@@ -1,21 +0,0 @@
-<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
deleted file mode 100644
index b47850f..0000000
--- a/inst/app/templates/content/estimators/add-estimators/descriptions/id.html
+++ /dev/null
@@ -1 +0,0 @@
-The incidence decay (ID) estimator assumes an exponential model and finds the parameters by minimizing the sum of the squared differences between the observed cases counts and the case counts  expected based on the assumed model.  The method assumes that the serial interval is known.   This means that the user needs to input the value of the serial interval.   The serial interval is the average time between the first infection and the time the first infected individual exhibits disease symptoms.  
diff --git a/inst/app/templates/content/estimators/add-estimators/descriptions/idea.html b/inst/app/templates/content/estimators/add-estimators/descriptions/idea.html
deleted file mode 100644
index edfbb79..0000000
--- a/inst/app/templates/content/estimators/add-estimators/descriptions/idea.html
+++ /dev/null
@@ -1 +0,0 @@
-This is a short description of the IDEA method.
diff --git a/inst/app/templates/content/estimators/add-estimators/descriptions/mu.html b/inst/app/templates/content/estimators/add-estimators/descriptions/mu.html
deleted file mode 100644
index 6e7bfe9..0000000
--- a/inst/app/templates/content/estimators/add-estimators/descriptions/mu.html
+++ /dev/null
@@ -1,7 +0,0 @@
-The serial interval (SI) is NOT one of the estimators.   
-
-<p>The SI is a parameter required by all of the estimators, and can also be estimated by the WP method.</p>
-
-<p>The SI is defined as the average time between successive infections in a chain of transmission i.e., the time between the infection of an infected and their subsequent transmissions. </p>
-
-<P> Make the tab a different shade (light gray) and then this won't have parameters.   It will let us not have to explain SI every single time.  We'll expand the description later.</p>
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
deleted file mode 100644
index f6df3ee..0000000
--- a/inst/app/templates/content/estimators/add-estimators/descriptions/seq_bayes.html
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 640b44d..0000000
--- a/inst/app/templates/content/estimators/add-estimators/descriptions/wp.html
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index a3159ca..0000000
--- a/inst/app/templates/content/estimators/add-estimators/parameters/id.html
+++ /dev/null
@@ -1 +0,0 @@
-{{ 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
deleted file mode 100644
index 379be84..0000000
--- a/inst/app/templates/content/estimators/add-estimators/parameters/idea.html
+++ /dev/null
@@ -1 +0,0 @@
-{{ htmlTemplate("templates/content/estimators/add-estimators/components/mu.html", id = "idea") }}
diff --git a/inst/app/templates/content/estimators/add-estimators/parameters/mu.html b/inst/app/templates/content/estimators/add-estimators/parameters/mu.html
deleted file mode 100644
index a3159ca..0000000
--- a/inst/app/templates/content/estimators/add-estimators/parameters/mu.html
+++ /dev/null
@@ -1 +0,0 @@
-{{ htmlTemplate("templates/content/estimators/add-estimators/components/mu.html", id = "id") }}
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
deleted file mode 100644
index bcc82b7..0000000
--- a/inst/app/templates/content/estimators/add-estimators/parameters/seq_bayes.html
+++ /dev/null
@@ -1,22 +0,0 @@
-<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
deleted file mode 100644
index b789a23..0000000
--- a/inst/app/templates/content/estimators/add-estimators/parameters/wp.html
+++ /dev/null
@@ -1,39 +0,0 @@
-<!-- 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
deleted file mode 100644
index e81fff6..0000000
--- a/inst/app/templates/content/estimators/view-estimates.html
+++ /dev/null
@@ -1,21 +0,0 @@
-<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>
-- 
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