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
---
 .../templates/content/estimation/about-estimators/id.html  |  5 +++++
 .../content/estimation/about-estimators/idea.html          |  1 +
 .../content/estimation/about-estimators/panel.html         | 14 ++++++++++++++
 .../content/estimation/about-estimators/seq_bayes.html     |  1 +
 .../templates/content/estimation/about-estimators/wp.html  |  1 +
 5 files changed, 22 insertions(+)
 create mode 100644 inst/app/templates/content/estimation/about-estimators/id.html
 create mode 100644 inst/app/templates/content/estimation/about-estimators/idea.html
 create mode 100644 inst/app/templates/content/estimation/about-estimators/panel.html
 create mode 100644 inst/app/templates/content/estimation/about-estimators/seq_bayes.html
 create mode 100644 inst/app/templates/content/estimation/about-estimators/wp.html

(limited to 'inst/app/templates/content/estimation/about-estimators')

diff --git a/inst/app/templates/content/estimation/about-estimators/id.html b/inst/app/templates/content/estimation/about-estimators/id.html
new file mode 100644
index 0000000..3200c00
--- /dev/null
+++ b/inst/app/templates/content/estimation/about-estimators/id.html
@@ -0,0 +1,5 @@
+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/estimation/about-estimators/idea.html b/inst/app/templates/content/estimation/about-estimators/idea.html
new file mode 100644
index 0000000..edfbb79
--- /dev/null
+++ b/inst/app/templates/content/estimation/about-estimators/idea.html
@@ -0,0 +1 @@
+This is a short description of the IDEA method.
diff --git a/inst/app/templates/content/estimation/about-estimators/panel.html b/inst/app/templates/content/estimation/about-estimators/panel.html
new file mode 100644
index 0000000..98fe155
--- /dev/null
+++ b/inst/app/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/app/templates/content/estimation/about-estimators/seq_bayes.html b/inst/app/templates/content/estimation/about-estimators/seq_bayes.html
new file mode 100644
index 0000000..f6df3ee
--- /dev/null
+++ b/inst/app/templates/content/estimation/about-estimators/seq_bayes.html
@@ -0,0 +1 @@
+This is a short description of the seqB method.
diff --git a/inst/app/templates/content/estimation/about-estimators/wp.html b/inst/app/templates/content/estimation/about-estimators/wp.html
new file mode 100644
index 0000000..640b44d
--- /dev/null
+++ b/inst/app/templates/content/estimation/about-estimators/wp.html
@@ -0,0 +1 @@
+This is a short description of the WP method.
-- 
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