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
---
 .../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 ----------------------
 5 files changed, 64 deletions(-)
 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

(limited to 'inst/app/templates/content/estimators/add-estimators/parameters')

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>
-- 
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