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
---
 inst/app/templates/content/about.html              | 28 ----------------
 inst/app/templates/content/data.html               | 12 -------
 inst/app/templates/content/data/enter-data.html    |  9 -----
 .../content/data/enter-data/load-samples.html      | 19 -----------
 .../content/data/enter-data/manual-entry.html      | 11 ------
 .../content/data/enter-data/required-format.html   | 25 --------------
 .../content/data/enter-data/upload-data.html       | 12 -------
 inst/app/templates/content/data/view-data.html     |  3 --
 .../content/data/view-data/data-plots.html         |  7 ----
 .../content/data/view-data/data-table.html         | 18 ----------
 inst/app/templates/content/estimation.html         | 13 --------
 .../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 -----------
 inst/app/templates/content/help.html               |  8 -----
 inst/app/templates/content/help/panel.html         | 12 -------
 .../templates/content/help/serial-interval.html    |  9 -----
 29 files changed, 383 deletions(-)
 delete mode 100644 inst/app/templates/content/about.html
 delete mode 100644 inst/app/templates/content/data.html
 delete mode 100644 inst/app/templates/content/data/enter-data.html
 delete mode 100644 inst/app/templates/content/data/enter-data/load-samples.html
 delete mode 100644 inst/app/templates/content/data/enter-data/manual-entry.html
 delete mode 100644 inst/app/templates/content/data/enter-data/required-format.html
 delete mode 100644 inst/app/templates/content/data/enter-data/upload-data.html
 delete mode 100644 inst/app/templates/content/data/view-data.html
 delete mode 100644 inst/app/templates/content/data/view-data/data-plots.html
 delete mode 100644 inst/app/templates/content/data/view-data/data-table.html
 delete mode 100644 inst/app/templates/content/estimation.html
 delete mode 100644 inst/app/templates/content/estimation/about-estimators.html
 delete mode 100644 inst/app/templates/content/estimation/about-estimators/id.html
 delete mode 100644 inst/app/templates/content/estimation/about-estimators/idea.html
 delete mode 100644 inst/app/templates/content/estimation/about-estimators/panel.html
 delete mode 100644 inst/app/templates/content/estimation/about-estimators/seq_bayes.html
 delete mode 100644 inst/app/templates/content/estimation/about-estimators/wp.html
 delete mode 100644 inst/app/templates/content/estimation/estimates.html
 delete mode 100644 inst/app/templates/content/estimation/estimates/add-estimators.html
 delete mode 100644 inst/app/templates/content/estimation/estimates/add-estimators/id.html
 delete mode 100644 inst/app/templates/content/estimation/estimates/add-estimators/idea.html
 delete mode 100644 inst/app/templates/content/estimation/estimates/add-estimators/mu.html
 delete mode 100644 inst/app/templates/content/estimation/estimates/add-estimators/parameters.html
 delete mode 100644 inst/app/templates/content/estimation/estimates/add-estimators/seq_bayes.html
 delete mode 100644 inst/app/templates/content/estimation/estimates/add-estimators/wp.html
 delete mode 100644 inst/app/templates/content/estimation/estimates/estimates-table.html
 delete mode 100644 inst/app/templates/content/help.html
 delete mode 100644 inst/app/templates/content/help/panel.html
 delete mode 100644 inst/app/templates/content/help/serial-interval.html

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

diff --git a/inst/app/templates/content/about.html b/inst/app/templates/content/about.html
deleted file mode 100644
index 73b75ea..0000000
--- a/inst/app/templates/content/about.html
+++ /dev/null
@@ -1,28 +0,0 @@
-<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</em><sub>0</sub>, is defined as the expected number of infections caused
-  by a single infectious individual when introduced into a totally susceptible population. 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. It is a useful indicator of the transmissibility of an infectious disease during
-  the early stages of its spread and detection.
-</p>
-<p>
-  If <em>R</em><sub>0</sub> &lt; 1, the disease will eventually die out. On the other hand, if
-  <em>R</em><sub>0</sub> &gt; 1, the disease will spread (the higher the <em>R</em><sub>0</sub>, the faster this will
-  happen). Due to uncertainty of known data about the disease, it is difficult to determine <em>R</em><sub>0</sub>
-  precisely. Therefore, many estimation methods exist, each based on different assumptions and yielding different
-  estimates. It is the responsibility of users to employ the most appropriate estimator (or suite of estimators) given
-  the situation at hand.
-</p>
diff --git a/inst/app/templates/content/data.html b/inst/app/templates/content/data.html
deleted file mode 100644
index 574f003..0000000
--- a/inst/app/templates/content/data.html
+++ /dev/null
@@ -1,12 +0,0 @@
-<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
deleted file mode 100644
index 254f1d7..0000000
--- a/inst/app/templates/content/data/enter-data.html
+++ /dev/null
@@ -1,9 +0,0 @@
-<form class="mb-5">
-  {{ htmlTemplate("templates/content/data/enter-data/required-format.html") }}
-  {{ htmlTemplate("templates/content/data/enter-data/manual-entry.html") }}
-  {{ htmlTemplate("templates/content/data/enter-data/upload-data.html") }}
-</form>
-<hr>
-<form>
-  {{ htmlTemplate("templates/content/data/enter-data/load-samples.html") }}
-</form>
diff --git a/inst/app/templates/content/data/enter-data/load-samples.html b/inst/app/templates/content/data/enter-data/load-samples.html
deleted file mode 100644
index 2a4f013..0000000
--- a/inst/app/templates/content/data/enter-data/load-samples.html
+++ /dev/null
@@ -1,19 +0,0 @@
-<h4 class="mb-3">Load samples</h4>
-<!-- Checkboxes for sample data. -->
-{{
-  checkboxInput(inputId = "covid_canada", label = "COVID-19 Canada, 2020/03/03 - 2020/03/31 (Weekly)",
-    value = FALSE, width = "100%"
-  )
-}}
-{{
-  checkboxInput(inputId = "covid_ontario", label = "COVID-19 Ontario, 2020/03/03 - 2020/03/31 (Weekly)",
-    value = FALSE, width = "100%"
-  )
-}}
-<!-- Warning text. -->
-<div>
-  <small id="data_samples_warn" class="form-text text-primary shiny-text-output"></small>
-</div>
-<button id="data_samples" type="button" class="btn btn-outline-primary btn-sm action-button mt-3">
-  <span class="glyphicon glyphicon-plus"></span> Add
-</button>
diff --git a/inst/app/templates/content/data/enter-data/manual-entry.html b/inst/app/templates/content/data/enter-data/manual-entry.html
deleted file mode 100644
index a6319d9..0000000
--- a/inst/app/templates/content/data/enter-data/manual-entry.html
+++ /dev/null
@@ -1,11 +0,0 @@
-<!-- Data input area (manual entry). -->
-<div class="my-4">
-  <label class="form-label" for="data_area">Enter manually</label>
-  <textarea id="data_area" class="form-control" rows="3" wrap="off"></textarea>
-  <div>
-    <small id="data_area_warn" class="form-text text-primary shiny-html-output"></small>
-  </div>
-  <button id="data_bulk" 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/app/templates/content/data/enter-data/required-format.html b/inst/app/templates/content/data/enter-data/required-format.html
deleted file mode 100644
index 724dd83..0000000
--- a/inst/app/templates/content/data/enter-data/required-format.html
+++ /dev/null
@@ -1,25 +0,0 @@
-<!-- Button to toggle help text. -->
-<button type="button" class="btn btn-outline-primary btn-sm" id="data-format-toggle"
-        data-bs-toggle="collapse" data-bs-target="#data-format">Show required format</button>
-<!-- Help text for data input format. -->
-<div class="collapse mt-2" id="data-format">
-  <div class="card card-body border-primary">
-    <p>Manually enter rows or upload a CSV file 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">
-      Disease A,Days,1,2,3,4,5,6,7,8,9<br>
-      Disease B,Weeks,3,1,4,1,5,2,9<br>
-      Disease C,Days,2,3,5,7,11,13,17,19
-    </p>
-  </div>
-</div>
diff --git a/inst/app/templates/content/data/enter-data/upload-data.html b/inst/app/templates/content/data/enter-data/upload-data.html
deleted file mode 100644
index 740047b..0000000
--- a/inst/app/templates/content/data/enter-data/upload-data.html
+++ /dev/null
@@ -1,12 +0,0 @@
-<!-- File input for data upload (hidden). -->
-<input class="form-control" type="file" id="data_upload" accept="text/csv,text/comma-separated-values,text/plain,.csv">
-<!-- Custom button to trigger file selector for data upload (visible). -->
-<label class="form-label" for="data-upload-select">Upload a CSV file</label>
-<div class="input-group">
-  <button id="data-upload-select" type="button" class="btn btn-outline-primary btn-sm">
-    <span class="glyphicon glyphicon-file"></span> Select file
-  </button>
-  <input type="text" id="data-upload-name" class="form-control" placeholder="No file selected" disabled>
-</div>
-<!-- Warning text. -->
-<small id="data_upload_warn" class="form-text text-primary shiny-html-output"></small>
diff --git a/inst/app/templates/content/data/view-data.html b/inst/app/templates/content/data/view-data.html
deleted file mode 100644
index 880cf7f..0000000
--- a/inst/app/templates/content/data/view-data.html
+++ /dev/null
@@ -1,3 +0,0 @@
-{{ htmlTemplate("templates/content/data/view-data/data-table.html") }}
-<hr>
-{{ htmlTemplate("templates/content/data/view-data/data-plots.html") }}
diff --git a/inst/app/templates/content/data/view-data/data-plots.html b/inst/app/templates/content/data/view-data/data-plots.html
deleted file mode 100644
index 5019088..0000000
--- a/inst/app/templates/content/data/view-data/data-plots.html
+++ /dev/null
@@ -1,7 +0,0 @@
-<h4>Data plots</h4>
-<div class="container my-5">
-  {{ plotly::plotlyOutput(outputId = "data_plot_days") }}
-</div>
-<div class="container">
-  {{ plotly::plotlyOutput(outputId = "data_plot_weeks") }}
-</div>
diff --git a/inst/app/templates/content/data/view-data/data-table.html b/inst/app/templates/content/data/view-data/data-table.html
deleted file mode 100644
index 590a5b9..0000000
--- a/inst/app/templates/content/data/view-data/data-table.html
+++ /dev/null
@@ -1,18 +0,0 @@
-<h4>Data table</h4>
-<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/estimation.html b/inst/app/templates/content/estimation.html
deleted file mode 100644
index 5764057..0000000
--- a/inst/app/templates/content/estimation.html
+++ /dev/null
@@ -1,13 +0,0 @@
-<nav class="nav nav-tabs">
-  <a class="nav-link active" data-bs-toggle="tab" href="#about-estimators">About the estimators</a>
-  <a class="nav-link" data-bs-toggle="tab" href="#estimates">Compute and view estimates</a>
-</nav>
-
-<div class="container-fluid tab-content">
-  <div id="about-estimators" class="pt-3 tab-pane fade show active">
-    {{ htmlTemplate("templates/content/estimation/about-estimators.html") }}
-  </div>
-  <div id="estimates" class="pt-3 tab-pane fade">
-    {{ htmlTemplate("templates/content/estimation/estimates.html") }}
-  </div>
-</div>
diff --git a/inst/app/templates/content/estimation/about-estimators.html b/inst/app/templates/content/estimation/about-estimators.html
deleted file mode 100644
index db2898b..0000000
--- a/inst/app/templates/content/estimation/about-estimators.html
+++ /dev/null
@@ -1,31 +0,0 @@
-<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/app/templates/content/estimation/about-estimators/id.html b/inst/app/templates/content/estimation/about-estimators/id.html
deleted file mode 100644
index fc70b1c..0000000
--- a/inst/app/templates/content/estimation/about-estimators/id.html
+++ /dev/null
@@ -1,3 +0,0 @@
-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/app/templates/content/estimation/about-estimators/idea.html b/inst/app/templates/content/estimation/about-estimators/idea.html
deleted file mode 100644
index 67548f8..0000000
--- a/inst/app/templates/content/estimation/about-estimators/idea.html
+++ /dev/null
@@ -1,4 +0,0 @@
-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/app/templates/content/estimation/about-estimators/panel.html b/inst/app/templates/content/estimation/about-estimators/panel.html
deleted file mode 100644
index 98fe155..0000000
--- a/inst/app/templates/content/estimation/about-estimators/panel.html
+++ /dev/null
@@ -1,14 +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/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
deleted file mode 100644
index 8f66ab4..0000000
--- a/inst/app/templates/content/estimation/about-estimators/seq_bayes.html
+++ /dev/null
@@ -1,9 +0,0 @@
-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/app/templates/content/estimation/about-estimators/wp.html b/inst/app/templates/content/estimation/about-estimators/wp.html
deleted file mode 100644
index c6f4580..0000000
--- a/inst/app/templates/content/estimation/about-estimators/wp.html
+++ /dev/null
@@ -1,6 +0,0 @@
-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/app/templates/content/estimation/estimates.html b/inst/app/templates/content/estimation/estimates.html
deleted file mode 100644
index bc9124e..0000000
--- a/inst/app/templates/content/estimation/estimates.html
+++ /dev/null
@@ -1,3 +0,0 @@
-{{ htmlTemplate("templates/content/estimation/estimates/estimates-table.html") }}
-<hr>
-{{ htmlTemplate("templates/content/estimation/estimates/add-estimators.html") }}
diff --git a/inst/app/templates/content/estimation/estimates/add-estimators.html b/inst/app/templates/content/estimation/estimates/add-estimators.html
deleted file mode 100644
index 60111c7..0000000
--- a/inst/app/templates/content/estimation/estimates/add-estimators.html
+++ /dev/null
@@ -1,16 +0,0 @@
-<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/app/templates/content/estimation/estimates/add-estimators/id.html b/inst/app/templates/content/estimation/estimates/add-estimators/id.html
deleted file mode 100644
index 7c35e55..0000000
--- a/inst/app/templates/content/estimation/estimates/add-estimators/id.html
+++ /dev/null
@@ -1 +0,0 @@
-{{ htmlTemplate("templates/content/estimation/estimates/add-estimators/mu.html", id = "id") }}
diff --git a/inst/app/templates/content/estimation/estimates/add-estimators/idea.html b/inst/app/templates/content/estimation/estimates/add-estimators/idea.html
deleted file mode 100644
index 781349f..0000000
--- a/inst/app/templates/content/estimation/estimates/add-estimators/idea.html
+++ /dev/null
@@ -1 +0,0 @@
-{{ htmlTemplate("templates/content/estimation/estimates/add-estimators/mu.html", id = "idea") }}
diff --git a/inst/app/templates/content/estimation/estimates/add-estimators/mu.html b/inst/app/templates/content/estimation/estimates/add-estimators/mu.html
deleted file mode 100644
index 8781574..0000000
--- a/inst/app/templates/content/estimation/estimates/add-estimators/mu.html
+++ /dev/null
@@ -1,22 +0,0 @@
-<!-- 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/app/templates/content/estimation/estimates/add-estimators/parameters.html b/inst/app/templates/content/estimation/estimates/add-estimators/parameters.html
deleted file mode 100644
index 5250e31..0000000
--- a/inst/app/templates/content/estimation/estimates/add-estimators/parameters.html
+++ /dev/null
@@ -1,7 +0,0 @@
-<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/app/templates/content/estimation/estimates/add-estimators/seq_bayes.html b/inst/app/templates/content/estimation/estimates/add-estimators/seq_bayes.html
deleted file mode 100644
index 028fabc..0000000
--- a/inst/app/templates/content/estimation/estimates/add-estimators/seq_bayes.html
+++ /dev/null
@@ -1,22 +0,0 @@
-<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/app/templates/content/estimation/estimates/add-estimators/wp.html b/inst/app/templates/content/estimation/estimates/add-estimators/wp.html
deleted file mode 100644
index 511170f..0000000
--- a/inst/app/templates/content/estimation/estimates/add-estimators/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/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/app/templates/content/estimation/estimates/estimates-table.html b/inst/app/templates/content/estimation/estimates/estimates-table.html
deleted file mode 100644
index 4704d03..0000000
--- a/inst/app/templates/content/estimation/estimates/estimates-table.html
+++ /dev/null
@@ -1,19 +0,0 @@
-<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>
diff --git a/inst/app/templates/content/help.html b/inst/app/templates/content/help.html
deleted file mode 100644
index df4e887..0000000
--- a/inst/app/templates/content/help.html
+++ /dev/null
@@ -1,8 +0,0 @@
-<div class="accordion accordion-flush" id="help-accordion">
-  {{
-    htmlTemplate("templates/content/help/panel.html",
-      id = "serial-interval",
-      header = "What is the serial interval?"
-    )
-  }}
-</div>
diff --git a/inst/app/templates/content/help/panel.html b/inst/app/templates/content/help/panel.html
deleted file mode 100644
index 9eb6e2e..0000000
--- a/inst/app/templates/content/help/panel.html
+++ /dev/null
@@ -1,12 +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 }}">
-      {{ 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>
diff --git a/inst/app/templates/content/help/serial-interval.html b/inst/app/templates/content/help/serial-interval.html
deleted file mode 100644
index e061115..0000000
--- a/inst/app/templates/content/help/serial-interval.html
+++ /dev/null
@@ -1,9 +0,0 @@
-<p>Reference: <a href="https://en.wikipedia.org/wiki/Serial_interval" target="_blank"><em>Wikipedia</em></a>
-<p>
-  The serial interval (SI) is not one of the estimators. It is a parameter required by most of the estimators, and can
-  also be estimated by some of them (if not specified).
-</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 individual and their subsequent transmissions).
-</p>
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