Update web app entry point

- Rename 'app' -> 'web'
- Return shiny app object in entry point function

5 files changed, 36 insertions, 0 deletions

diff --git a/inst/web/templates/content/estimation/about-estimators/id.html b/inst/web/templates/content/estimation/about-estimators/id.html
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+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
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+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
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+<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
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+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
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+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.