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Diffstat (limited to 'inst/app/templates/content/estimation')
15 files changed, 0 insertions, 197 deletions
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 (κ) - <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> |