diff options
Diffstat (limited to 'inst/app/templates/content/estimators')
14 files changed, 0 insertions, 156 deletions
diff --git a/inst/app/templates/content/estimators/add-estimators.html b/inst/app/templates/content/estimators/add-estimators.html deleted file mode 100644 index 0d7562e..0000000 --- a/inst/app/templates/content/estimators/add-estimators.html +++ /dev/null @@ -1,19 +0,0 @@ -<div class="accordion accordion-flush" id="estimators-accordion"> - {{ - htmlTemplate("templates/content/estimators/add-estimators/components/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/estimators/add-estimators/components/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/estimators/add-estimators/components/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/estimators/add-estimators/components/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/estimators/add-estimators/components/mu.html b/inst/app/templates/content/estimators/add-estimators/components/mu.html deleted file mode 100644 index f25a1c8..0000000 --- a/inst/app/templates/content/estimators/add-estimators/components/mu.html +++ /dev/null @@ -1,20 +0,0 @@ -<!-- Serial interval label and help tooltip. --> -<label class="form-label" for="mu_{{ id }}"> - Serial interval (μ) - <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. --> -<small id="mu_{{ id }}_warn" class="form-text text-primary shiny-text-output"></small> diff --git a/inst/app/templates/content/estimators/add-estimators/components/panel.html b/inst/app/templates/content/estimators/add-estimators/components/panel.html deleted file mode 100644 index b1e0378..0000000 --- a/inst/app/templates/content/estimators/add-estimators/components/panel.html +++ /dev/null @@ -1,21 +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/estimators/add-estimators/descriptions/", id, ".html")) }}</p> - <h5>Parameters</h5> - <form class="my-3"> - {{ htmlTemplate(paste0("templates/content/estimators/add-estimators/parameters/", id, ".html")) }} - </form> - <button id="add_{{ id }}" type="button" class="btn btn-outline-primary btn-sm action-button"> - <span class="glyphicon glyphicon-plus"></span> Add - </button> - </div> - </div> -</div> diff --git a/inst/app/templates/content/estimators/add-estimators/descriptions/id.html b/inst/app/templates/content/estimators/add-estimators/descriptions/id.html deleted file mode 100644 index b47850f..0000000 --- a/inst/app/templates/content/estimators/add-estimators/descriptions/id.html +++ /dev/null @@ -1 +0,0 @@ -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/estimators/add-estimators/descriptions/idea.html b/inst/app/templates/content/estimators/add-estimators/descriptions/idea.html deleted file mode 100644 index edfbb79..0000000 --- a/inst/app/templates/content/estimators/add-estimators/descriptions/idea.html +++ /dev/null @@ -1 +0,0 @@ -This is a short description of the IDEA method. diff --git a/inst/app/templates/content/estimators/add-estimators/descriptions/mu.html b/inst/app/templates/content/estimators/add-estimators/descriptions/mu.html deleted file mode 100644 index 6e7bfe9..0000000 --- a/inst/app/templates/content/estimators/add-estimators/descriptions/mu.html +++ /dev/null @@ -1,7 +0,0 @@ -The serial interval (SI) is NOT one of the estimators. - -<p>The SI is a parameter required by all of the estimators, and can also be estimated by the WP method.</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 and their subsequent transmissions. </p> - -<P> Make the tab a different shade (light gray) and then this won't have parameters. It will let us not have to explain SI every single time. We'll expand the description later.</p> diff --git a/inst/app/templates/content/estimators/add-estimators/descriptions/seq_bayes.html b/inst/app/templates/content/estimators/add-estimators/descriptions/seq_bayes.html deleted file mode 100644 index f6df3ee..0000000 --- a/inst/app/templates/content/estimators/add-estimators/descriptions/seq_bayes.html +++ /dev/null @@ -1 +0,0 @@ -This is a short description of the seqB method. diff --git a/inst/app/templates/content/estimators/add-estimators/descriptions/wp.html b/inst/app/templates/content/estimators/add-estimators/descriptions/wp.html deleted file mode 100644 index 640b44d..0000000 --- a/inst/app/templates/content/estimators/add-estimators/descriptions/wp.html +++ /dev/null @@ -1 +0,0 @@ -This is a short description of the WP method. 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 (κ) - <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> diff --git a/inst/app/templates/content/estimators/view-estimates.html b/inst/app/templates/content/estimators/view-estimates.html deleted file mode 100644 index e81fff6..0000000 --- a/inst/app/templates/content/estimators/view-estimates.html +++ /dev/null @@ -1,21 +0,0 @@ -<h4>Estimates table</h4> -<!-- Estimates table. --> -<div class="my-3"> - {{ DT::dataTableOutput(outputId = "estimates_table") }} -</div> -<!-- Display inactive delete button when no columns are selected. --> -<button type="button" class="btn btn-primary btn-sm text-white" disabled - data-display-if="'estimates_table_columns_selected' in input && - input.estimates_table_columns_selected.length == 0"> - <span class="glyphicon glyphicon-remove"></span> Delete column(s) -</button> -<!-- Display active delete button when at least one column is selected. --> -<button id="estimators_delete" type="button" class="btn btn-primary btn-sm action-button text-white" - data-display-if="'estimates_table_columns_selected' in input && - input.estimates_table_columns_selected.length != 0"> - <span class="glyphicon glyphicon-remove"></span> Delete column(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> |