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Diffstat (limited to 'inst/app/templates')
33 files changed, 0 insertions, 445 deletions
diff --git a/inst/app/templates/content.html b/inst/app/templates/content.html deleted file mode 100644 index da69f08..0000000 --- a/inst/app/templates/content.html +++ /dev/null @@ -1,14 +0,0 @@ -<div class="container-fluid tab-content px-3 py-3"> - <div id="about" class="tab-pane fade show active px-1"> - {{ htmlTemplate("templates/content/about.html") }} - </div> - <div id="data" class="tab-pane fade"> - {{ htmlTemplate("templates/content/data.html") }} - </div> - <div id="estimation" class="tab-pane fade"> - {{ htmlTemplate("templates/content/estimation.html") }} - </div> - <div id="help" class="tab-pane fade"> - {{ htmlTemplate("templates/content/help.html") }} - </div> -</div> 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> < 1, the disease will eventually die out. On the other hand, if - <em>R</em><sub>0</sub> > 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 (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> 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> diff --git a/inst/app/templates/footer.html b/inst/app/templates/footer.html deleted file mode 100644 index 19d4b0c..0000000 --- a/inst/app/templates/footer.html +++ /dev/null @@ -1,7 +0,0 @@ -<footer class="container-fluid mt-auto text-center"> - <em> - Released under the - <a href="https://www.gnu.org/licenses/agpl-3.0.html" target="_blank">AGPLv3</a> - or later. - </em> -</footer> diff --git a/inst/app/templates/navbar.html b/inst/app/templates/navbar.html deleted file mode 100644 index d447fba..0000000 --- a/inst/app/templates/navbar.html +++ /dev/null @@ -1,27 +0,0 @@ -<nav class="navbar navbar-expand-sm"> - <div class="container-fluid"> - <!-- Project name and description. --> - <a class="navbar-brand text-primary" href="/">Rnaught Web</a> - <span class="navbar-text d-none d-md-block"> - An estimation suite for <em>R</em><sub>0</sub> - </span> - <!-- Navigation toggler for smaller screens. --> - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#nav-toggle"> - <span class="glyphicon glyphicon-menu-hamburger text-primary"></span> - </button> - <!-- Navigation links. --> - <div class="collapse navbar-collapse justify-content-end" id="nav-toggle"> - <div class="navbar-nav"> - <a class="nav-link text-primary" href="https://MI2YorkU.github.io/Rnaught" target="_blank"> - <span class="glyphicon glyphicon-book"></span> Documentation - </a> - <a class="nav-link text-primary" href="https://github.com/MI2Yorku/Rnaught" target="_blank"> - <span class="glyphicon glyphicon-console"></span> Source - </a> - <a class="nav-link text-primary" href="https://doi.org/10.1371/journal.pone.0269306" target="_blank"> - <span class="glyphicon glyphicon-education"></span> Article - </a> - </div> - </div> - </div> -</nav> diff --git a/inst/app/templates/tabs.html b/inst/app/templates/tabs.html deleted file mode 100644 index 351b480..0000000 --- a/inst/app/templates/tabs.html +++ /dev/null @@ -1,14 +0,0 @@ -<nav class="nav nav-pills nav-fill"> - <a class="nav-link rounded-0 active" data-bs-toggle="pill" href="#about"> - About <span class="glyphicon glyphicon-info-sign"></span> - </a> - <a class="nav-link rounded-0" data-bs-toggle="pill" href="#data"> - Data <span class="glyphicon glyphicon-list-alt"></span> - </a> - <a class="nav-link rounded-0" data-bs-toggle="pill" href="#estimation"> - Estimation <span class="glyphicon glyphicon-random"></span> - </a> - <a class="nav-link rounded-0" data-bs-toggle="pill" href="#help"> - Help <span class="glyphicon glyphicon-question-sign"></span> - </a> -</nav> |