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-<title>Estimate the Basic Reproduction Number of Infectious Diseases • Rnaught</title>
+<title>Estimate the Basic Reproduction Number (R0) of Infectious Diseases • Rnaught</title>
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-<meta name="description" content="A collection of methods for estimating the basic reproduction number (R0) of infectious diseases. Optionally available as a web application using the shiny framework.">
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+<meta name="description" content="An R package and web application for estimating the basic reproduction number (R0) of infectious diseases.">
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<p>Rnaught is an R package and web application for estimating the <a href="https://en.wikipedia.org/wiki/Basic_reproduction_number" class="external-link">basic reproduction number (<em>R</em><sub>0</sub>)</a> of infectious diseases.</p>
-<p>Currently, this estimation can be done in the web application via four different methods: White and Panago (WP), sequential Bayes (seqB), incidence decay (ID), and incidence decay and exponential adjustment (IDEA).</p>
-<p>Datasets can be uploaded as a .csv file, or can be entered manually into the application. The data is visualized in the application through plots that show the case counts (either weekly or daily). If multiple datasets are uploaded/manually entered, the trends corresponding to these datasets are populated in the same plot and can be compared. This plot can be exported as a .png file. Further, the dataset entered can be exported into a .csv file. Two sample datasets are included: weekly Canadian COVID-19 case count data from March 3rd, 2020 to March 31st, 2020, and weekly Ontario COVID-19 case count data from March 3rd, 2020 to March 31st, 2020.</p>
-<p>To estimate the basic reproductive number, the user can choose their preferred estimator, and if applicable, must enter the known serial interval prior to estimation. If multiple estimates of the basic reproductive number are calculated, they are all included in a table where each row represents an estimate. If multiple datasets are being considered, the basic reproductive number is estimated for all datasets and the columns of the table correspond to the different datasets uploaded into the application. The table also consists of a column corresponding to the value of the serial interval. This table can be exported as a .csv file.</p>
-<p>In progress…</p>
+<p>An instance of the web application is available at <a href="https://immune.math.yorku.ca/Rnaught" class="external-link uri">https://immune.math.yorku.ca/Rnaught</a>.</p>
+<div class="section level2">
+<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
+</h2>
+<p>You can install the development version of Rnaught using the <a href="https://devtools.r-lib.org" class="external-link">devtools</a> package. Run the following commands in an R session:</p>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"devtools"</span><span class="op">)</span> <span class="co"># If not already installed.</span></span>
+<span><span class="fu">devtools</span><span class="fu">::</span><span class="fu">install_github</span><span class="op">(</span><span class="st">"MI2YorkU/Rnaught"</span>, build_vignettes <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+</div>
+<div class="section level2">
+<h2 id="documentation">Documentation<a class="anchor" aria-label="anchor" href="#documentation"></a>
+</h2>
+<p>The package documentation is available online at <a href="https://MI2YorkU.github.io/Rnaught" class="uri">https://MI2YorkU.github.io/Rnaught</a>.</p>
+<p>For a quick introduction, see the <a href="https://MI2YorkU.github.io/Rnaught/articles/Rnaught.html">Get started</a> page. This can also be accessed from an R session with <code><a href="articles/Rnaught.html">vignette("Rnaught", package = "Rnaught")</a></code>.</p>
+<p>To view the documentation locally, run <code>?Rnaught::<function></code>. A list of all functions is shown in the package index by executing <code><a href="https://MI2YorkU.github.io/Rnaught/reference">help(package = "Rnaught")</a></code>.</p>
+</div>
+<div class="section level2">
+<h2 id="contributing">Contributing<a class="anchor" aria-label="anchor" href="#contributing"></a>
+</h2>
+<p>The source code for this package is available on <a href="https://github.com/MI2YorkU/Rnaught" class="external-link">GitHub</a>.</p>
+<p>To report a bug, request a new feature, give feedback, or ask questions, open a new <a href="https://github.com/MI2YorkU/Rnaught/issues" class="external-link">issue</a>.</p>
+<p>Submit new estimators, features, bug fixes, or patches by creating a <a href="https://github.com/MI2YorkU/Rnaught/pulls" class="external-link">pull request</a>.</p>
+</div>
+<div class="section level2">
+<h2 id="license">License<a class="anchor" aria-label="anchor" href="#license"></a>
+</h2>
+<p>This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.</p>
+<p>This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.</p>
+<p>You should have received a copy of the GNU Affero General Public License along with this program. If not, see <a href="https://www.gnu.org/licenses" class="external-link uri">https://www.gnu.org/licenses</a>.</p>
+</div>
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-<li>Sawitree Boonpatcharanon <br><small class="roles"> Author </small> </li>
-<li>Jane Heffernan <br><small class="roles"> Author </small> </li>
-<li>Hanna Jankowski <br><small class="roles"> Author </small> </li>
-<li>Naeem Model <br><small class="roles"> Author, maintainer </small> </li>
+<li>Naeem Model <br><small class="roles"> Author, maintainer </small> </li>
+<li>Sawitree Boonpatcharanon <br><small class="roles"> Author </small> </li>
+<li>Jane Heffernan <br><small class="roles"> Author </small> </li>
+<li>Hanna Jankowski <br><small class="roles"> Author </small> </li>
+<li>Tatiana Krikella <br><small class="roles"> Author </small> </li>
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+<div class="dev-status">
+<h2 data-toc-skip>Dev status</h2>
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+<li><a href="https://github.com/MI2YorkU/Rnaught/actions/workflows/R-CMD-check.yaml" class="external-link"><img src="https://github.com/MI2YorkU/Rnaught/actions/workflows/R-CMD-check.yaml/badge.svg" alt="R-CMD-check"></a></li>
+</ul>
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- <p>Developed by Sawitree Boonpatcharanon, Jane Heffernan, Hanna Jankowski, Naeem Model.</p>
+ <p>Developed by Naeem Model, Sawitree Boonpatcharanon, Jane Heffernan, Hanna Jankowski, Tatiana Krikella.</p>
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- <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
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