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   8 <title>Estimate the Basic Reproduction Number (R0) of Infectious Diseases • Rnaught</title>
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  20 <meta name="description" content="An R package and web application for estimating the basic reproduction number (R0) of infectious diseases.">
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  46 <li><a class="dropdown-item" href="articles/seq_bayes_post.html">Sequential Bayes: Utilizing the Posterior Distribution</a></li>
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  65 <img src="logo.svg" class="logo" alt=""><h1 id="rnaught-">Rnaught
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  71 <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>
  72 <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>
  73 <div class="section level2">
  74 <h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
  75 </h2>
  76 <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>
  77 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
  78 <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>
  79 <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>
  80 </div>
  81 <div class="section level2">
  82 <h2 id="documentation">Documentation<a class="anchor" aria-label="anchor" href="#documentation"></a>
  83 </h2>
  84 <p>The package documentation is available online at <a href="https://MI2YorkU.github.io/Rnaught" class="uri">https://MI2YorkU.github.io/Rnaught</a>.</p>
  85 <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>
  86 <p>To view the documentation locally, run <code>?Rnaught::&lt;function&gt;</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>
  87 </div>
  88 <div class="section level2">
  89 <h2 id="contributing">Contributing<a class="anchor" aria-label="anchor" href="#contributing"></a>
  90 </h2>
  91 <p>The source code for this package is available on <a href="https://github.com/MI2YorkU/Rnaught" class="external-link">GitHub</a>.</p>
  92 <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>
  93 <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>
  94 </div>
  95 <div class="section level2">
  96 <h2 id="license">License<a class="anchor" aria-label="anchor" href="#license"></a>
  97 </h2>
  98 <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>
  99 <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>
 100 <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>
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 104 <h2 data-toc-skip>Links</h2>
 105 <ul class="list-unstyled">
 106 <li><a href="https://github.com/MI2YorkU/Rnaught/" class="external-link">Browse source code</a></li>
 107 <li><a href="https://github.com/MI2YorkU/Rnaught/issues" class="external-link">Report a bug</a></li>
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 112 <h2 data-toc-skip>License</h2>
 113 <ul class="list-unstyled">
 114 <li>AGPL (&gt;= 3)</li>
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 119 <div class="citation">
 120 <h2 data-toc-skip>Citation</h2>
 121 <ul class="list-unstyled">
 122 <li><a href="authors.html#citation">Citing Rnaught</a></li>
 123 </ul>
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 125
 126 <div class="developers">
 127 <h2 data-toc-skip>Developers</h2>
 128 <ul class="list-unstyled">
 129 <li>Naeem Model <br><small class="roles"> Author, maintainer </small>  </li>
 130 <li>Sawitree Boonpatcharanon <br><small class="roles"> Author </small>  </li>
 131 <li>Jane Heffernan <br><small class="roles"> Author </small>  </li>
 132 <li>Hanna Jankowski <br><small class="roles"> Author </small>  </li>
 133 <li><a href="authors.html">More about authors...</a></li>
 134 </ul>
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 138 <h2 data-toc-skip>Dev status</h2>
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 140 <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>
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 149   <p>Developed by Naeem Model, Sawitree Boonpatcharanon, Jane Heffernan, Hanna Jankowski.</p>
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