<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<title>Estimate the Basic Reproduction Number of Infectious Diseases • Rnaught</title>
+<title>Estimate the Basic Reproduction Number (R0) of Infectious Diseases • Rnaught</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="favicon-96x96.png">
+<link rel="icon" type="”image/svg+xml”" href="favicon.svg">
+<link rel="apple-touch-icon" sizes="180x180" href="apple-touch-icon.png">
+<link rel="icon" sizes="any" href="favicon.ico">
+<link rel="manifest" href="site.webmanifest">
<script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
-<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
-<link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
-<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Estimate the Basic Reproduction Number of Infectious Diseases">
-<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.">
-<meta property="og: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.">
+<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
+<link href="deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Estimate the Basic Reproduction Number (R0) of Infectious Diseases">
+<meta name="description" content="An R package and web application for estimating the basic reproduction number (R0) of infectious diseases.">
+<meta property="og:description" content="An R package and web application for estimating the basic reproduction number (R0) of infectious diseases.">
<meta property="og:image" content="https://MI2YorkU.github.io/Rnaught/logo.svg">
</head>
<body>
<div id="navbar" class="collapse navbar-collapse ms-3">
<ul class="navbar-nav me-auto">
+<li class="nav-item"><a class="nav-link" href="articles/Rnaught.html">Get started</a></li>
<li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
<li class="nav-item dropdown">
<button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
<a class="anchor" aria-label="anchor" href="#rnaught-"></a>
</h1>
</div>
+<!-- badges: start -->
+
<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>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>
</div>
</main><aside class="col-md-3"><div class="links">
<h2 data-toc-skip>Links</h2>
<div class="developers">
<h2 data-toc-skip>Developers</h2>
<ul class="list-unstyled">
-<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>
</ul>
</div>
-
+<div class="dev-status">
+<h2 data-toc-skip>Dev status</h2>
+<ul class="list-unstyled">
+<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>
+</div>
</aside>
</div>
<footer><div class="pkgdown-footer-left">
- <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>
</div>
<div class="pkgdown-footer-right">
- <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p>
</div>
</footer>
git.nmode.ca / Rnaught / blobdiff
