--- /dev/null
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<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>Introduction to Rnaught • Rnaught</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<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-6.5.2/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="Introduction to Rnaught">
+</head>
+<body>
+ <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+
+
+ <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
+
+ <a class="navbar-brand me-2" href="../index.html">Rnaught</a>
+
+ <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
+
+
+ <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+ <span class="navbar-toggler-icon"></span>
+ </button>
+
+ <div id="navbar" class="collapse navbar-collapse ms-3">
+ <ul class="navbar-nav me-auto">
+<li class="active 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>
+ <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/seq_bayes_post.html">Sequential Bayes: Utilizing the Posterior Distribution</a></li>
+ <li><a class="dropdown-item" href="../articles/wp_serial.html">White and Pagano: Utilizing the Serial Distribution</a></li>
+ </ul>
+</li>
+ </ul>
+<ul class="navbar-nav">
+<li class="nav-item"><form class="form-inline" role="search">
+ <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json">
+</form></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/MI2YorkU/Rnaught/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+ </ul>
+</div>
+
+
+ </div>
+</nav><div class="container template-article">
+
+
+
+
+<div class="row">
+ <main id="main" class="col-md-9"><div class="page-header">
+ <img src="../logo.svg" class="logo" alt=""><h1>Introduction to Rnaught</h1>
+
+
+ <small class="dont-index">Source: <a href="https://github.com/MI2YorkU/Rnaught/blob/master/vignettes/Rnaught.Rmd" class="external-link"><code>vignettes/Rnaught.Rmd</code></a></small>
+ <div class="d-none name"><code>Rnaught.Rmd</code></div>
+ </div>
+
+
+
+<p>The goal of Rnaught is to provide a a collection of methods for
+estimating the <a href="https://en.wikipedia.org/wiki/Basic_reproduction_number" class="external-link">basic
+reproduction number</a>
+(<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>R</mi><mn>0</mn></msub><annotation encoding="application/x-tex">R_0</annotation></semantics></math>)
+of infectious diseases.</p>
+<div class="section level2">
+<h2 id="estimators">Estimators<a class="anchor" aria-label="anchor" href="#estimators"></a>
+</h2>
+<p>The following estimators are currently available:</p>
+<ul>
+<li>
+<code><a href="../reference/id.html">id()</a></code>: Incidence Decay (ID)</li>
+<li>
+<code><a href="../reference/idea.html">idea()</a></code>: Incidence Decay and Exponential Adjustment
+(IDEA)</li>
+<li>
+<code><a href="../reference/seq_bayes.html">seq_bayes()</a></code>: Sequential Bayes (seqB)</li>
+<li>
+<code><a href="../reference/wp.html">wp()</a></code>: White and Pagano (WP)</li>
+</ul>
+<p>Every estimator employs its own model, has its own set of parameters,
+and is better suited to particular scenarios. You should consult each
+method’s documentation for technical details. Below is a short example
+computing estimates for a given set of case counts.</p>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://MI2YorkU.github.io/Rnaught">Rnaught</a></span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># Weekly case counts.</span></span>
+<span><span class="va">cases</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">4</span>, <span class="fl">10</span>, <span class="fl">5</span>, <span class="fl">3</span>, <span class="fl">4</span>, <span class="fl">19</span>, <span class="fl">3</span>, <span class="fl">3</span>, <span class="fl">14</span>, <span class="fl">4</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># Compute estimates of R0, assuming a serial interval of five days.</span></span>
+<span><span class="va">mu</span> <span class="op"><-</span> <span class="fl">5</span> <span class="op">/</span> <span class="fl">7</span></span>
+<span></span>
+<span><span class="fu"><a href="../reference/id.html">id</a></span><span class="op">(</span><span class="va">cases</span>, <span class="va">mu</span><span class="op">)</span></span>
+<span><span class="co">#> [1] 1.245734</span></span>
+<span><span class="fu"><a href="../reference/idea.html">idea</a></span><span class="op">(</span><span class="va">cases</span>, <span class="va">mu</span><span class="op">)</span></span>
+<span><span class="co">#> [1] 1.419546</span></span>
+<span><span class="fu"><a href="../reference/seq_bayes.html">seq_bayes</a></span><span class="op">(</span><span class="va">cases</span>, <span class="va">mu</span><span class="op">)</span></span>
+<span><span class="co">#> [1] 1.026563</span></span>
+<span><span class="fu"><a href="../reference/wp.html">wp</a></span><span class="op">(</span><span class="va">cases</span>, <span class="va">mu</span><span class="op">)</span></span>
+<span><span class="co">#> [1] 1.107862</span></span></code></pre></div>
+</div>
+<div class="section level2">
+<h2 id="web-application">Web Application<a class="anchor" aria-label="anchor" href="#web-application"></a>
+</h2>
+<p>This serves as a graphical interface for the package. An instance is
+available at <a href="https://immune.math.yorku.ca/Rnaught" class="external-link uri">https://immune.math.yorku.ca/Rnaught</a>. It can also be run
+locally by invoking the <code><a href="../reference/web.html">web()</a></code> function.</p>
+<p>Datasets can be uploaded as a CSV file, or entered manually. The data
+is visualized in the application through plots that show the case counts
+(either daily or weekly). If multiple datasets are added, the trends
+corresponding to these datasets are populated in the same plot. This
+plot can be exported as a PNG image. Furthermore, the datasets entered
+can be exported as a CSV.</p>
+<p>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 <a href="https://en.wikipedia.org/wiki/Serial_interval" class="external-link">serial interval</a>
+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 reproduction number is estimated for all datasets and the columns
+of the table correspond to the different datasets. The table also
+consists of a column corresponding to the value of the serial interval.
+This table can also be exported as a CSV.</p>
+</div>
+<div class="section level2">
+<h2 id="datasets">Datasets<a class="anchor" aria-label="anchor" href="#datasets"></a>
+</h2>
+<p>The package includes two datasets provided by the <a href="https://github.com/ccodwg/CovidTimelineCanada" class="external-link">COVID-19 Canada
+Open Data Working Group</a>. These report the national and provincial
+case counts of COVID-19 in Canada. For details, see
+<code><a href="../reference/COVIDCanada.html">?COVIDCanada</a></code> and <code><a href="../reference/COVIDCanadaPT.html">?COVIDCanadaPT</a></code>. They are also
+available as <a href="https://github.com/MI2YorkU/Rnaught/tree/master/inst/extdata" class="external-link">CSV
+files</a>.</p>
+</div>
+ </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+ </nav></aside>
+</div>
+
+
+
+ <footer><div class="pkgdown-footer-left">
+ <p>Developed by Naeem Model, Sawitree Boonpatcharanon, Jane Heffernan, Hanna Jankowski.</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>
+</div>
+
+ </footer>
+</div>
+
+
+
+
+
+ </body>
+</html>
git.nmode.ca / Rnaught / blobdiff
