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  64   <main id="main" class="col-md-9"><div class="page-header">
  65       <img src="../logo.svg" class="logo" alt=""><h1>Introduction to Rnaught</h1>
  66
  67
  68       <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>
  69       <div class="d-none name"><code>Rnaught.Rmd</code></div>
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  71
  72
  73
  74 <p>The goal of Rnaught is to provide a a collection of methods for
  75 estimating the <a href="https://en.wikipedia.org/wiki/Basic_reproduction_number" class="external-link">basic
  76 reproduction number</a>
  77 (<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>)
  78 of infectious diseases.</p>
  79 <div class="section level2">
  80 <h2 id="estimators">Estimators<a class="anchor" aria-label="anchor" href="#estimators"></a>
  81 </h2>
  82 <p>The following estimators are currently available:</p>
  83 <ul>
  84 <li>
  85 <code><a href="../reference/id.html">id()</a></code>: Incidence Decay (ID)</li>
  86 <li>
  87 <code><a href="../reference/idea.html">idea()</a></code>: Incidence Decay and Exponential Adjustment
  88 (IDEA)</li>
  89 <li>
  90 <code><a href="../reference/seq_bayes.html">seq_bayes()</a></code>: Sequential Bayes (seqB)</li>
  91 <li>
  92 <code><a href="../reference/wp.html">wp()</a></code>: White and Pagano (WP)</li>
  93 </ul>
  94 <p>Every estimator employs its own model, has its own set of parameters,
  95 and is better suited to particular scenarios. You should consult each
  96 method’s documentation for technical details. Below is a short example
  97 computing estimates for a given set of case counts.</p>
  98 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
  99 <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>
 100 <span></span>
 101 <span><span class="co"># Weekly case counts.</span></span>
 102 <span><span class="va">cases</span> <span class="op">&lt;-</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>
 103 <span></span>
 104 <span><span class="co"># Compute estimates of R0, assuming a serial interval of five days.</span></span>
 105 <span><span class="va">mu</span> <span class="op">&lt;-</span> <span class="fl">5</span> <span class="op">/</span> <span class="fl">7</span></span>
 106 <span></span>
 107 <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>
 108 <span><span class="co">#&gt; [1] 1.245734</span></span>
 109 <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>
 110 <span><span class="co">#&gt; [1] 1.419546</span></span>
 111 <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>
 112 <span><span class="co">#&gt; [1] 1.026563</span></span>
 113 <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>
 114 <span><span class="co">#&gt; [1] 1.107862</span></span></code></pre></div>
 115 </div>
 116 <div class="section level2">
 117 <h2 id="web-application">Web Application<a class="anchor" aria-label="anchor" href="#web-application"></a>
 118 </h2>
 119 <p>This serves as a graphical interface for the package. An instance is
 120 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
 121 locally by invoking the <code><a href="../reference/web.html">web()</a></code> function.</p>
 122 <p>Datasets can be uploaded as a CSV file, or entered manually. The data
 123 is visualized in the application through plots that show the case counts
 124 (either daily or weekly). If multiple datasets are added, the trends
 125 corresponding to these datasets are populated in the same plot. This
 126 plot can be exported as a PNG image. Furthermore, the datasets entered
 127 can be exported as a CSV.</p>
 128 <p>Two sample datasets are included: weekly Canadian COVID-19 case count
 129 data from March 3rd, 2020 to March 31st, 2020, and weekly Ontario
 130 COVID-19 case count data from March 3rd, 2020 to March 31st, 2020.</p>
 131 <p>To estimate the basic reproductive number, the user can choose their
 132 preferred estimator, and if applicable, must enter the known <a href="https://en.wikipedia.org/wiki/Serial_interval" class="external-link">serial interval</a>
 133 prior to estimation. If multiple estimates of the basic reproductive
 134 number are calculated, they are all included in a table where each row
 135 represents an estimate. If multiple datasets are being considered, the
 136 basic reproduction number is estimated for all datasets and the columns
 137 of the table correspond to the different datasets. The table also
 138 consists of a column corresponding to the value of the serial interval.
 139 This table can also be exported as a CSV.</p>
 140 </div>
 141 <div class="section level2">
 142 <h2 id="datasets">Datasets<a class="anchor" aria-label="anchor" href="#datasets"></a>
 143 </h2>
 144 <p>The package includes two datasets provided by the <a href="https://github.com/ccodwg/CovidTimelineCanada" class="external-link">COVID-19 Canada
 145 Open Data Working Group</a>. These report the national and provincial
 146 case counts of COVID-19 in Canada. For details, see
 147 <code><a href="../reference/COVIDCanada.html">?COVIDCanada</a></code> and <code><a href="../reference/COVIDCanadaPT.html">?COVIDCanadaPT</a></code>. They are also
 148 available as <a href="https://github.com/MI2YorkU/Rnaught/tree/master/inst/extdata" class="external-link">CSV
 149 files</a>.</p>
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