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  64       <img src="../logo.svg" class="logo" alt=""><h1>Introduction to Rnaught</h1>
  65
  66
  67       <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>
  68       <div class="d-none name"><code>Rnaught.Rmd</code></div>
  69     </div>
  70
  71
  72
  73 <p>The goal of Rnaught is to provide a collection of methods for
  74 estimating the <a href="https://en.wikipedia.org/wiki/Basic_reproduction_number" class="external-link">basic
  75 reproduction number</a>
  76 (<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>)
  77 of infectious diseases.</p>
  78 <div class="section level2">
  79 <h2 id="estimators">Estimators<a class="anchor" aria-label="anchor" href="#estimators"></a>
  80 </h2>
  81 <p>The following estimators are currently available:</p>
  82 <ul>
  83 <li>
  84 <code><a href="../reference/id.html">id()</a></code>: Incidence Decay (ID)</li>
  85 <li>
  86 <code><a href="../reference/idea.html">idea()</a></code>: Incidence Decay and Exponential Adjustment
  87 (IDEA)</li>
  88 <li>
  89 <code><a href="../reference/seq_bayes.html">seq_bayes()</a></code>: Sequential Bayes (seqB)</li>
  90 <li>
  91 <code><a href="../reference/wp.html">wp()</a></code>: White and Pagano (WP)</li>
  92 </ul>
  93 <p>Every estimator employs its own model, has its own set of parameters,
  94 and is better suited to particular scenarios. You should consult each
  95 method’s documentation for technical details. Below is a short example
  96 computing estimates for a given set of case counts.</p>
  97 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
  98 <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>
  99 <span></span>
 100 <span><span class="co"># Weekly case counts.</span></span>
 101 <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>
 102 <span></span>
 103 <span><span class="co"># Compute estimates of R0, assuming a serial interval of five days.</span></span>
 104 <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>
 105 <span></span>
 106 <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>
 107 <span><span class="co">#&gt; [1] 1.245734</span></span>
 108 <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>
 109 <span><span class="co">#&gt; [1] 1.419546</span></span>
 110 <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>
 111 <span><span class="co">#&gt; [1] 1.026563</span></span>
 112 <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>
 113 <span><span class="co">#&gt; [1] 1.107862</span></span></code></pre></div>
 114 </div>
 115 <div class="section level2">
 116 <h2 id="web-application">Web Application<a class="anchor" aria-label="anchor" href="#web-application"></a>
 117 </h2>
 118 <p>This serves as a graphical interface for the package. An instance is
 119 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
 120 locally by invoking the <code><a href="../reference/web.html">web()</a></code> function.</p>
 121 <p>Datasets can be uploaded as a CSV file, or entered manually. The data
 122 is visualized in the application through plots that show the case counts
 123 (either daily or weekly). If multiple datasets are added, the trends
 124 corresponding to these datasets are populated in the same plot. This
 125 plot can be exported as a PNG image. Furthermore, the datasets entered
 126 can be exported as a CSV.</p>
 127 <p>Two sample datasets are included: weekly Canadian COVID-19 case count
 128 data from March 3rd, 2020 to March 31st, 2020, and weekly Ontario
 129 COVID-19 case count data from March 3rd, 2020 to March 31st, 2020.</p>
 130 <p>To estimate the basic reproductive number, the user can choose their
 131 preferred estimator, and if applicable, must enter the known <a href="https://en.wikipedia.org/wiki/Serial_interval" class="external-link">serial interval</a>
 132 prior to estimation. If multiple estimates of the basic reproductive
 133 number are calculated, they are all included in a table where each row
 134 represents an estimate. If multiple datasets are being considered, the
 135 basic reproduction number is estimated for all datasets and the columns
 136 of the table correspond to the different datasets. The table also
 137 consists of a column corresponding to the value of the serial interval.
 138 This table can also be exported as a CSV.</p>
 139 </div>
 140 <div class="section level2">
 141 <h2 id="datasets">Datasets<a class="anchor" aria-label="anchor" href="#datasets"></a>
 142 </h2>
 143 <p>The package includes two datasets provided by the <a href="https://github.com/ccodwg/CovidTimelineCanada" class="external-link">COVID-19 Canada
 144 Open Data Working Group</a>. These report the national and provincial
 145 case counts of COVID-19 in Canada. For details, see
 146 <code><a href="../reference/COVIDCanada.html">?COVIDCanada</a></code> and <code><a href="../reference/COVIDCanadaPT.html">?COVIDCanadaPT</a></code>. They are also
 147 available as <a href="https://github.com/MI2YorkU/Rnaught/tree/master/inst/extdata" class="external-link">CSV
 148 files</a>.</p>
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