nmode's Git Repositories - Rnaught/blob - reference/idea.html

   1 <!DOCTYPE html>
   2 <!-- 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>Incidence Decay and Exponential Adjustment (IDEA) — idea • Rnaught</title><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="Incidence Decay and Exponential Adjustment (IDEA) — idea"><meta name="description" content="This function implements a least squares estimation method of R0 due to
   3 Fisman et al. (PloS One, 2013). See details for implementation notes."><meta property="og:description" content="This function implements a least squares estimation method of R0 due to
   4 Fisman et al. (PloS One, 2013). See details for implementation notes."><meta property="og:image" content="https://MI2YorkU.github.io/Rnaught/logo.svg"></head><body>
   5     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
   6
   7
   8     <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
   9
  10     <a class="navbar-brand me-2" href="../index.html">Rnaught</a>
  11
  12     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
  13
  14
  15     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
  16       <span class="navbar-toggler-icon"></span>
  17     </button>
  18
  19     <div id="navbar" class="collapse navbar-collapse ms-3">
  20       <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
  21 <li class="nav-item dropdown">
  22   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
  23   <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>
  24     <li><a class="dropdown-item" href="../articles/wp_serial.html">White and Pagano: Utilizing the Serial Distribution</a></li>
  25   </ul></li>
  26       </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
  27  <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>
  28 <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>
  29       </ul></div>
  30
  31
  32   </div>
  33 </nav><div class="container template-reference-topic">
  34 <div class="row">
  35   <main id="main" class="col-md-9"><div class="page-header">
  36       <img src="../logo.svg" class="logo" alt=""><h1>Incidence Decay and Exponential Adjustment (IDEA)</h1>
  37       <small class="dont-index">Source: <a href="https://github.com/MI2YorkU/Rnaught/blob/master/R/idea.R" class="external-link"><code>R/idea.R</code></a></small>
  38       <div class="d-none name"><code>idea.Rd</code></div>
  39     </div>
  40
  41     <div class="ref-description section level2">
  42     <p>This function implements a least squares estimation method of R0 due to
  43 Fisman et al. (PloS One, 2013). See details for implementation notes.</p>
  44     </div>
  45
  46     <div class="section level2">
  47     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
  48     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">idea</span><span class="op">(</span><span class="va">cases</span>, <span class="va">mu</span><span class="op">)</span></span></code></pre></div>
  49     </div>
  50
  51     <div class="section level2">
  52     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
  53
  54
  55 <dl><dt id="arg-cases">cases<a class="anchor" aria-label="anchor" href="#arg-cases"></a></dt>
  56 <dd><p>Vector of case counts. The vector must be of length at least two
  57 and only contain positive integers.</p></dd>
  58
  59
  60 <dt id="arg-mu">mu<a class="anchor" aria-label="anchor" href="#arg-mu"></a></dt>
  61 <dd><p>Mean of the serial distribution. This must be a positive number.
  62 The value should match the case counts in time units. For example, if case
  63 counts are weekly and the serial distribution has a mean of seven days,
  64 then <code>mu</code> should be set to <code>1</code>. If case counts are daily and the serial
  65 distribution has a mean of seven days, then <code>mu</code> should be set to <code>7</code>.</p></dd>
  66
  67 </dl></div>
  68     <div class="section level2">
  69     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
  70     <p>An estimate of the basic reproduction number (R0).</p>
  71     </div>
  72     <div class="section level2">
  73     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
  74     <p>This method is closely related to that implemented in <code><a href="id.html">id()</a></code>. The method is
  75 based on an incidence decay model. The estimate of R0 is the value which
  76 minimizes the sum of squares between observed case counts and case counts
  77 expected under the model.</p>
  78 <p>This method is based on an approximation of the SIR model, which is most
  79 valid at the beginning of an epidemic. The method assumes that the mean of
  80 the serial distribution (sometimes called the serial interval) is known. The
  81 final estimate can be quite sensitive to this value, so sensitivity testing
  82 is strongly recommended. Users should be careful about units of time (e.g.,
  83 are counts observed daily or weekly?) when implementing.</p>
  84     </div>
  85     <div class="section level2">
  86     <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
  87     <p><a href="https://doi.org/10.1371/journal.pone.0083622" class="external-link">Fisman et al. (PloS One, 2013)</a></p>
  88     </div>
  89     <div class="section level2">
  90     <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
  91     <div class="dont-index"><p><code><a href="id.html">id()</a></code> for a similar method.</p></div>
  92     </div>
  93
  94     <div class="section level2">
  95     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
  96     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Weekly data.</span></span></span>
  97 <span class="r-in"><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></span>
  98 <span class="r-in"><span></span></span>
  99 <span class="r-in"><span><span class="co"># Obtain R0 when the serial distribution has a mean of five days.</span></span></span>
 100 <span class="r-in"><span><span class="fu">idea</span><span class="op">(</span><span class="va">cases</span>, mu <span class="op">=</span> <span class="fl">5</span> <span class="op">/</span> <span class="fl">7</span><span class="op">)</span></span></span>
 101 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.419546</span>
 102 <span class="r-in"><span></span></span>
 103 <span class="r-in"><span><span class="co"># Obtain R0 when the serial distribution has a mean of three days.</span></span></span>
 104 <span class="r-in"><span><span class="fu">idea</span><span class="op">(</span><span class="va">cases</span>, mu <span class="op">=</span> <span class="fl">3</span> <span class="op">/</span> <span class="fl">7</span><span class="op">)</span></span></span>
 105 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.233927</span>
 106 </code></pre></div>
 107     </div>
 108   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
 109     </nav></aside></div>
 110
 111
 112     <footer><div class="pkgdown-footer-left">
 113   <p>Developed by Sawitree Boonpatcharanon, Jane Heffernan, Hanna Jankowski, Naeem Model.</p>
 114 </div>
 115
 116 <div class="pkgdown-footer-right">
 117   <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 118 </div>
 119
 120     </footer></div>
 121
 122
 123
 124
 125
 126   </body></html>
 127