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sim_ctd.html
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sim_ctd.html
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<meta property="og:description" content="This function simulates contact data from a transmission tree. The
model assumes that all transmission pairs have experienced contact, and that
there is no false-positive reporting of contacts. The probability of contact
occuring between a non-transmision pair is given by the parameter lambda. The
probability of reporting a contact (transmission pair or not) is given by the
parameters eps." />
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<h1>Simulate contact data from a transmission tree</h1>
<div class="hidden name"><code>sim_ctd.Rd</code></div>
</div>
<div class="ref-description">
<p>This function simulates contact data from a transmission tree. The
model assumes that all transmission pairs have experienced contact, and that
there is no false-positive reporting of contacts. The probability of contact
occuring between a non-transmision pair is given by the parameter lambda. The
probability of reporting a contact (transmission pair or not) is given by the
parameters eps.</p>
</div>
<pre class="usage"><span class='fu'>sim_ctd</span><span class='op'>(</span><span class='va'>tTree</span>, <span class='va'>eps</span>, <span class='va'>lambda</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>tTree</th>
<td><p>a dataframe or matrix of two columns, with each row providing
the ids (numerical or as characters) of a transmission pair</p></td>
</tr>
<tr>
<th>eps</th>
<td><p>the contact reporting coverage, defined as the probability of
reporting a contact (transmission pair or not)</p></td>
</tr>
<tr>
<th>lambda</th>
<td><p>the non-infectious contact rate, defined as the probability
of contact between a non-transmission pair.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
<p>Finlay Campbell (<a href='mailto:finlaycampbell93@gmail.com'>finlaycampbell93@gmail.com</a>)</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'>
<span class='co'>## load data</span>
<span class='va'>x</span> <span class='op'><-</span> <span class='va'>fake_outbreak</span>
<span class='va'>tTree</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>from <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>ances</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq_along</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>ances</span><span class='op'>)</span><span class='op'>)</span>
<span class='co'>## simulate contact data with coverage of 80% and 10% probability of</span>
<span class='co'>## contact between non-transmission pairs</span>
<span class='va'>ctd</span> <span class='op'><-</span> <span class='fu'>outbreaker2</span><span class='fu'>:::</span><span class='fu'>sim_ctd</span><span class='op'>(</span><span class='va'>tTree</span>, eps <span class='op'>=</span> <span class='fl'>0.8</span>, lambda <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>
<span class='co'>## inspect contact data</span>
<span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span><span class='op'>(</span><span class='va'>ctd</span><span class='op'>)</span>
</div><div class='output co'>#> i j
#> 1 6 9
#> 2 3 5
#> 3 4 7
#> 4 13 25
#> 5 13 30
#> 6 10 20</div></pre>
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