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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'>&lt;-</span> <span class='va'>fake_outbreak</span>

<span class='va'>tTree</span> <span class='op'>&lt;-</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'>&lt;-</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'>#&gt;    i  j

#&gt; 1  6  9

#&gt; 2  3  5

#&gt; 3  4  7

#&gt; 4 13 25

#&gt; 5 13 30

#&gt; 6 10 20</div></pre>

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