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<h1>Small simulated outbreak</h1>
<div class="hidden name"><code>fake_outbreak.Rd</code></div>
</div>
<div class="ref-description">
<p>This dataset is a small (30 cases) simulated outbreak originally used to
illustrate <code>outbreaker</code>, and used for the same purposes in
<code>outbreaker2</code>. This list contains the following:</p>
</div>
<pre class="usage"><span class='va'>fake_outbreak</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>An object of class <code>list</code> of length 6.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<ul>
<li><p><code>$onset</code>: A vector of integers representing dates of onset.</p></li>
<li><p><code>$sample</code>: A vector of integers representing the dates of isolation.</p></li>
<li><p><code>$dna</code>: A DNAbin matrix of pathogen genome sequences.</p></li>
<li><p><code>$w</code>: A numeric vector giving the empirical distribution of the
generation time.</p></li>
<li><p><code>$ances</code>: A vector of integers indicating, for each case, the true
infectors. <code>NA</code> represents imported cases.</p></li>
</ul>
<h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
<p>Thibaut Jombart <a href='mailto:thibautjombart@gmail.com'>thibautjombart@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='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>fake_outbreak</span><span class='op'>)</span>
</div><div class='output co'>#> [1] "onset" "sample" "dna" "w" "ances" "ctd" </div><div class='input'><span class='va'>fake_outbreak</span>
</div><div class='output co'>#> $onset
#> [1] 0 2 4 4 6 6 6 7 7 8 8 8 8 9 9 9 9 10 10 10 10 10 10 10 10
#> [26] 10 10 10 11 11
#>
#> $sample
#> [1] 3 5 6 6 7 9 8 9 9 9 11 10 10 10 10 11 11 12 11 13 12 13 11 12 11
#> [26] 11 13 12 14 14
#>
#> $dna
#> 30 DNA sequences in binary format stored in a matrix.
#>
#> All sequences of same length: 10000
#>
#> Labels:
#> ...
#>
#> Base composition:
#> a c g t
#> 0.251 0.242 0.251 0.256
#> (Total: 300 kb)
#>
#> $w
#> [1] 0.04255319 0.21276596 0.42553191 0.31914894
#>
#> $ances
#> [1] NA 1 2 NA 3 4 4 5 6 6 7 8 9 5 5 7 7 8 9 10 11 11 13 13 13
#> [26] 17 17 NA 10 13
#>
#> $ctd
#> i j
#> 1 4 7
#> 2 10 29
#> 3 13 30
#> 4 11 22
#> 5 13 25
#> 6 16 7
#> 7 13 23
#> 8 10 6
#> 9 18 8
#> 10 14 5
#> 11 17 26
#> 12 11 21
#> 13 3 5
#> 14 17 27
#> 15 2 3
#> 16 17 7
#> 17 19 9
#> 18 12 8
#> 19 22 6
#> 20 30 9
#> 21 17 20
#> 22 21 29
#> 23 11 14
#> 24 18 9
#> 25 25 29
#> 26 1 17
#> 27 23 7
#> 28 25 3
#> 29 3 9
#> 30 1 4
#> 31 13 4
#> 32 21 27
#> 33 16 2
#> 34 29 3
#> 35 21 5
#> </div><div class='input'>
</div></pre>
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