|
a |
|
b/docs/reference/outbreaker_data.html |
|
|
1 |
<!-- Generated by pkgdown: do not edit by hand --> |
|
|
2 |
<!DOCTYPE html> |
|
|
3 |
<html lang="en"> |
|
|
4 |
<head> |
|
|
5 |
<meta charset="utf-8"> |
|
|
6 |
<meta http-equiv="X-UA-Compatible" content="IE=edge"> |
|
|
7 |
<meta name="viewport" content="width=device-width, initial-scale=1.0"> |
|
|
8 |
|
|
|
9 |
<title>Process input data for outbreaker — outbreaker_data • outbreaker2</title> |
|
|
10 |
|
|
|
11 |
|
|
|
12 |
<!-- jquery --> |
|
|
13 |
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> |
|
|
14 |
<!-- Bootstrap --> |
|
|
15 |
|
|
|
16 |
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> |
|
|
17 |
|
|
|
18 |
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> |
|
|
19 |
|
|
|
20 |
<!-- bootstrap-toc --> |
|
|
21 |
<link rel="stylesheet" href="../bootstrap-toc.css"> |
|
|
22 |
<script src="../bootstrap-toc.js"></script> |
|
|
23 |
|
|
|
24 |
<!-- Font Awesome icons --> |
|
|
25 |
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" /> |
|
|
26 |
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" /> |
|
|
27 |
|
|
|
28 |
<!-- clipboard.js --> |
|
|
29 |
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script> |
|
|
30 |
|
|
|
31 |
<!-- headroom.js --> |
|
|
32 |
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> |
|
|
33 |
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> |
|
|
34 |
|
|
|
35 |
<!-- pkgdown --> |
|
|
36 |
<link href="../pkgdown.css" rel="stylesheet"> |
|
|
37 |
<script src="../pkgdown.js"></script> |
|
|
38 |
|
|
|
39 |
|
|
|
40 |
|
|
|
41 |
|
|
|
42 |
<meta property="og:title" content="Process input data for outbreaker — outbreaker_data" /> |
|
|
43 |
<meta property="og:description" content="This function performs various checks on input data given to outbreaker. It |
|
|
44 |
takes a list of named items as input, performs various checks, set defaults |
|
|
45 |
where arguments are missing, and return a correct list of data input. If no |
|
|
46 |
input is given, it returns the default settings." /> |
|
|
47 |
|
|
|
48 |
|
|
|
49 |
|
|
|
50 |
|
|
|
51 |
<!-- mathjax --> |
|
|
52 |
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> |
|
|
53 |
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> |
|
|
54 |
|
|
|
55 |
<!--[if lt IE 9]> |
|
|
56 |
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> |
|
|
57 |
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> |
|
|
58 |
<![endif]--> |
|
|
59 |
|
|
|
60 |
|
|
|
61 |
|
|
|
62 |
</head> |
|
|
63 |
|
|
|
64 |
<body data-spy="scroll" data-target="#toc"> |
|
|
65 |
<div class="container template-reference-topic"> |
|
|
66 |
<header> |
|
|
67 |
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> |
|
|
68 |
<div class="container"> |
|
|
69 |
<div class="navbar-header"> |
|
|
70 |
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> |
|
|
71 |
<span class="sr-only">Toggle navigation</span> |
|
|
72 |
<span class="icon-bar"></span> |
|
|
73 |
<span class="icon-bar"></span> |
|
|
74 |
<span class="icon-bar"></span> |
|
|
75 |
</button> |
|
|
76 |
<span class="navbar-brand"> |
|
|
77 |
<a class="navbar-link" href="../index.html">outbreaker2</a> |
|
|
78 |
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span> |
|
|
79 |
</span> |
|
|
80 |
</div> |
|
|
81 |
|
|
|
82 |
<div id="navbar" class="navbar-collapse collapse"> |
|
|
83 |
<ul class="nav navbar-nav"> |
|
|
84 |
<li> |
|
|
85 |
<a href="../index.html"> |
|
|
86 |
<span class="fas fa-home fa-lg"></span> |
|
|
87 |
|
|
|
88 |
</a> |
|
|
89 |
</li> |
|
|
90 |
<li> |
|
|
91 |
<a href="../reference/index.html">Reference</a> |
|
|
92 |
</li> |
|
|
93 |
<li class="dropdown"> |
|
|
94 |
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> |
|
|
95 |
Articles |
|
|
96 |
|
|
|
97 |
<span class="caret"></span> |
|
|
98 |
</a> |
|
|
99 |
<ul class="dropdown-menu" role="menu"> |
|
|
100 |
<li> |
|
|
101 |
<a href="../articles/customisation.html">Using custom priors, likelihood, or movements in outbreaker2</a> |
|
|
102 |
</li> |
|
|
103 |
<li> |
|
|
104 |
<a href="../articles/introduction.html">Introduction to outbreaker2</a> |
|
|
105 |
</li> |
|
|
106 |
<li> |
|
|
107 |
<a href="../articles/overview.html">outbreaker2: package overview</a> |
|
|
108 |
</li> |
|
|
109 |
<li> |
|
|
110 |
<a href="../articles/Rcpp_API.html">outbreaker2: Rcpp API</a> |
|
|
111 |
</li> |
|
|
112 |
</ul> |
|
|
113 |
</li> |
|
|
114 |
<li> |
|
|
115 |
<a href="../news/index.html">Changelog</a> |
|
|
116 |
</li> |
|
|
117 |
</ul> |
|
|
118 |
<ul class="nav navbar-nav navbar-right"> |
|
|
119 |
|
|
|
120 |
</ul> |
|
|
121 |
|
|
|
122 |
</div><!--/.nav-collapse --> |
|
|
123 |
</div><!--/.container --> |
|
|
124 |
</div><!--/.navbar --> |
|
|
125 |
|
|
|
126 |
|
|
|
127 |
|
|
|
128 |
</header> |
|
|
129 |
|
|
|
130 |
<div class="row"> |
|
|
131 |
<div class="col-md-9 contents"> |
|
|
132 |
<div class="page-header"> |
|
|
133 |
<h1>Process input data for outbreaker</h1> |
|
|
134 |
|
|
|
135 |
<div class="hidden name"><code>outbreaker_data.Rd</code></div> |
|
|
136 |
</div> |
|
|
137 |
|
|
|
138 |
<div class="ref-description"> |
|
|
139 |
<p>This function performs various checks on input data given to outbreaker. It |
|
|
140 |
takes a list of named items as input, performs various checks, set defaults |
|
|
141 |
where arguments are missing, and return a correct list of data input. If no |
|
|
142 |
input is given, it returns the default settings.</p> |
|
|
143 |
</div> |
|
|
144 |
|
|
|
145 |
<pre class="usage"><span class='fu'>outbreaker_data</span><span class='op'>(</span><span class='va'>...</span>, data <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</span><span class='op'>)</span></pre> |
|
|
146 |
|
|
|
147 |
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> |
|
|
148 |
<table class="ref-arguments"> |
|
|
149 |
<colgroup><col class="name" /><col class="desc" /></colgroup> |
|
|
150 |
<tr> |
|
|
151 |
<th>...</th> |
|
|
152 |
<td><p>a list of data items to be processed (see description)</p></td> |
|
|
153 |
</tr> |
|
|
154 |
<tr> |
|
|
155 |
<th>data</th> |
|
|
156 |
<td><p>optionally, an existing list of data item as returned by <code>outbreaker_data</code>.</p></td> |
|
|
157 |
</tr> |
|
|
158 |
</table> |
|
|
159 |
|
|
|
160 |
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> |
|
|
161 |
|
|
|
162 |
<p>Acceptables arguments for ... are:</p><dl> |
|
|
163 |
<dt>dates</dt><dd><p>dates a vector indicating the collection dates, provided either as |
|
|
164 |
integer numbers or in a usual date format such as <code>Date</code> or |
|
|
165 |
<code>POSIXct</code> format. By convention, zero will indicate the oldest date. If |
|
|
166 |
the vector is named, the vector names will be used for matching cases to |
|
|
167 |
contact tracing data and labelled DNA sequences.</p></dd> |
|
|
168 |
|
|
|
169 |
<dt>dna</dt><dd><p>the DNA sequences in <code>DNAbin</code> format (see |
|
|
170 |
<code><a href='https://rdrr.io/pkg/ape/man/read.dna.html'>read.dna</a></code> in the ape package); this can be imported from a |
|
|
171 |
fasta file (extension .fa, .fas, or .fasta) using <code>adegenet</code>'s function |
|
|
172 |
<a href='https://rdrr.io/pkg/adegenet/man/fasta2DNAbin.html'>fasta2DNAbin</a>.</p></dd> |
|
|
173 |
|
|
|
174 |
<dt>ctd</dt><dd><p>the contact tracing data provided as a matrix/dataframe of two |
|
|
175 |
columns, indicating a reported contact between the two individuals whose ids |
|
|
176 |
are provided in a given row of the data, or an epicontacts object. In the case |
|
|
177 |
of the latter, linelist IDs will be used for matching dates and DNA |
|
|
178 |
sequences</p></dd> |
|
|
179 |
|
|
|
180 |
<dt>w_dens</dt><dd><p>a vector of numeric values indicating the generation time |
|
|
181 |
distribution, reflecting the infectious potential of a case t = 1, 2, ... |
|
|
182 |
time steps after infection. By convention, it is assumed that |
|
|
183 |
newly infected patients cannot see new infections on the same time step. If not |
|
|
184 |
standardized, this distribution is rescaled to sum to 1.</p></dd> |
|
|
185 |
|
|
|
186 |
<dt>f_dens</dt><dd><p>similar to <code>w_dens</code>, except that this is the distribution |
|
|
187 |
of the colonization time, i_e. time interval during which the pathogen can |
|
|
188 |
be sampled from the patient.</p></dd> |
|
|
189 |
</dl> |
|
|
190 |
|
|
|
191 |
<h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> |
|
|
192 |
|
|
|
193 |
<p>Thibaut Jombart (<a href='mailto:thibautjombart@gmail.com'>thibautjombart@gmail.com</a>)</p> |
|
|
194 |
|
|
|
195 |
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
|
|
196 |
<pre class="examples"><div class='input'> |
|
|
197 |
<span class='va'>x</span> <span class='op'><-</span> <span class='va'>fake_outbreak</span> |
|
|
198 |
<span class='fu'>outbreaker_data</span><span class='op'>(</span>dates <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>sample</span>, dna <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>dna</span>, w_dens <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>w</span><span class='op'>)</span> |
|
|
199 |
</div><div class='output co'>#> $dates |
|
|
200 |
#> [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 |
|
|
201 |
#> [26] 11 13 12 14 14 |
|
|
202 |
#> |
|
|
203 |
#> $w_dens |
|
|
204 |
#> [1] 4.254894e-02 2.127447e-01 4.254894e-01 3.191170e-01 6.320574e-05 |
|
|
205 |
#> [6] 2.325209e-05 8.553966e-06 3.146828e-06 1.157653e-06 4.258769e-07 |
|
|
206 |
#> [11] 1.566714e-07 5.763617e-08 2.120316e-08 7.800208e-09 2.869536e-09 |
|
|
207 |
#> [16] 1.055643e-09 3.883495e-10 1.428658e-10 5.255739e-11 1.933478e-11 |
|
|
208 |
#> [21] 7.112869e-12 |
|
|
209 |
#> |
|
|
210 |
#> $f_dens |
|
|
211 |
#> [1] 4.254894e-02 2.127447e-01 4.254894e-01 3.191170e-01 6.320574e-05 |
|
|
212 |
#> [6] 2.325209e-05 8.553966e-06 3.146828e-06 1.157653e-06 4.258769e-07 |
|
|
213 |
#> [11] 1.566714e-07 5.763617e-08 2.120316e-08 7.800208e-09 2.869536e-09 |
|
|
214 |
#> [16] 1.055643e-09 3.883495e-10 1.428658e-10 5.255739e-11 1.933478e-11 |
|
|
215 |
#> [21] 7.112869e-12 |
|
|
216 |
#> |
|
|
217 |
#> $dna |
|
|
218 |
#> 30 DNA sequences in binary format stored in a matrix. |
|
|
219 |
#> |
|
|
220 |
#> All sequences of same length: 10000 |
|
|
221 |
#> |
|
|
222 |
#> Labels: |
|
|
223 |
#> 1 |
|
|
224 |
#> 2 |
|
|
225 |
#> 3 |
|
|
226 |
#> 4 |
|
|
227 |
#> 5 |
|
|
228 |
#> 6 |
|
|
229 |
#> ... |
|
|
230 |
#> |
|
|
231 |
#> Base composition: |
|
|
232 |
#> a c g t |
|
|
233 |
#> 0.251 0.242 0.251 0.256 |
|
|
234 |
#> (Total: 300 kb) |
|
|
235 |
#> |
|
|
236 |
#> $ctd |
|
|
237 |
#> NULL |
|
|
238 |
#> |
|
|
239 |
#> $N |
|
|
240 |
#> [1] 30 |
|
|
241 |
#> |
|
|
242 |
#> $L |
|
|
243 |
#> [1] 10000 |
|
|
244 |
#> |
|
|
245 |
#> $D |
|
|
246 |
#> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 |
|
|
247 |
#> 1 0 1 2 26 3 30 26 3 33 31 28 3 34 4 5 28 28 3 34 34 29 28 37 35 36 |
|
|
248 |
#> 2 1 0 1 27 2 31 27 2 34 32 29 2 35 3 4 29 29 2 35 35 30 29 38 36 37 |
|
|
249 |
#> 3 2 1 0 28 1 32 28 1 35 33 30 1 36 2 3 30 30 1 36 36 31 30 39 37 38 |
|
|
250 |
#> 4 26 27 28 0 29 4 0 29 7 5 2 29 8 30 31 2 2 29 8 8 3 2 11 9 10 |
|
|
251 |
#> 5 3 2 1 29 0 33 29 0 36 34 31 0 37 1 2 31 31 0 37 37 32 31 40 38 39 |
|
|
252 |
#> 6 30 31 32 4 33 0 4 33 3 1 6 33 4 34 35 6 6 33 4 4 7 6 7 5 6 |
|
|
253 |
#> 7 26 27 28 0 29 4 0 29 7 5 2 29 8 30 31 2 2 29 8 8 3 2 11 9 10 |
|
|
254 |
#> 8 3 2 1 29 0 33 29 0 36 34 31 0 37 1 2 31 31 0 37 37 32 31 40 38 39 |
|
|
255 |
#> 9 33 34 35 7 36 3 7 36 0 4 9 36 1 37 38 9 9 36 1 7 10 9 4 2 3 |
|
|
256 |
#> 10 31 32 33 5 34 1 5 34 4 0 7 34 5 35 36 7 7 34 5 3 8 7 8 6 7 |
|
|
257 |
#> 11 28 29 30 2 31 6 2 31 9 7 0 31 10 32 33 4 4 31 10 10 1 0 13 11 12 |
|
|
258 |
#> 12 3 2 1 29 0 33 29 0 36 34 31 0 37 1 2 31 31 0 37 37 32 31 40 38 39 |
|
|
259 |
#> 13 34 35 36 8 37 4 8 37 1 5 10 37 0 38 39 10 10 37 2 8 11 10 3 1 2 |
|
|
260 |
#> 14 4 3 2 30 1 34 30 1 37 35 32 1 38 0 3 32 32 1 38 38 33 32 41 39 40 |
|
|
261 |
#> 15 5 4 3 31 2 35 31 2 38 36 33 2 39 3 0 33 33 2 39 39 34 33 42 40 41 |
|
|
262 |
#> 16 28 29 30 2 31 6 2 31 9 7 4 31 10 32 33 0 4 31 10 10 5 4 13 11 12 |
|
|
263 |
#> 17 28 29 30 2 31 6 2 31 9 7 4 31 10 32 33 4 0 31 10 10 5 4 13 11 12 |
|
|
264 |
#> 18 3 2 1 29 0 33 29 0 36 34 31 0 37 1 2 31 31 0 37 37 32 31 40 38 39 |
|
|
265 |
#> 19 34 35 36 8 37 4 8 37 1 5 10 37 2 38 39 10 10 37 0 8 11 10 5 3 4 |
|
|
266 |
#> 20 34 35 36 8 37 4 8 37 7 3 10 37 8 38 39 10 10 37 8 0 11 10 11 9 10 |
|
|
267 |
#> 21 29 30 31 3 32 7 3 32 10 8 1 32 11 33 34 5 5 32 11 11 0 1 14 12 13 |
|
|
268 |
#> 22 28 29 30 2 31 6 2 31 9 7 0 31 10 32 33 4 4 31 10 10 1 0 13 11 12 |
|
|
269 |
#> 23 37 38 39 11 40 7 11 40 4 8 13 40 3 41 42 13 13 40 5 11 14 13 0 4 5 |
|
|
270 |
#> 24 35 36 37 9 38 5 9 38 2 6 11 38 1 39 40 11 11 38 3 9 12 11 4 0 3 |
|
|
271 |
#> 25 36 37 38 10 39 6 10 39 3 7 12 39 2 40 41 12 12 39 4 10 13 12 5 3 0 |
|
|
272 |
#> 26 29 30 31 3 32 7 3 32 10 8 5 32 11 33 34 5 1 32 11 11 6 5 14 12 13 |
|
|
273 |
#> 27 29 30 31 3 32 7 3 32 10 8 5 32 11 33 34 5 1 32 11 11 6 5 14 12 13 |
|
|
274 |
#> 28 28 29 30 32 31 36 32 31 39 37 34 31 40 32 33 34 34 31 40 40 35 34 43 41 42 |
|
|
275 |
#> 29 31 32 33 5 34 1 5 34 4 0 7 34 5 35 36 7 7 34 5 3 8 7 8 6 7 |
|
|
276 |
#> 30 36 37 38 10 39 6 10 39 3 7 12 39 2 40 41 12 12 39 4 10 13 12 5 3 4 |
|
|
277 |
#> 26 27 28 29 30 |
|
|
278 |
#> 1 29 29 28 31 36 |
|
|
279 |
#> 2 30 30 29 32 37 |
|
|
280 |
#> 3 31 31 30 33 38 |
|
|
281 |
#> 4 3 3 32 5 10 |
|
|
282 |
#> 5 32 32 31 34 39 |
|
|
283 |
#> 6 7 7 36 1 6 |
|
|
284 |
#> 7 3 3 32 5 10 |
|
|
285 |
#> 8 32 32 31 34 39 |
|
|
286 |
#> 9 10 10 39 4 3 |
|
|
287 |
#> 10 8 8 37 0 7 |
|
|
288 |
#> 11 5 5 34 7 12 |
|
|
289 |
#> 12 32 32 31 34 39 |
|
|
290 |
#> 13 11 11 40 5 2 |
|
|
291 |
#> 14 33 33 32 35 40 |
|
|
292 |
#> 15 34 34 33 36 41 |
|
|
293 |
#> 16 5 5 34 7 12 |
|
|
294 |
#> 17 1 1 34 7 12 |
|
|
295 |
#> 18 32 32 31 34 39 |
|
|
296 |
#> 19 11 11 40 5 4 |
|
|
297 |
#> 20 11 11 40 3 10 |
|
|
298 |
#> 21 6 6 35 8 13 |
|
|
299 |
#> 22 5 5 34 7 12 |
|
|
300 |
#> 23 14 14 43 8 5 |
|
|
301 |
#> 24 12 12 41 6 3 |
|
|
302 |
#> 25 13 13 42 7 4 |
|
|
303 |
#> 26 0 2 35 8 13 |
|
|
304 |
#> 27 2 0 35 8 13 |
|
|
305 |
#> 28 35 35 0 37 42 |
|
|
306 |
#> 29 8 8 37 0 7 |
|
|
307 |
#> 30 13 13 42 7 0 |
|
|
308 |
#> |
|
|
309 |
#> $max_range |
|
|
310 |
#> [1] 11 |
|
|
311 |
#> |
|
|
312 |
#> $can_be_ances |
|
|
313 |
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] |
|
|
314 |
#> [1,] FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
315 |
#> [2,] TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
316 |
#> [3,] TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
317 |
#> [4,] TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
318 |
#> [5,] TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
319 |
#> [6,] TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
320 |
#> [7,] TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE |
|
|
321 |
#> [8,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE |
|
|
322 |
#> [9,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE |
|
|
323 |
#> [10,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE |
|
|
324 |
#> [11,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE |
|
|
325 |
#> [12,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE |
|
|
326 |
#> [13,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
327 |
#> [14,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
328 |
#> [15,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
329 |
#> [16,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
330 |
#> [17,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
331 |
#> [18,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
332 |
#> [19,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
333 |
#> [20,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
334 |
#> [21,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
335 |
#> [22,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
336 |
#> [23,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
337 |
#> [24,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
338 |
#> [25,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
339 |
#> [26,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
340 |
#> [27,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
341 |
#> [28,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
342 |
#> [29,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
343 |
#> [30,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
344 |
#> [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] |
|
|
345 |
#> [1,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
346 |
#> [2,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
347 |
#> [3,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
348 |
#> [4,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
349 |
#> [5,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
350 |
#> [6,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
351 |
#> [7,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
352 |
#> [8,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
353 |
#> [9,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
354 |
#> [10,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
355 |
#> [11,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
356 |
#> [12,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
357 |
#> [13,] FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
358 |
#> [14,] TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
359 |
#> [15,] TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
360 |
#> [16,] TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
361 |
#> [17,] TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
362 |
#> [18,] TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
363 |
#> [19,] TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE |
|
|
364 |
#> [20,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE |
|
|
365 |
#> [21,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE |
|
|
366 |
#> [22,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE |
|
|
367 |
#> [23,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE |
|
|
368 |
#> [24,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE |
|
|
369 |
#> [25,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
370 |
#> [26,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
371 |
#> [27,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
372 |
#> [28,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
373 |
#> [29,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
374 |
#> [30,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
375 |
#> [,25] [,26] [,27] [,28] [,29] [,30] |
|
|
376 |
#> [1,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
377 |
#> [2,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
378 |
#> [3,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
379 |
#> [4,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
380 |
#> [5,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
381 |
#> [6,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
382 |
#> [7,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
383 |
#> [8,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
384 |
#> [9,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
385 |
#> [10,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
386 |
#> [11,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
387 |
#> [12,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
388 |
#> [13,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
389 |
#> [14,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
390 |
#> [15,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
391 |
#> [16,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
392 |
#> [17,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
393 |
#> [18,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
394 |
#> [19,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
395 |
#> [20,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
396 |
#> [21,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
397 |
#> [22,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
398 |
#> [23,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
399 |
#> [24,] TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
400 |
#> [25,] FALSE TRUE TRUE TRUE TRUE TRUE |
|
|
401 |
#> [26,] TRUE FALSE TRUE TRUE TRUE TRUE |
|
|
402 |
#> [27,] TRUE TRUE FALSE TRUE TRUE TRUE |
|
|
403 |
#> [28,] TRUE TRUE TRUE FALSE TRUE TRUE |
|
|
404 |
#> [29,] TRUE TRUE TRUE TRUE FALSE TRUE |
|
|
405 |
#> [30,] TRUE TRUE TRUE TRUE TRUE FALSE |
|
|
406 |
#> |
|
|
407 |
#> $log_w_dens |
|
|
408 |
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] |
|
|
409 |
#> [1,] -3.1571 -1.547663 -0.8545153 -1.142197 -9.669115 -10.66912 -11.66912 |
|
|
410 |
#> [,8] [,9] [,10] [,11] [,12] [,13] [,14] |
|
|
411 |
#> [1,] -12.66912 -13.66912 -14.66912 -15.66912 -16.66912 -17.66912 -18.66912 |
|
|
412 |
#> [,15] [,16] [,17] [,18] [,19] [,20] [,21] |
|
|
413 |
#> [1,] -19.66912 -20.66912 -21.66912 -22.66912 -23.66912 -24.66912 -25.66912 |
|
|
414 |
#> |
|
|
415 |
#> $log_f_dens |
|
|
416 |
#> [1] -3.1571004 -1.5476625 -0.8545153 -1.1421974 -9.6691155 -10.6691155 |
|
|
417 |
#> [7] -11.6691155 -12.6691155 -13.6691155 -14.6691155 -15.6691155 -16.6691155 |
|
|
418 |
#> [13] -17.6691155 -18.6691155 -19.6691155 -20.6691155 -21.6691155 -22.6691155 |
|
|
419 |
#> [19] -23.6691155 -24.6691155 -25.6691155 |
|
|
420 |
#> |
|
|
421 |
#> $contacts |
|
|
422 |
#> <0 x 0 matrix> |
|
|
423 |
#> |
|
|
424 |
#> $C_combn |
|
|
425 |
#> NULL |
|
|
426 |
#> |
|
|
427 |
#> $C_nrow |
|
|
428 |
#> NULL |
|
|
429 |
#> |
|
|
430 |
#> $ids |
|
|
431 |
#> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" |
|
|
432 |
#> [16] "16" "17" "18" "19" "20" "21" "22" "23" "24" "25" "26" "27" "28" "29" "30" |
|
|
433 |
#> |
|
|
434 |
#> $has_dna |
|
|
435 |
#> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
436 |
#> [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE |
|
|
437 |
#> |
|
|
438 |
#> $id_in_dna |
|
|
439 |
#> [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 |
|
|
440 |
#> [26] 26 27 28 29 30 |
|
|
441 |
#> </div><div class='input'> |
|
|
442 |
</div></pre> |
|
|
443 |
</div> |
|
|
444 |
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
|
|
445 |
<nav id="toc" data-toggle="toc" class="sticky-top"> |
|
|
446 |
<h2 data-toc-skip>Contents</h2> |
|
|
447 |
</nav> |
|
|
448 |
</div> |
|
|
449 |
</div> |
|
|
450 |
|
|
|
451 |
|
|
|
452 |
<footer> |
|
|
453 |
<div class="copyright"> |
|
|
454 |
<p>Developed by Thibaut Jombart, Finlay Campbell, Rich Fitzjohn.</p> |
|
|
455 |
</div> |
|
|
456 |
|
|
|
457 |
<div class="pkgdown"> |
|
|
458 |
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> |
|
|
459 |
</div> |
|
|
460 |
|
|
|
461 |
</footer> |
|
|
462 |
</div> |
|
|
463 |
|
|
|
464 |
|
|
|
465 |
|
|
|
466 |
|
|
|
467 |
</body> |
|
|
468 |
</html> |
|
|
469 |
|
|
|
470 |
|