-
Notifications
You must be signed in to change notification settings - Fork 42
/
getCommunitySlope.html
309 lines (255 loc) · 14.4 KB
/
getCommunitySlope.html
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
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Calculate the slope of the community abundance — getCommunitySlope • mizer</title>
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<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>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<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" />
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js -->
<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>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script>
<!-- docsearch -->
<script src="../docsearch.js"></script>
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.3/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
<link href="../docsearch.css" rel="stylesheet">
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
<meta property="og:title" content="Calculate the slope of the community abundance — getCommunitySlope" />
<meta property="og:description" content="Calculates the slope of the community abundance through time by performing a
linear regression on the logged total numerical abundance at weight and
logged weights (natural logs, not log to base 10, are used). You can specify
minimum and maximum weight or length range for the species. Lengths take
precedence over weights (i.e. if both min_l and min_w are supplied, only
min_l will be used). You can also specify the species to be used in the
calculation." />
<meta name="robots" content="noindex">
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<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>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mizer</a>
<span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">2.0.2.9001</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
<li>
<a href="../articles/mizer.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/model_description.html">The General Mizer Size-spectrum Model</a>
</li>
<li>
<a href="../articles/community_model.html">The Community Model</a>
</li>
<li>
<a href="../articles/trait_model.html">The Trait-Based Model</a>
</li>
<li>
<a href="../articles/multispecies_model.html">The Multi Species Model</a>
</li>
<li>
<a href="../articles/running_a_simulation.html">Running a Simulation</a>
</li>
<li>
<a href="../articles/exploring_the_simulation_results.html">Exploring the Simulation Results</a>
</li>
<li>
<a href="../articles/a_multispecies_model_of_the_north_sea.html">A Multi-Species Model Of The North Sea</a>
</li>
<li>
<a href="../articles/plotting.html">Using ggplot2 and plotly with mizer</a>
</li>
<li class="divider"></li>
<li class="dropdown-header">For developers</li>
<li>
<a href="../articles/developer_vignette.html">Developer Guide</a>
</li>
<li>
<a href="../articles/working_with_git.html">Working with git and GitHub</a>
</li>
<li>
<a href="../articles/developer_FAQ.html">Developer FAQ</a>
</li>
<li>
<a href="../articles/editing_website.html">Editing the Mizer Website</a>
</li>
</ul>
</li>
<li>
<a href="../articles/publications.html">Publications</a>
</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/sizespectrum/mizer/">
<span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
</ul>
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
<div class="form-group">
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
</div>
</form>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Calculate the slope of the community abundance</h1>
<small class="dont-index">Source: <a href='https://github.com/sizespectrum/mizer/blob/master/R/summary_methods.R'><code>R/summary_methods.R</code></a></small>
<div class="hidden name"><code>getCommunitySlope.Rd</code></div>
</div>
<div class="ref-description">
<p>Calculates the slope of the community abundance through time by performing a
linear regression on the logged total numerical abundance at weight and
logged weights (natural logs, not log to base 10, are used). You can specify
minimum and maximum weight or length range for the species. Lengths take
precedence over weights (i.e. if both min_l and min_w are supplied, only
min_l will be used). You can also specify the species to be used in the
calculation.</p>
</div>
<pre class="usage"><span class='fu'>getCommunitySlope</span>(
<span class='no'>sim</span>,
<span class='kw'>species</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq_len</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>nrow</a></span>(<span class='fu'><a href='setParams.html'>species_params</a></span>(<span class='fu'><a href='getParams.html'>getParams</a></span>(<span class='no'>sim</span>)))),
<span class='kw'>biomass</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='no'>...</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>sim</th>
<td><p>A <a href='MizerSim-class.html'>MizerSim</a> object</p></td>
</tr>
<tr>
<th>species</th>
<td><p>Numeric or character vector of species to include in the
calculation.</p></td>
</tr>
<tr>
<th>biomass</th>
<td><p>Boolean. If TRUE (default), the abundance is based on biomass,
if FALSE the abundance is based on numbers.</p></td>
</tr>
<tr>
<th>...</th>
<td><p>Arguments passed on to <code><a href='get_size_range_array.html'>get_size_range_array</a></code></p><dl>
<dt><code>min_w</code></dt><dd><p>Smallest weight in size range. Defaults to smallest weight in
the model.</p></dd>
<dt><code>max_w</code></dt><dd><p>Largest weight in size range. Defaults to largest weight in the
model.</p></dd>
<dt><code>min_l</code></dt><dd><p>Smallest length in size range. If supplied, this takes
precedence over <code>min_w</code>.</p></dd>
<dt><code>max_l</code></dt><dd><p>Largest length in size range. If supplied, this takes precedence
over <code>max_w</code>.</p></dd>
</dl></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A data.frame with four columns: time step, slope, intercept and the
coefficient of determination R^2.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>Other functions for calculating indicators:
<code><a href='getMeanMaxWeight.html'>getMeanMaxWeight</a>()</code>,
<code><a href='getMeanWeight.html'>getMeanWeight</a>()</code>,
<code><a href='getProportionOfLargeFish.html'>getProportionOfLargeFish</a>()</code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'><a href='newMultispeciesParams.html'>newMultispeciesParams</a></span>(<span class='no'>NS_species_params_gears</span>, <span class='no'>inter</span>)
<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'><a href='project.html'>project</a></span>(<span class='no'>params</span>, <span class='kw'>effort</span><span class='kw'>=</span><span class='fl'>1</span>, <span class='kw'>t_max</span><span class='kw'>=</span><span class='fl'>40</span>, <span class='kw'>dt</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>t_save</span> <span class='kw'>=</span> <span class='fl'>1</span>)
<span class='co'># Slope based on biomass, using all species and sizes</span>
<span class='no'>slope_biomass</span> <span class='kw'><-</span> <span class='fu'>getCommunitySlope</span>(<span class='no'>sim</span>)
<span class='co'># Slope based on numbers, using all species and sizes</span>
<span class='no'>slope_numbers</span> <span class='kw'><-</span> <span class='fu'>getCommunitySlope</span>(<span class='no'>sim</span>, <span class='kw'>biomass</span><span class='kw'>=</span><span class='fl'>FALSE</span>)
<span class='co'># Slope based on biomass, using all species and sizes between 10g and 1000g</span>
<span class='no'>slope_biomass</span> <span class='kw'><-</span> <span class='fu'>getCommunitySlope</span>(<span class='no'>sim</span>, <span class='kw'>min_w</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>max_w</span> <span class='kw'>=</span> <span class='fl'>1000</span>)
<span class='co'># Slope based on biomass, using only demersal species and sizes between 10g and 1000g</span>
<span class='no'>dem_species</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Dab"</span>,<span class='st'>"Whiting"</span>,<span class='st'>"Sole"</span>,<span class='st'>"Gurnard"</span>,<span class='st'>"Plaice"</span>,<span class='st'>"Haddock"</span>, <span class='st'>"Cod"</span>,<span class='st'>"Saithe"</span>)
<span class='no'>slope_biomass</span> <span class='kw'><-</span> <span class='fu'>getCommunitySlope</span>(<span class='no'>sim</span>, <span class='kw'>species</span> <span class='kw'>=</span> <span class='no'>dem_species</span>, <span class='kw'>min_w</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>max_w</span> <span class='kw'>=</span> <span class='fl'>1000</span>)
}</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.york.ac.uk/maths/staff/gustav-delius/'>Gustav Delius</a>, Finlay Scott, <a href='http://www.utas.edu.au/profiles/staff/imas/julia-blanchard'>Julia Blanchard</a>, <a href='https://ken.haste.dk/'>Ken Andersen</a>.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>
</div>
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
<script>
docsearch({
apiKey: '96e9641255d3fff35a4fd16d1a1bf70c',
indexName: 'sizespectrum_mizer',
inputSelector: 'input#search-input.form-control',
transformData: function(hits) {
return hits.map(function (hit) {
hit.url = updateHitURL(hit);
return hit;
});
}
});
</script>
</body>
</html>