-
Notifications
You must be signed in to change notification settings - Fork 0
/
README.html
339 lines (321 loc) · 16.1 KB
/
README.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
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
<meta charset="utf-8">
<meta name="generator" content="quarto-1.2.269">
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
<title>readme</title>
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
div.columns{display: flex; gap: min(4vw, 1.5em);}
div.column{flex: auto; overflow-x: auto;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
ul.task-list li input[type="checkbox"] {
width: 0.8em;
margin: 0 0.8em 0.2em -1.6em;
vertical-align: middle;
}
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
div.sourceCode { margin: 1em 0; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
pre > code.sourceCode { white-space: pre-wrap; }
pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
{ counter-reset: source-line 0; }
pre.numberSource code > span
{ position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
{ content: counter(source-line);
position: relative; left: -1em; text-align: right; vertical-align: baseline;
border: none; display: inline-block;
-webkit-touch-callout: none; -webkit-user-select: none;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
color: #aaaaaa;
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode
{ }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span.al { color: #ff0000; font-weight: bold; } /* Alert */
code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #7d9029; } /* Attribute */
code span.bn { color: #40a070; } /* BaseN */
code span.bu { color: #008000; } /* BuiltIn */
code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4070a0; } /* Char */
code span.cn { color: #880000; } /* Constant */
code span.co { color: #60a0b0; font-style: italic; } /* Comment */
code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #ba2121; font-style: italic; } /* Documentation */
code span.dt { color: #902000; } /* DataType */
code span.dv { color: #40a070; } /* DecVal */
code span.er { color: #ff0000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #40a070; } /* Float */
code span.fu { color: #06287e; } /* Function */
code span.im { color: #008000; font-weight: bold; } /* Import */
code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #007020; font-weight: bold; } /* Keyword */
code span.op { color: #666666; } /* Operator */
code span.ot { color: #007020; } /* Other */
code span.pp { color: #bc7a00; } /* Preprocessor */
code span.sc { color: #4070a0; } /* SpecialChar */
code span.ss { color: #bb6688; } /* SpecialString */
code span.st { color: #4070a0; } /* String */
code span.va { color: #19177c; } /* Variable */
code span.vs { color: #4070a0; } /* VerbatimString */
code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
</style>
<script src="README_files/libs/clipboard/clipboard.min.js"></script>
<script src="README_files/libs/quarto-html/quarto.js"></script>
<script src="README_files/libs/quarto-html/popper.min.js"></script>
<script src="README_files/libs/quarto-html/tippy.umd.min.js"></script>
<script src="README_files/libs/quarto-html/anchor.min.js"></script>
<link href="README_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="README_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
<script src="README_files/libs/bootstrap/bootstrap.min.js"></script>
<link href="README_files/libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
<link href="README_files/libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light">
</head>
<body class="fullcontent">
<div id="quarto-content" class="page-columns page-rows-contents page-layout-article">
<main class="content" id="quarto-document-content">
<h1 align="center">
Autocorrelation-informed home range estimation:<br> a review and practical guide
</h1>
<div data-align="center">
<p> <a href="https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.13786"><img border="0" alt="Manuscript" src="https://assets.dryicons.com/uploads/icon/svg/4926/home.svg" width="35" height="35"></a> <a href="mailto:[email protected]"><img border="0" alt="Email" src="https://assets.dryicons.com/uploads/icon/svg/8007/c804652c-fae4-43d7-b539-187d6a408254.svg" width="35" height="35"></a> <a href="https://twitter.com/ecoisilva"><img border="0" alt="Twitter" src="https://assets.dryicons.com/uploads/icon/svg/8385/c23f7ffc-ca8d-4246-8978-ce9f6d5bcc99.svg" width="35" height="35"></a> </p>
</div>
<section id="about" class="level1">
<h1>About:</h1>
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="files/graphical-abstract.png" class="img-fluid figure-img"></p>
<p></p><figcaption class="figure-caption">Graphical abstract</figcaption><p></p>
</figure>
</div>
<p>This repository is a companion piece to the manuscript <em>“Autocorrelation-informed home range estimation: a review and practical guide”</em>, published in <a href="https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.13786">Methods in Ecology and Evolution</a>. Click <a href="https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.13786">here</a> to download the full-text. Preprint is also available on <a href="https://ecoevorxiv.org/repository/view/4026/">EcoEvoRxiv</a>.</p>
<blockquote class="blockquote">
<p>Home range estimation is a key output from tracking datasets, but the inherent properties of animal movement can lead traditional methods to under- or overestimated their size. <strong>Autocorrelated Kernel Density Estimation (AKDE)</strong> methods were designed to be statistically efficient while explicitly dealing with the complexities and biases of modern movement data, such as <em>autocorrelation</em>, <em>small sample sizes</em>, and <em>missing or irregularly sampled data</em>.</p>
</blockquote>
<p>Here, we provide:</p>
<ol type="1">
<li><a href="https://ecoisilva.github.io/AKDE_minireview/code/AKDE_R-tutorial.html">R tutorial</a> as a GitHub page (or as a <a href="files/SuppFile2_R-tutorial.pdf">.pdf</a> file).</li>
<li>Simulation <a href="data/data_sims.csv">data</a> and corresponding <a href="AKDE_sims.R">R script</a>.</li>
</ol>
<section id="citation" class="level3">
<h3 class="anchored" data-anchor-id="citation">Citation:</h3>
<blockquote class="blockquote">
<p>Silva, I., Fleming, C. H., Noonan, M. J., Alston, J., Folta, C., Fagan, W. F., & Calabrese, J. M. (2022). Autocorrelation‐informed home range estimation: A review and practical guide. Methods in Ecology and Evolution, 13(3), 534-544. https://doi.org/10.1111/2041-210X.13786</p>
</blockquote>
</section>
</section>
<section id="r-tutorial" class="level1">
<h1>R tutorial:</h1>
<p>The <strong>AKDE</strong> family of home range estimators will be run using <code>R</code> software and the <code>ctmm</code> package (Calabrese <em>et al.</em>, <a href="https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12559">2016</a>). If you are not familiar with <code>R</code>, make sure you follow these steps:</p>
<ol type="1">
<li>Install <code>R</code> from <a href="https://www.r-project.org" class="uri">https://www.r-project.org</a>.</li>
<li>Install <code>RStudio Desktop</code> from <a href="https://rstudio.com/products/rstudio/download/#download">here</a> for a graphical interface for <code>R</code>.</li>
<li>Install the required <code>R</code> packages with the following code:</li>
</ol>
<div class="sourceCode" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">"ctmm"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>We provide a guide to <strong>home range estimation</strong> using the following workflow:</p>
<ul>
<li><strong>Step 1.</strong> – Formatting and loading an animal tracking dataset;</li>
<li><strong>Step 2.</strong> – Checking for the <em>range residency</em> assumption;</li>
<li><strong>Step 3.</strong> – Selecting the best-fit movement model through <em>model selection</em>;</li>
<li><strong>Step 4.</strong> – Feeding a movement model into the <em>home range estimator</em>;</li>
<li><strong>Step 5.</strong> – Evaluating additional <em>biases</em>, applying <em>mitigation measures</em>.</li>
</ul>
<p>Click <a href="https://ecoisilva.github.io/AKDE_minireview/code/AKDE_R-tutorial.html">here</a> for the tutorial as a GitHub page (or <a href="files/SuppFile2_R-tutorial.pdf">here</a> as a .pdf file). The tutorial was generated with <code>R</code> version <code>4.2.3</code>, and <code>ctmm</code> version <code>1.1.1</code>.</p>
</section>
<section id="simulations" class="level1">
<h1>Simulations:</h1>
<blockquote class="blockquote">
<p>To quantify the level of improvement offered by each mitigation measure and to explore the tradeoff between accuracy and computational cost, we performed a detailed simulation study. For more details, check our manuscript <a href="https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.13786">here</a>.</p>
</blockquote>
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="files/methods-comparison.png" class="img-fluid figure-img"></p>
<p></p><figcaption class="figure-caption">Methods comparison - error and computational cost</figcaption><p></p>
</figure>
</div>
<section id="metadata" class="level2">
<h2 class="anchored" data-anchor-id="metadata">Metadata</h2>
<p>The <a href="/data">:file_folder: <strong>data</strong></a> directory contains:</p>
<ul>
<li><a href="data_sims.csv">:memo: data_sims.csv</a>: Output from simulations.
<ul>
<li><code>method</code> - home range estimator method</li>
<li><code>duration</code> - sampling duration (in days)</li>
<li><code>bias</code> - difference between the 95% home range estimate and the true 95% area</li>
<li><code>cost</code> - computational cost (in seconds)</li>
<li><code>relArea</code> - Relative home range area (true home range area is scaled to 1)</li>
<li><code>error</code> - Relative error of home range area</li>
<li><code>tau_p</code> - position autocorrelation timescale (in sec)</li>
<li><code>tau_v</code> - velocity autocorrelation timescale (in sec)</li>
</ul></li>
<li><a href="example_data_longlat.csv">:memo: example_data_longlat.csv</a>: Example dataset with coordinates as latitude/longitude.</li>
<li><a href="example_data_utm.csv">:memo: example_data_utm.csv</a>: Example dataset with UTM coordinates.</li>
</ul>
</section>
</section>
<section id="useful-links" class="level1">
<h1>Useful links:</h1>
<ul>
<li><a href="https://ourcodingclub.github.io/tutorials.html">Coding Club</a>: collection of coding tutorials with examples in R.</li>
<li><a href="https://rstudio.github.io/learnr/"><code>learn</code> R package</a>: interactive tutorials for R.</li>
</ul>
<p>For further documentation on using the <code>ctmm</code> package: - https://cran.r-project.org/web/packages/ctmm/ctmm.pdf - https://ctmm-initiative.github.io/ctmm/</p>
</section>
</main>
<!-- /main column -->
<script id="quarto-html-after-body" type="application/javascript">
window.document.addEventListener("DOMContentLoaded", function (event) {
const toggleBodyColorMode = (bsSheetEl) => {
const mode = bsSheetEl.getAttribute("data-mode");
const bodyEl = window.document.querySelector("body");
if (mode === "dark") {
bodyEl.classList.add("quarto-dark");
bodyEl.classList.remove("quarto-light");
} else {
bodyEl.classList.add("quarto-light");
bodyEl.classList.remove("quarto-dark");
}
}
const toggleBodyColorPrimary = () => {
const bsSheetEl = window.document.querySelector("link#quarto-bootstrap");
if (bsSheetEl) {
toggleBodyColorMode(bsSheetEl);
}
}
toggleBodyColorPrimary();
const icon = "";
const anchorJS = new window.AnchorJS();
anchorJS.options = {
placement: 'right',
icon: icon
};
anchorJS.add('.anchored');
const clipboard = new window.ClipboardJS('.code-copy-button', {
target: function(trigger) {
return trigger.previousElementSibling;
}
});
clipboard.on('success', function(e) {
// button target
const button = e.trigger;
// don't keep focus
button.blur();
// flash "checked"
button.classList.add('code-copy-button-checked');
var currentTitle = button.getAttribute("title");
button.setAttribute("title", "Copied!");
let tooltip;
if (window.bootstrap) {
button.setAttribute("data-bs-toggle", "tooltip");
button.setAttribute("data-bs-placement", "left");
button.setAttribute("data-bs-title", "Copied!");
tooltip = new bootstrap.Tooltip(button,
{ trigger: "manual",
customClass: "code-copy-button-tooltip",
offset: [0, -8]});
tooltip.show();
}
setTimeout(function() {
if (tooltip) {
tooltip.hide();
button.removeAttribute("data-bs-title");
button.removeAttribute("data-bs-toggle");
button.removeAttribute("data-bs-placement");
}
button.setAttribute("title", currentTitle);
button.classList.remove('code-copy-button-checked');
}, 1000);
// clear code selection
e.clearSelection();
});
function tippyHover(el, contentFn) {
const config = {
allowHTML: true,
content: contentFn,
maxWidth: 500,
delay: 100,
arrow: false,
appendTo: function(el) {
return el.parentElement;
},
interactive: true,
interactiveBorder: 10,
theme: 'quarto',
placement: 'bottom-start'
};
window.tippy(el, config);
}
const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
for (var i=0; i<noterefs.length; i++) {
const ref = noterefs[i];
tippyHover(ref, function() {
// use id or data attribute instead here
let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href');
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
return note.innerHTML;
});
}
const findCites = (el) => {
const parentEl = el.parentElement;
if (parentEl) {
const cites = parentEl.dataset.cites;
if (cites) {
return {
el,
cites: cites.split(' ')
};
} else {
return findCites(el.parentElement)
}
} else {
return undefined;
}
};
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
for (var i=0; i<bibliorefs.length; i++) {
const ref = bibliorefs[i];
const citeInfo = findCites(ref);
if (citeInfo) {
tippyHover(citeInfo.el, function() {
var popup = window.document.createElement('div');
citeInfo.cites.forEach(function(cite) {
var citeDiv = window.document.createElement('div');
citeDiv.classList.add('hanging-indent');
citeDiv.classList.add('csl-entry');
var biblioDiv = window.document.getElementById('ref-' + cite);
if (biblioDiv) {
citeDiv.innerHTML = biblioDiv.innerHTML;
}
popup.appendChild(citeDiv);
});
return popup.innerHTML;
});
}
}
});
</script>
</div> <!-- /content -->
</body></html>