forked from datacarpentry/R-ecology-lesson
-
Notifications
You must be signed in to change notification settings - Fork 0
/
index.html
455 lines (383 loc) · 15.2 KB
/
index.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
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<meta name="author" content="François Michonneau & Auriel Fournier (Lesson Maintainers)" />
<title>Data Carpentry: R for data analysis and visualization of Ecological Data</title>
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/bootstrap.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/font-awesome-4.5.0/css/font-awesome.min.css" rel="stylesheet" />
<style type="text/css">
h1 {
font-size: 34px;
}
h1.title {
font-size: 38px;
}
h2 {
font-size: 30px;
}
h3 {
font-size: 24px;
}
h4 {
font-size: 18px;
}
h5 {
font-size: 16px;
}
h6 {
font-size: 12px;
}
.table th:not([align]) {
text-align: left;
}
</style>
<link rel="stylesheet" href="style.css" type="text/css" />
</head>
<body>
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
height: auto;
}
.tabbed-pane {
padding-top: 12px;
}
button.code-folding-btn:focus {
outline: none;
}
</style>
<style type="text/css">
/* padding for bootstrap navbar */
body {
padding-top: 51px;
padding-bottom: 40px;
}
/* offset scroll position for anchor links (for fixed navbar) */
.section h1 {
padding-top: 56px;
margin-top: -56px;
}
.section h2 {
padding-top: 56px;
margin-top: -56px;
}
.section h3 {
padding-top: 56px;
margin-top: -56px;
}
.section h4 {
padding-top: 56px;
margin-top: -56px;
}
.section h5 {
padding-top: 56px;
margin-top: -56px;
}
.section h6 {
padding-top: 56px;
margin-top: -56px;
}
</style>
<script>
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
if (href === "")
href = "index.html";
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
});
</script>
<div class="container-fluid main-container">
<!-- tabsets -->
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
</script>
<!-- code folding -->
<script>
$(document).ready(function () {
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')
.children('h1,h2,h3,h4,h5').addClass('toc-ignore');
// establish options
var options = {
selectors: "h1,h2,h3",
theme: "bootstrap3",
context: '.toc-content',
hashGenerator: function (text) {
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase();
},
ignoreSelector: ".toc-ignore",
scrollTo: 0
};
options.showAndHide = false;
options.smoothScroll = true;
// tocify
var toc = $("#TOC").tocify(options).data("toc-tocify");
});
</script>
<style type="text/css">
#TOC {
margin: 25px 0px 20px 0px;
}
@media (max-width: 768px) {
#TOC {
position: relative;
width: 100%;
}
}
.toc-content {
padding-left: 30px;
padding-right: 40px;
}
div.main-container {
max-width: 1200px;
}
div.tocify {
width: 20%;
max-width: 260px;
max-height: 85%;
}
@media (min-width: 768px) and (max-width: 991px) {
div.tocify {
width: 25%;
}
}
@media (max-width: 767px) {
div.tocify {
width: 100%;
max-width: none;
}
}
.tocify ul, .tocify li {
line-height: 20px;
}
.tocify-subheader .tocify-item {
font-size: 0.90em;
padding-left: 25px;
text-indent: 0;
}
.tocify .list-group-item {
border-radius: 0px;
}
.tocify-subheader {
display: inline;
}
.tocify-subheader .tocify-item {
font-size: 0.95em;
}
</style>
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
</div>
<div class="toc-content col-xs-12 col-sm-8 col-md-9">
<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">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html"></a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">Home</a>
</li>
<li>
<a href="00-before-we-start.html">Before we start</a>
</li>
<li>
<a href="01-intro-to-r.html">Intro to R</a>
</li>
<li>
<a href="02-starting-with-data.html">Starting with data</a>
</li>
<li>
<a href="03-dplyr.html">Manipulating data frames</a>
</li>
<li>
<a href="04-visualization-ggplot2.html">Visualizing data</a>
</li>
<li>
<a href="05-r-and-databases.html">R and SQL</a>
</li>
<li>
<a href="code-handout.R">Code Handout</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/datacarpentry/R-ecology-lesson">
<span class="fa fa-github fa-lg"></span>
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<h1 class="title toc-ignore">Data Carpentry: R for data analysis and visualization of Ecological Data</h1>
<h4 class="author"><em>François Michonneau & Auriel Fournier (Lesson Maintainers)</em></h4>
</div>
<p>
</p>
<div style="text-align: center; margin-top: 30px; margin-bottom: 30px;">
<div class="figure">
<img src="img/DC-logo-vision.png" />
</div>
</div>
<p>
</p>
<p>Data Carpentry’s aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain. The lessons below were designed for those interested in working with ecology data in R.</p>
<p>This is an introduction to R designed for participants with no programming experience. These lessons can be taught in a day. They start with some basic information about R syntax, the RStudio interface, and move through how to import CSV files, the structure of data frames, how to deal with factors, how to add/remove rows and columns, and finish with how to calculate summary statistics for each level and a very brief introduction to plotting.</p>
<div id="chapters" class="section level2">
<h2>Chapters</h2>
<ol style="list-style-type: decimal">
<li><a href="00-before-we-start.html">Before we start</a></li>
<li><a href="01-intro-to-r.html">Introduction to R</a></li>
<li><a href="02-starting-with-data.html">Starting with data</a></li>
<li><a href="03-dplyr.html">Aggregating and analyzing data with dplyr</a></li>
<li><a href="04-visualization-ggplot2.html">Data visualization with ggplot2</a></li>
<li><a href="05-r-and-databases.html">R and Databases</a></li>
</ol>
</div>
<div id="requirements" class="section level2">
<h2>Requirements</h2>
<p>Data Carpentry’s teaching is hands-on, so participants are encouraged to use their own computers to ensure the proper setup of tools for an efficient workflow. <em>These lessons assume no prior knowledge of the skills or tools</em>, but working through this lesson requires working copies of the software described below. To most effectively use these materials, please make sure to download the data and install everything <em>before</em> working through this lesson.</p>
<div id="data" class="section level3">
<h3>Data</h3>
<p>Data files for the lesson are available here: <a href="http://dx.doi.org/10.6084/m9.figshare.1314459" class="uri">http://dx.doi.org/10.6084/m9.figshare.1314459</a></p>
<p>Please download the <em>*.csv</em> (Comma Separated Value) files: <em>species.csv</em>, <em>plots.csv</em>, <em>surveys.csv</em>, and <em>combined.csv</em>.</p>
</div>
<div id="setup-instructions" class="section level3">
<h3>Setup instructions</h3>
<p><strong>R</strong> and <strong>RStudio</strong> are separate downloads and installations. R is the underlying statistical computing environment, but using R alone is no fun. RStudio is a graphical integrated development environment (IDE) that makes using R much easier and more interactive. You need to install R before you install RStudio. After installing both programs, you will need to install the <code>tidyverse</code> package from within RStudio. Follow the instructions below for your operating system, and then follow the instructions to install <code>tidyverse</code> and <code>RSQLite</code>.</p>
<div id="windows" class="section level4">
<h4>Windows</h4>
<div id="if-you-already-have-r-and-rstudio-installed" class="section level5">
<h5>If you already have R and RStudio installed</h5>
<ul>
<li>Open RStudio, and click on “Help” > “Check for updates”. If a new version is available, quit RStudio, and download the latest version for RStudio.</li>
<li>To check which version of R you are using, start RStudio and the first thing that appears in the console indicates the version of R you are running. Alternatively, you can type <code>sessionInfo()</code>, which will also display which version of R you are running. Go on the <a href="https://cran.r-project.org/bin/windows/base/">CRAN website</a> and check whether a more recent version is available. If so, please download and install it. You can <a href="https://cran.r-project.org/bin/windows/base/rw-FAQ.html#How-do-I-UNinstall-R_003f">check here</a> for more information on how to remove old versions from your system if you wish to do so.</li>
</ul>
</div>
<div id="if-you-dont-have-r-and-rstudio-installed" class="section level5">
<h5>If you don’t have R and RStudio installed</h5>
<ul>
<li>Download R from the <a href="http://cran.r-project.org/bin/windows/base/release.htm">CRAN website</a>.</li>
<li>Run the <code>.exe</code> file that was just downloaded</li>
<li>Go to the <a href="https://www.rstudio.com/products/rstudio/download/#download">RStudio download page</a></li>
<li>Under <em>Installers</em> select <strong>RStudio x.yy.zzz - Windows XP/Vista/7/8</strong> (where x, y, and z represent version numbers)</li>
<li>Double click the file to install it</li>
<li>Once it’s installed, open RStudio to make sure it works and you don’t get any error messages.</li>
</ul>
</div>
</div>
<div id="macos-x" class="section level4">
<h4>MacOS X</h4>
<div id="if-you-already-have-r-and-rstudio-installed-1" class="section level5">
<h5>If you already have R and RStudio installed</h5>
<ul>
<li>Open RStudio, and click on “Help” > “Check for updates”. If a new version is available, quit RStudio, and download the latest version for RStudio.</li>
<li>To check the version of R you are using, start RStudio and the first thing that appears on the terminal indicates the version of R you are running. Alternatively, you can type <code>sessionInfo()</code>, which will also display which version of R you are running. Go on the <a href="https://cran.r-project.org/bin/macosx/">CRAN website</a> and check whether a more recent version is available. If so, please download and install it. You may also want to consider removing your old version of R. You can <a href="https://cran.r-project.org/bin/windows/base/rw-FAQ.html#How-do-I-UNinstall-R_003f">check here</a> for more information.</li>
</ul>
</div>
<div id="if-you-dont-have-r-and-rstudio-installed-1" class="section level5">
<h5>If you don’t have R and RStudio installed</h5>
<ul>
<li>Download R from the <a href="http://cran.r-project.org/bin/macosx">CRAN website</a>.</li>
<li>Select the <code>.pkg</code> file for the version of OS X that you have and the file will download</li>
<li>Double clik on the downloaded file to install R</li>
<li>Go to the <a href="https://www.rstudio.com/products/rstudio/download/#download">RStudio download page</a></li>
<li>Under <em>Installers</em> select <strong>RStudio x.yy.zzz - Mac OS X 10.6+ (64-bit)</strong> (where x, y, and z represent version numbers)</li>
<li>Double click the file to install RStudio</li>
<li>Once it’s installed, open RStudio to make sure it works and you don’t get any error messages.</li>
</ul>
</div>
</div>
<div id="linux" class="section level4">
<h4>Linux</h4>
<ul>
<li>Follow the instructions for your distribution from <a href="https://cloud.r-project.org/bin/linux">CRAN</a>, they provide information to get the most recent version of R for your distribution. For most distributions, you could use your package manager (e.g., for Debian/Ubuntu run <code>sudo apt-get install r-base</code>, and for Fedora <code>sudo yum install R</code>), but the versions provided by this approach are usually out of date. In any case, make sure you have at least R 3.3.1</li>
<li>Go to the <a href="https://www.rstudio.com/products/rstudio/download/#download">RStudio download page</a></li>
<li>Under <em>Installers</em> select the version that matches your distribution, and install it with your preferred method (e.g., with Debian/Ubuntu <code>sudo dpkg -i rstudio-x.yy.zzz-amd64.deb</code> at the terminal).</li>
<li>Once it’s installed, open RStudio to make sure it works and you don’t get any error messages.</li>
</ul>
</div>
<div id="for-everyone" class="section level4">
<h4>For everyone</h4>
<p><strong>After installing R and RStudio, you need to install the “tidyverse” and “RSQLite” packages.</strong></p>
<ul>
<li>After starting RStudio, at the console type: <code>install.packages(c("tidyverse", "RSQLite"))</code></li>
</ul>
</div>
</div>
</div>
<div id="contributors" class="section level2">
<h2>Contributors</h2>
<p>The list of contributors to this lesson is available <a href="AUTHORS">here</a>,</p>
</div>
<hr/>
<p><a href="http://datacarpentry.org/">Data Carpentry</a>, 2017. <br/>
<a href="LICENSE.html">License</a>. Questions? Feedback?
Please <a href="https://github.com/datacarpentry/R-ecology-lesson/issues/new">file
an issue on GitHub</a>. <br/>
On Twitter: <a href="https://twitter.com/datacarpentry">@datacarpentry</a></p>
</div>
</div>
</div>
<script>
// add bootstrap table styles to pandoc tables
function bootstrapStylePandocTables() {
$('tr.header').parent('thead').parent('table').addClass('table table-condensed');
}
$(document).ready(function () {
bootstrapStylePandocTables();
});
</script>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
script.src = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>