This repository has been archived by the owner on Aug 4, 2020. It is now read-only.
-
-
Notifications
You must be signed in to change notification settings - Fork 76
/
00-before-we-start.html
418 lines (347 loc) · 12.3 KB
/
00-before-we-start.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
<!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="Data Carpentry contributors" />
<title>Before we start</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-5.0.13/css/fa-svg-with-js.css" rel="stylesheet" />
<script src="site_libs/font-awesome-5.0.13/js/fontawesome-all.min.js"></script>
<script src="site_libs/font-awesome-5.0.13/js/fa-v4-shims.min.js"></script>
<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;
}
.html-widget {
margin-bottom: 20px;
}
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-data-frames.html">Data frames</a>
</li>
<li>
<a href="04-dplyr.html">The dplyr package</a>
</li>
<li>
<a href="05-data-visualization.html">Data visualization</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/data-lessons/R-genomics">
<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">Before we start</h1>
<h4 class="author"><em>Data Carpentry contributors</em></h4>
</div>
<hr />
<blockquote>
<h2 id="learning-objectives">Learning Objectives</h2>
<ul>
<li>Describe the purpose of RStudio’s script, console, environment, and file/plot/help windows.</li>
<li>Create an R project.</li>
<li>Organize files and directories for a set of analyses as an R Project.</li>
<li>Use the built-in RStudio help interface to search for more information on R functions.</li>
</ul>
</blockquote>
<hr />
<div id="presentation-of-rstudio" class="section level1">
<h1>Presentation of RStudio</h1>
<p>Start RStudio – Let’s start by learning about our tool.</p>
<ul>
<li>Console, Scripts, Environments, Plots</li>
<li>Code and workflow are more reproducible if we can document everything that we do.</li>
<li>Our end goal is not just to “do stuff” but to do it in a way that anyone can easily and exactly replicate our workflow and results.</li>
</ul>
</div>
<div id="before-we-get-started" class="section level1">
<h1>Before we get started</h1>
<ul>
<li>Under the <code>File</code> menu, click on <code>New project</code>, choose <code>New directory</code>, then <code>Empty project</code></li>
<li>Enter a name for this new folder, and choose a convenient location for it. This will be your <strong>working directory</strong> for the rest of the day (e.g., <code>~/data-carpentry</code>)</li>
<li>Confirm that the folder named in the <code>Create project as a sub-directory of</code> box is where you want the working directory created. Use the <code>Browse</code> button to navigate folders if changes are needed.</li>
<li>Click on “Create project”</li>
<li>Under the <code>Files</code> tab on the right of the screen, click on <code>New Folder</code> and create a folder named <code>data</code> within your newly created working directory. (e.g., <code>~/data-carpentry/data</code>)</li>
<li>Create a new R script (File > New File > R script) and save it in your working directory (e.g. <code>data-carpentry-script.R</code>)</li>
</ul>
<p>Your working directory should now look like this:</p>
<div class="figure">
<img src="img/r_starting_how_it_should_like.png" alt="How it should look like at the beginning of this lesson" />
<p class="caption">How it should look like at the beginning of this lesson</p>
</div>
</div>
<div id="interacting-with-r" class="section level1">
<h1>Interacting with R</h1>
<p>There are two main ways of interacting with R: using the console or by using script files (plain text files that contain your code).</p>
<p>The console window (in RStudio, the bottom left panel) is the place where R is waiting for you to tell it what to do, and where it will show the results of a command. You can type commands directly into the console, but they will be forgotten when you close the session. It is better to enter the commands in the script editor, and save the script. This way, you have a complete record of what you did, you can easily show others how you did it and you can do it again later on if needed. You can copy-paste into the R console, but the Rstudio script editor allows you to ‘send’ the current line or the currently selected text to the R console using the <code>Ctrl-Enter</code> shortcut.</p>
<p>If R is ready to accept commands, the R console shows a <code>></code> prompt. If it receives a command (by typing, copy-pasting or sent from the script editor using <kbd>Ctrl</kbd>-<kbd>Enter</kbd>), R will try to execute it, and when ready, show the results and come back with a new <code>></code> prompt to wait for new commands.</p>
<p>If R is still waiting for you to enter more data because it isn’t complete yet, the console will show a <code>+</code> prompt. It means that you haven’t finished entering a complete command. This is because you have not ‘closed’ a parenthesis or quotation. If you’re in Rstudio and this happens, click inside the console window and press <kbd>Esc</kbd>; this should help you out of trouble.</p>
</div>
<div id="basics-of-r" class="section level1">
<h1>Basics of R</h1>
<p>R is a versatile, open source programming/scripting language that’s useful both for statistics but also data science. Inspired by the programming language S.</p>
<ul>
<li>Open source software under GPL.</li>
<li>Superior (if not just comparable) to commercial alternatives. R has over 7,000 user contributed packages at this time. It’s widely used both in academia and industry.</li>
<li>Available on all platforms.</li>
<li>Not just for statistics, but also general purpose programming.</li>
<li>For people who have experience in programmming: R is both an object-oriented and a so-called <a href="http://adv-r.had.co.nz/Functional-programming.html">functional language</a></li>
<li>Large and growing community of peers.</li>
</ul>
<div id="organizing-your-working-directory" class="section level2">
<h2>Organizing your working directory</h2>
<p>You should separate the original data (raw data) from intermediate datasets that you may create for the need of a particular analysis. For instance, you may want to create a <code>data/</code> directory within your working directory that stores the raw data, and have a <code>data_output/</code> directory for intermediate datasets and a <code>figure_output/</code> directory for the plots you will generate.</p>
</div>
</div>
<hr/>
<p><a href="http://datacarpentry.org/">Data Carpentry</a>,
2017-2018. <a href="LICENSE.html">License</a>. <a href="CONTRIBUTING.html">Contributing</a>. <br/>
Questions? Feedback?
Please <a href="https://github.com/datacarpentry/R-genomics/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://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>