forked from FukamiLab/BIO202
-
Notifications
You must be signed in to change notification settings - Fork 0
/
01-A-R-intro.html
548 lines (470 loc) · 19.8 KB
/
01-A-R-intro.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
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
<!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="Jes & Tad" />
<title>Introduction to R and RStudio</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>
<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-computer-setup.html">Computer Setup</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
W1
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="01-A-R-intro.html">Intro to R</a>
</li>
<li>
<a href="01-B-Rmarkdown-intro.html">R markdown</a>
</li>
<li>
<a href="01-C-R-workshop.html">R workshop</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
W2
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="02-A-tidyr.html">ggplot2 and tidyr</a>
</li>
<li>
<a href="02-B-git-intro.html">Intro to git</a>
</li>
<li>
<a href="02-C-student-projects.html">Project introductions</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
W3
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="03-A-data-exploration.html">Data exploration</a>
</li>
<li>
<a href="03-B-linear-models.html">Linear models</a>
</li>
<li>
<a href="03-C-heterogeneity.html">Heterogeneity</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
W4
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="04-A-mixed-models.html">Mixed effects models</a>
</li>
<li>
<a href="04-B-binary-data.html">Binary & proportional data</a>
</li>
<li>
<a href="04-C-zero-data.html">Zero-inflated data</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
W5
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="05-A-Bayesian-linear-models.html">Bayesian linear models</a>
</li>
<li>
<a href="05-B-Bayesian-priors.html">Bayesian inference with prior information</a>
</li>
<li>
<a href="05-C-Advanced-bayesian-example.html">Advanced Bayesian model example</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
W6
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="06-A-unconstrained-ordination.html">Unconstrained ordination</a>
</li>
<li>
<a href="06-B-constrained-ordination.html">Constrained ordination</a>
</li>
<li>
<a href="06-C-matrix-comparison.html">Comparing multivariate data</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
W8
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="08-A-mapping.html">Visualizing spatial data</a>
</li>
<li>
<a href="08-B-spatial-regression.html">Spatial regression</a>
</li>
<li>
<a href="08-C-spatial-ordination.html">Ordination approach to spatial analysis</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
W9
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="09-A-time-series.html">Time series</a>
</li>
<li>
<a href="09-B-networks.html">Network analysis</a>
</li>
<li>
<a href="09-C-occupancy-models.html">Occupancy models</a>
</li>
</ul>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<h1 class="title toc-ignore">Introduction to R and RStudio</h1>
<h4 class="author"><em>Jes & Tad</em></h4>
</div>
<div id="key-points" class="section level3">
<h3>Key Points</h3>
<ul>
<li>R is a widely-used program for statistical computing.</li>
<li>RStudio is a program that allows users to easily document and run reproducible analyses with R.</li>
<li>Analyses are saved as text files (e.g. “code”) that can be re-run and edited as a reproducible record of the research process.</li>
<li>Well-organized research projects have clear locations for saving code, data, and analysis output (figures, tables, written documents).</li>
<li>Organizing an analysis as an RStudio project makes it easy to collaborate on research because the directory structure is self-contained, facilitating file transfer and version control.</li>
</ul>
</div>
<div id="how-we-will-use-r" class="section level3">
<h3>How we will use R</h3>
<p>R is a popular free and open program for statistical computing (<a href="https://www.r-project.org/about.html" class="uri">https://www.r-project.org/about.html</a>). R can be run from the command line or from a graphical user interface that is automatically installed when you install R (if you open the R program installed on your computer, this is what will open up). We will be using a program called RStudio (see <a href="https://www.rstudio.com/about/" class="uri">https://www.rstudio.com/about/</a>) to interface with the R program. RStudio is what is known as an <em>integrated development environment</em> that makes it easier for R users to write and execute code and organize research projects. Some of the features that we can take advantage of are:</p>
<ul>
<li>Text highlighting that makes it easier to spot typos and see the structure of code.</li>
<li>Easy rendering of Rmarkdown formatting to html documents for our course website.</li>
<li>Project management that automatically defines your working directory and makes projects transferable across computers.</li>
<li>Integrated version control with Git that make it (mostly) unnecessary to use the command line.</li>
</ul>
<p>Today we will focus on setting up an RStudio project for the research project you will complete during this class and in the process, introduce you to how RStudio is set up and some basics of using and writing R code.</p>
</div>
<div id="setting-up-your-research-project" class="section level3">
<h3>Setting up your research project</h3>
<p>Open RStudio and click File > New Project. Make this project in a new directory and select “Empty Project”. You will be prompted to type a name for the project and choose a directory on your computer where you want to save it. The new project can be saved anywhere on your computer that makes sense and you should choose an informative project name <strong>with no spaces</strong>. If you think that you might want to track changes to this project using version control or save the code to GitHub, be sure to check the “Create a git repository” box. We will have a <a href="02-B-git-intro.html">lesson on Git</a> on Wednesday, October 4th.</p>
<p>You will now have three windows displayed in RStudio:</p>
<ul>
<li><strong>Console</strong>: This is where the R code that you run will show up and display results.</li>
<li><strong>Files/Plots/Packages/Help/Viewer</strong>: This should currently show the <em>working directory</em> and the files in it. It is also where graphics and help pages will show up. (Try clicking the other tabs!)</li>
<li><strong>Environment/History</strong>: This will show any <em>objects</em> that you define when running R code and (if you click the History tab) a record of previous R code that you have run. It should currently be empty.</li>
</ul>
<p>Let’s make a new <em>R script</em>- a text file where you save R code that performs an analysis. Click File > New File > R Script. This will open a new window with a tab for your R script called “Untitled1”. The first thing you should do when starting an analysis is to make a new R script and save it with a descriptive name (no spaces!). The best practice for project organization is to save all code scripts in a folder named “code”. In the Files window, click “New Folder” and make a folder named “code”. Then save your new script into this folder. Now you are ready to start an analysis!</p>
</div>
<div id="how-r-works" class="section level3">
<h3>How R works</h3>
<div id="code-vs.the-console" class="section level4">
<h4>Code vs. The Console</h4>
<p>R is a fancy calculator that can remember previous calculations and store them for future use (see the section Objects and Functions). You can use R by typing commands directing into the console. For example, try doing some simple arithmetic. Place your cursor in the Console window in front of the <code>></code> symbol and type <code>3 + 5</code>. Then press Enter.</p>
<blockquote>
<p><strong>Exercise:</strong></p>
<p>Convince yourself that R follows the order of operations.</p>
</blockquote>
<p>Note: If you see a <code>+</code> symbol that means that R is waiting for further input from you before it can finish a calculation. Hit Escape if you aren’t sure what it is waiting for and want to try again.</p>
<p>Typing code into the console is inefficient and doesn’t allow you to easily save your work or edit previous work. Therefore you should always type R code into an R script and then run the code in the script. The R script is saved as a text file on your computer that you can open again later or send to colleagues.</p>
<p>Try typing some arithmetic expressions into the blank R script that you just made. Note each line corresponds to a new command to be sent to the R console. What happened in the R console after you typed the lines? Hopefully nothing.</p>
<p>R code that you type in a script will not be executed unless you tell RStudio to run it.</p>
<ul>
<li>To run a single line of code in a script place your cursor anywhere on the line and press Ctrl+Enter or Cmd+Enter or click the green “Run” arrow at the upper right of the script window.</li>
<li>To run a portion of a line of code, use your cursor to highlight just the part you want and then press Ctrl+Enter or Cmd+Enter or click the green “Run” arrow at the upper right of the script window.</li>
<li>To run multiple lines of code use your cursor to highlight all of the lines you want and then press Ctrl+Enter or Cmd+Enter or click the green “Run” arrow at the upper right of the script window.</li>
<li>To run all the code in a script click the “Source” button at the upper right of the script window. Note that the Console displays <code>source('~/filepath/name-of-script.R')</code>, but doesn’t give any output. The <code>source()</code> function allows you to run any code file without opening it in RStudio (which may be useful to you later).</li>
</ul>
</div>
<div id="documenting-your-code" class="section level4">
<h4>Documenting your code</h4>
<p>The most important part of you code are the <em>comments</em> that document what the code is supposed to do. This is most useful for reminding you of what you are trying to accomplish in an analysis as well as for anyone else who might need to read your code.</p>
<p>Any text in an R script that follows the <code>#</code> is interpretted as a <em>comment</em>- a piece of descriptive text that doesn’t cause R to do any calculations.</p>
<p>The best practice is to begin any R script with comments that give the title, author (with email), date, and short description of what the code does.</p>
<blockquote>
<p><strong>Exercise</strong></p>
<p>Add a header to your R script describing what will eventually be contained in it.</p>
</blockquote>
</div>
<div id="editing-r-code" class="section level4">
<h4>Editing R Code</h4>
<p>In this class we will often be working with and modifying existing R code that others have written. Many scientists learn R by borrowing code and modifying it to suit their purposes. Therefore it is useful to start right away learning how to search for answers and troubleshoot.</p>
<p>Download <a href="https://github.com/FukamiLab/BIO202/blob/master/code/01-A-r-intro-exercise-code.R">this R script</a> and save it in your code folder in the research project you created today. You will need to click the ‘Raw’ button and then download the text file that appears. Be sure to remove the .txt extension that may have been added when you saved the file to your computer so that the file ends in .R. Then, open the downloaded script in your current RStudio session.</p>
<p>This R script makes a new folder called ‘data’ and downloads a csv file from our course website into this folder. The csv file contains data on trees sampled by students in the BIO46 winter quarter class in 2017. It then reads the data into R and saves it as an object named <code>raw_data</code>. The <code>raw_data</code> object is a dataframe, which is basically a table where rows are observations and columns are attributes. It is a very useful data structure for performing statistical analyses. The code then goes on to calculate the mean value of latitude across all observations in the dataset and count the number of each species of tree sampled. Run the code so that you can see how it works.</p>
<blockquote>
<p><strong>Exercise:</strong></p>
<ol style="list-style-type: decimal">
<li>Save the R script you downloaded as a new R script named “analysis_2017-09-25.R” into the code folder in this project.</li>
<li>Copy a csv file from your computer containing data that you are interested in working with. If you don’t have a csv file yet, go to the <a href="http://data.neonscience.org/browse-data">Neon Data Portal</a> and download precipitation data from the Toolik Lake Core site in Alaska.</li>
<li>Modify your R script so that it reads the data file into R and calculates the maximum value in one of the columns.</li>
</ol>
</blockquote>
<p>If you get stuck, use the Help tab in RStudio as well as internet searches to figure out how to accomplish this task. Ask your classmates for help too!</p>
<p><strong>Don’t forget to press save periodically!</strong> RStudio does not automatically save changes to documents.</p>
</div>
</div>
</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>