-
Notifications
You must be signed in to change notification settings - Fork 6
/
Rmarkdown_intro.html
2502 lines (2337 loc) · 84.2 KB
/
Rmarkdown_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
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<title>Introduction to R markdown</title>
<script src="site_libs/header-attrs-2.20/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/flatly.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>
<style>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;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<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>
<script src="site_libs/navigation-1.1/codefolding.js"></script>
<script src="site_libs/kePrint-0.0.1/kePrint.js"></script>
<link href="site_libs/lightable-0.0.1/lightable.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-162377463-2"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'UA-162377463-2');
</script>
<style type="text/css">
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
span.underline{text-decoration: underline;}
div.column{display: inline-block; vertical-align: top; width: 50%;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
</style>
<style type="text/css">
code {
white-space: pre;
}
.sourceCode {
overflow: visible;
}
</style>
<style type="text/css" data-origin="pandoc">
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
{ background-color: #f8f8f8; }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span.al { color: #ef2929; } /* Alert */
code span.an { color: #8f5902; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #204a87; } /* Attribute */
code span.bn { color: #0000cf; } /* BaseN */
code span.cf { color: #204a87; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4e9a06; } /* Char */
code span.cn { color: #8f5902; } /* Constant */
code span.co { color: #8f5902; font-style: italic; } /* Comment */
code span.cv { color: #8f5902; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #8f5902; font-weight: bold; font-style: italic; } /* Documentation */
code span.dt { color: #204a87; } /* DataType */
code span.dv { color: #0000cf; } /* DecVal */
code span.er { color: #a40000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #0000cf; } /* Float */
code span.fu { color: #204a87; font-weight: bold; } /* Function */
code span.im { } /* Import */
code span.in { color: #8f5902; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #204a87; font-weight: bold; } /* Keyword */
code span.op { color: #ce5c00; font-weight: bold; } /* Operator */
code span.ot { color: #8f5902; } /* Other */
code span.pp { color: #8f5902; font-style: italic; } /* Preprocessor */
code span.sc { color: #ce5c00; font-weight: bold; } /* SpecialChar */
code span.ss { color: #4e9a06; } /* SpecialString */
code span.st { color: #4e9a06; } /* String */
code span.va { color: #000000; } /* Variable */
code span.vs { color: #4e9a06; } /* VerbatimString */
code span.wa { color: #8f5902; font-weight: bold; font-style: italic; } /* Warning */
.sourceCode .row {
width: 100%;
}
.sourceCode {
overflow-x: auto;
}
.code-folding-btn {
margin-right: -30px;
}
</style>
<script>
// apply pandoc div.sourceCode style to pre.sourceCode instead
(function() {
var sheets = document.styleSheets;
for (var i = 0; i < sheets.length; i++) {
if (sheets[i].ownerNode.dataset["origin"] !== "pandoc") continue;
try { var rules = sheets[i].cssRules; } catch (e) { continue; }
var j = 0;
while (j < rules.length) {
var rule = rules[j];
// check if there is a div.sourceCode rule
if (rule.type !== rule.STYLE_RULE || rule.selectorText !== "div.sourceCode") {
j++;
continue;
}
var style = rule.style.cssText;
// check if color or background-color is set
if (rule.style.color === '' && rule.style.backgroundColor === '') {
j++;
continue;
}
// replace div.sourceCode by a pre.sourceCode rule
sheets[i].deleteRule(j);
sheets[i].insertRule('pre.sourceCode{' + style + '}', j);
}
}
})();
</script>
<link rel="stylesheet" href="custom.css" type="text/css" />
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
img {
max-width:100%;
}
.tabbed-pane {
padding-top: 12px;
}
.html-widget {
margin-bottom: 20px;
}
button.code-folding-btn:focus {
outline: none;
}
summary {
display: list-item;
}
details > summary > p:only-child {
display: inline;
}
pre code {
padding: 0;
}
</style>
<style type="text/css">
.dropdown-submenu {
position: relative;
}
.dropdown-submenu>.dropdown-menu {
top: 0;
left: 100%;
margin-top: -6px;
margin-left: -1px;
border-radius: 0 6px 6px 6px;
}
.dropdown-submenu:hover>.dropdown-menu {
display: block;
}
.dropdown-submenu>a:after {
display: block;
content: " ";
float: right;
width: 0;
height: 0;
border-color: transparent;
border-style: solid;
border-width: 5px 0 5px 5px;
border-left-color: #cccccc;
margin-top: 5px;
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
}
.dropdown-submenu.pull-left>.dropdown-menu {
left: -100%;
margin-left: 10px;
border-radius: 6px 0 6px 6px;
}
</style>
<script type="text/javascript">
// 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 the anchor link active (and if it's in a dropdown, also mark that active)
var dropdown = menuAnchor.closest('li.dropdown');
if (window.bootstrap) { // Bootstrap 4+
menuAnchor.addClass('active');
dropdown.find('> .dropdown-toggle').addClass('active');
} else { // Bootstrap 3
menuAnchor.parent().addClass('active');
dropdown.addClass('active');
}
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
<!-- tabsets -->
<style type="text/css">
.tabset-dropdown > .nav-tabs {
display: inline-table;
max-height: 500px;
min-height: 44px;
overflow-y: auto;
border: 1px solid #ddd;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "\e259";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "\e258";
font-family: 'Glyphicons Halflings';
border: none;
}
.tabset-dropdown > .nav-tabs > li.active {
display: block;
}
.tabset-dropdown > .nav-tabs > li > a,
.tabset-dropdown > .nav-tabs > li > a:focus,
.tabset-dropdown > .nav-tabs > li > a:hover {
border: none;
display: inline-block;
border-radius: 4px;
background-color: transparent;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
display: block;
float: none;
}
.tabset-dropdown > .nav-tabs > li {
display: none;
}
</style>
<!-- code folding -->
<style type="text/css">
.code-folding-btn { margin-bottom: 4px; }
</style>
<style type="text/css">
#TOC {
margin: 25px 0px 20px 0px;
}
@media (max-width: 768px) {
#TOC {
position: relative;
width: 100%;
}
}
@media print {
.toc-content {
/* see https://github.com/w3c/csswg-drafts/issues/4434 */
float: right;
}
}
.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;
}
.tocify .list-group-item {
border-radius: 0px;
}
.tocify-subheader {
display: inline;
}
.tocify-subheader .tocify-item {
font-size: 0.95em;
}
</style>
</head>
<body>
<div class="container-fluid main-container">
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row">
<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-bs-toggle="collapse" data-target="#navbar" data-bs-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">Intro2R</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="setup.html">
<span class="fa fa-cog"></span>
Setup
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-book"></span>
R Book
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="https://intro2r.com">
<span class="fa fa-firefox"></span>
Web book
</a>
</li>
<li class="divider"></li>
<li>
<a href="https://github.com/alexd106/Rbook/raw/master/docs/Rbook.pdf">
<span class="fa fa-file-pdf"></span>
PDF book
</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-university"></span>
Learn R
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="howto.html">
<span class="fa fa-tv"></span>
How-to
</a>
</li>
<li class="divider"></li>
<li>
<a href="lectures.html">
<span class="fa fa-chalkboard"></span>
Lectures
</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-file-contract"></span>
Exercises
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="exercises.html">
<span class="fa fa-folder"></span>
Excercises
</a>
</li>
<li class="divider"></li>
<li>
<a href="exercise_solutions.html">
<span class="fa fa-folder"></span>
Exercise solutions
</a>
</li>
</ul>
</li>
<li>
<a href="data.html">
<span class="fa fa-download"></span>
Data
</a>
</li>
<li>
<a href="Tutorials.html">
<span class="fa fa-desktop"></span>
Tutorials
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-question-circle"></span>
Info
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="syllabus.html">
<span class="fa fa-graduation-cap"></span>
Syllabus
</a>
</li>
<li class="divider"></li>
<li>
<a href="People.html">
<span class="fa fa-user-friends"></span>
People
</a>
</li>
<li class="divider"></li>
<li>
<a href="resources.html">
<span class="fa fa-book"></span>
Resources
</a>
</li>
<li>
<a href="https://forms.gle/U7MbyhRWyLomjyFY7">
<span class="fa fa-commenting"></span>
Feedback
</a>
</li>
<li class="divider"></li>
<li>
<a href="People.html">
<span class="fa fa-envelope fa-lg"></span>
Contact
</a>
</li>
<li>
<a href="https://github.com/alexd106/intro2R">
<span class="fa fa-github fa-lg"></span>
Source code
</a>
</li>
<li>
<a href="https://twitter.com/Scedacity">
<span class="fa fa-twitter fa-lg"></span>
Twitter
</a>
</li>
</ul>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div id="header">
<div class="btn-group pull-right float-right">
<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm dropdown-toggle" data-toggle="dropdown" data-bs-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span>Code</span> <span class="caret"></span></button>
<ul class="dropdown-menu dropdown-menu-right" style="min-width: 50px;">
<li><a id="rmd-show-all-code" href="#">Show All Code</a></li>
<li><a id="rmd-hide-all-code" href="#">Hide All Code</a></li>
</ul>
</div>
<h1 class="title toc-ignore">Introduction to R markdown</h1>
</div>
<p> </p>
<p>This short tutorial will introduce you to creating reproducible
reports using R markdown to encourage best (or better) practice to
facilitate open science. It will first describe what R markdown is and
why you might want to consider using it, describe how to create an R
markdown document using RStudio and then how to convert this document to
a html or pdf formatted report. During this tutorial you will learn
about the different components of an R markdown document, how to format
text, graphics and tables within the document and finally how to avoid
some of the common difficulties using R markdown. There are also a
couple of exercises for you to complete if you wish.</p>
<p>I estimate that this tutorial should take you roughly 1.5 to 2.5
hours to complete in one sitting, but feel free to dip in and out over a
longer period if that suits you better.</p>
<p> </p>
<div id="what-is-r-markdown" class="section level2">
<h2>What is R markdown?</h2>
<p> </p>
<p>R markdown is a simple and easy to use plain text language used to
combine your R code, results from your data analysis (including plots
and tables) and written commentary into a single nicely formatted and
reproducible document (like a report, publication, thesis chapter or a
web page like this one).</p>
<p>Technically, R markdown is a variant of another language (yet another
language!) called Markdown and both are a type of ‘markup’ language. A
markup language simply provides a way of creating an easy to read plain
text file which can incorporate formatted text, images, headers and
links to other documents. Don’t worry about the details for the moment,
although if you’re interested you can find more information about markup
languages <a
href="https://en.wikipedia.org/wiki/Markup_language">here</a>. Actually,
if it makes you feel any better all of you will have been exposed to a
markup language before, as most of the internet content you digest every
day is underpinned by a markup language called HTML
(<strong>H</strong>yper<strong>t</strong>ext <strong>M</strong>arkup
<strong>L</strong>anguage). Anyway, the main point is that R markdown is
very easy to learn (much, much easier than HTML) and when used with
RStudio it’s ridiculously easy to integrate into your workflow to
produce feature rich content (so why wouldn’t you?!).</p>
<p> </p>
</div>
<div id="why-use-r-markdown" class="section level2">
<h2>Why use R markdown?</h2>
<p> </p>
<p>During our previous R course we talked a lot about conducting your
research in a robust and reproducible manner to facilitate open science.
In a nutshell, open science is about doing all we can to make our data,
methods, results and inferences transparent and available to everyone.
Some of the main tenets of open science are described <a
href="http://openscience.org/what-exactly-is-open-science/">here</a> and
include:</p>
<p> </p>
<ul>
<li>Transparency in experimental methodology, observation, collection of
data and analytical methods.</li>
<li>Public availability and re-usability of scientific data</li>
<li>Public accessibility and transparency of scientific
communication</li>
<li>Using web-based tools to facilitate scientific collaboration</li>
</ul>
<p> </p>
<p>By now all of you will (hopefully) be using R to explore and analyse
your interesting data. As such, you’re already well along the road to
making your analysis more reproducible, transparent and shareable.
However, perhaps your current workflow looks something like this:</p>
<p> </p>
<p><img src="images/workflow1.png" width="90%" style="display: block; margin: auto;" /></p>
<p> </p>
<p>Your data is imported from your favourite spreadsheet software into
RStudio (or R), you write your R code to explore and analyse your data,
you save plots as external files, copy tables of analysis output and
then manually combine all of this and your written prose into a single
MS Word document (maybe a paper or thesis chapter). Whilst there is
nothing particularly wrong with this approach (and it’s certainly better
than using point and click software to analyse your data) there are some
limitations:</p>
<p> </p>
<ul>
<li><p>It’s not particularly reproducible. Because this workflow
separates your R code from the final document there are multiple
opportunities for undocumented decisions to be made (which plots did you
use? what analysis did/didn’t you include? etc).</p></li>
<li><p>It’s inefficient. If you need to go back and change something
(create a new plot or update your analysis etc) you will need to create
or amend multiple documents increasing the risk of mistakes creeping
into your workflow.</p></li>
<li><p>It’s difficult to maintain. If your analysis changes you again
need to update multiple files and documents.</p></li>
<li><p>It can be difficult to decide what to share with others. Do you
share all of your code (initial data exploration, model validation etc)
or just the code specific to your final document? It’s quite a common
(and bad!) practice for researchers to maintain two R scripts, one used
for the actual analysis and one to share with the final paper or thesis
chapter. This can be both time consuming and confusing and should be
avoided.</p></li>
</ul>
<p> </p>
<p>Perhaps a more efficient and robust workflow would look something
like this:</p>
<p> </p>
<p><img src="images/workflow2.png" width="90%" style="display: block; margin: auto;" /></p>
<p> </p>
<p>Your data is imported into RStudio (or R) as before but this time all
of the R code you used to analyse your data, produce your plots and your
written text (Introduction, Materials and Methods, Discussion etc) is
contained within a single R markdown document which is then used (along
with your data) to automatically create your final document. This is
exactly what R markdown allows you to do.</p>
<p> </p>
<p>Some of the advantages of using R markdown include:</p>
<p> </p>
<ul>
<li><p>Explicitly links your data with your R code and output creating a
fully reproducible workflow. <strong>ALL</strong> of the R code used to
explore, summarise and analyse your data can be included in a single
easy to read document. You can decide what to include in your final
document (as you will learn below) but all of your R code can be
included in the R markdown document.</p></li>
<li><p>You can create a wide variety of output formats (pdf, html web
pages, MS Word and many others) from a single R markdown document which
enhances both collaboration and communication.</p></li>
<li><p>Enhances transparency of your research. Your data and R markdown
file can be included with your publication or thesis chapter as
supplementary material or hosted on a GitHub repository (more about this
in future tutorial).</p></li>
<li><p>Increases the efficiency of your workflow. If you need to modify
or extend your current analysis you just need to update your R markdown
document and these changes will automatically be included in your final
document.</p></li>
</ul>
<p> </p>
</div>
<div id="getting-started-with-r-markdown" class="section level2">
<h2>Getting started with R markdown</h2>
<p> </p>
<p>This tutorial assumes that you have already installed the latest
versions of R and RStudio. If you haven’t done this yet you can find
instructions <a href="setup.html">here</a>. To use R markdown you will
first need to install the <code>rmarkdown</code> package in RStudio (or
in the R console if you’re not using RStudio) and any package
dependencies. You can find instructions on how to do this for both
Windows and Mac OSX operating systems <a
href="install_rmarkdown.html">here</a>. If you would like to create pdf
documents (or MS Word documents) from your R markdown file you will also
need to install a version of LaTeX on your computer. If you’ve not
installed LaTeX before, I recommend that you install <a
href="https://yihui.name/tinytex/">TinyTeX</a>. Again, instructions on
how to do this can be found <a
href="install_rmarkdown.html">here</a>.</p>
<p> </p>
</div>
<div id="new_rm" class="section level2">
<h2>Creating an R markdown document</h2>
<p> </p>
<p>Right, time to create your first R markdown document. Within RStudio,
click on the menu <code>File</code> -> <code>New File</code> ->
<code>R Markdown...</code>. In the pop up window, give the document a
‘Title’ and enter the ‘Author’ information (your name) and select HTML
as the default output. We can change all of this later so don’t worry
about it for the moment.</p>
<p> </p>
<p><img src="images/new_rm2.png" width="70%" style="display: block; margin: auto;" /></p>
<p> </p>
<p>You will notice that when your new R markdown document is created it
includes some example R markdown code. Normally you would just highlight
and delete everything in the document except the information at the top
between the <code>---</code> delimiters (this is called the YAML header
which we will discuss in a bit) and then start writing your own code.
However, just for now we will use this document to practice converting R
markdown to both html and pdf formats and check everything is
working.</p>
<p> </p>
<p><img src="images/new_file_rm.png" width="70%" style="display: block; margin: auto;" /></p>
<p> </p>
<p>Once you’ve created your R markdown document it’s good practice to
save this file somewhere convenient. You can do this by selecting
<code>File</code> -> <code>Save</code> from RStudio menu (or use the
keyboard shortcut ctrl + s on Windows or cmd + s on a Mac) and enter an
appropriate file name (maybe call it <code>my_first_rmarkdown</code>).
Notice the file extension of your new R markdown file is
<code>.Rmd</code>.</p>
<p>Now, to convert your <code>.Rmd</code> file to a HTML document click
on the little black triangle next to the <code>Knit</code> icon at the
top of the source window and select <code>knit to HTML</code></p>
<p> </p>
<p><img src="images/knit_rm.png" width="80%" style="display: block; margin: auto;" /></p>
<p> </p>
<p>RStudio will now ‘knit’ (or render) your <code>.Rmd</code> file into
a HTML file. Notice that there is a new <code>R Markdown</code> tab in
your console window which provides you with information on the rendering
process and will also display any errors if something goes wrong.</p>
<p> </p>
<p><img src="images/Rmarkdown_console.png" width="70%" style="display: block; margin: auto;" /></p>
<p> </p>
<p>If everything went smoothly a new HTML file will have been created
and saved in the same directory as your <code>.Rmd</code> file (ours
will be called <code>my_first_rmarkdown.html</code>). To view this
document simply double click on the file to open in a browser (like
Chrome or Firefox) to display the rendered content. RStudio will also
display a preview of the rendered file in a new window for you to check
out (your window might look slightly different if you’re using a Windows
computer).</p>
<p> </p>
<p><img src="images/html_rendered.png" width="70%" style="display: block; margin: auto;" /></p>
<p> </p>
<p>Great, you’ve just rendered your first R markdown document. If you
want to knit your <code>.Rmd</code> file to a pdf document then all you
need to do is choose <code>knit to PDF</code> instead of
<code>knit to HTML</code> when you click on the <code>knit</code> icon.
This will create a file called <code>my_first_rmarkdown.pdf</code> which
you can double click to open. Give it a go!</p>
<p> </p>
<p>You can also knit an <code>.Rmd</code> file using the command line in
the console rather than by clicking on the knit icon. To do this, just
use the <code>render()</code> function from the <code>rmarkdown</code>
package as shown below. Again, you can change the output format using
the <code>output_format=</code> argument as well as many other
options.</p>
<p> </p>
<div class="sourceCode" id="cb1"><pre
class="sourceCode r fold-show"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">library</span>(rmarkdown)</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="fu">render</span>(<span class="st">'my_first_rmarkdown.Rmd'</span>, <span class="at">output_format =</span> <span class="st">'html_document'</span>)</span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a></span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a><span class="co"># alternatively if you don't want to load the rmarkdown package</span></span>
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a></span>
<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a>rmarkdown<span class="sc">::</span><span class="fu">render</span>(<span class="st">'my_first_rmarkdown.Rmd'</span>, <span class="at">output_format =</span> <span class="st">'html_document'</span>)</span>
<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a></span>
<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a><span class="co"># see ?render for more options</span></span></code></pre></div>
<p> </p>
</div>
<div id="r-markdown-anatomy" class="section level2">
<h2>R markdown anatomy</h2>
<p> </p>
<p>OK, now that you can render an R markdown file in RStudio into both
HTML and pdf formats let’s take a closer look at the different
components of a typical R markdown document. Normally each R markdown
document is composed of 3 main components, 1) a YAML header, 2)
formatted text and 3) one or more code chunks. </p>
<p><img src="images/rm_components.png" width="80%" style="display: block; margin: auto auto auto 0;" /></p>
<p> </p>
<div id="yaml-header" class="section level3">
<h3>YAML header</h3>
<p>YAML stands for ‘<strong>Y</strong>AML <strong>A</strong>in’t
<strong>M</strong>arkup <strong>L</strong>anguage’ (it’s an ‘in’ <a
href="https://en.wikipedia.org/wiki/Recursive_acronym">joke</a>!) and
this optional component contains the metadata and options for the entire
document such as the author name, date, output format, etc. The YAML
header is surrounded before and after by a <code>---</code> on its own
line. In RStudio a minimal YAML header is automatically created for you
when you create a new R markdown document as we did <a
href="#new_rm">above</a> but you can change this any time. A simple YAML
header may look something like this:</p>
<p> </p>
<div class="sourceCode" id="cb2"><pre
class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a></span>
<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="pp">---</span></span>
<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a><span class="fu">title</span><span class="kw">:</span><span class="at"> My first R markdown document</span></span>
<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a><span class="fu">author</span><span class="kw">:</span><span class="at"> Jane Doe</span></span>
<span id="cb2-5"><a href="#cb2-5" tabindex="-1"></a><span class="fu">date</span><span class="kw">:</span><span class="at"> March 01, 2020</span></span>
<span id="cb2-6"><a href="#cb2-6" tabindex="-1"></a><span class="fu">output</span><span class="kw">:</span><span class="at"> html_document</span></span>
<span id="cb2-7"><a href="#cb2-7" tabindex="-1"></a><span class="pp">---</span></span>
<span id="cb2-8"><a href="#cb2-8" tabindex="-1"></a><span class="at"> </span></span></code></pre></div>
<p> </p>
<p>In the YAML header above the output format is set to HTML. If you
would like to change the output to pdf format then you can change it
from <code>output: html_document</code> to
<code>output: pdf_document</code> (you can also set more than one output
format if you like). You can also change the default font and font size
for the whole document and even include fancy options such as a table of
contents and inline references and a bibliography. If you want to
explore the plethora of other options see <a
href="https://bookdown.org/yihui/rmarkdown/html-document.html">here</a>.
Just a note of caution, many of the options you can specify in the YAML
header will work with both HTML and pdf formatted documents, but not
all. If you need multiple output formats for your R markdown document
check whether your YAML options are compatible between these formats.
Also, indentation in the YAML header has a meaning to be careful when
aligning text. For example, if you want to include a table of contents
you would modify the <code>output:</code> field in the YAML header as
follows</p>
<p> </p>
<div class="sourceCode" id="cb3"><pre
class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a></span>
<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a><span class="pp">---</span></span>
<span id="cb3-3"><a href="#cb3-3" tabindex="-1"></a><span class="fu">title</span><span class="kw">:</span><span class="at"> My first R markdown document</span></span>
<span id="cb3-4"><a href="#cb3-4" tabindex="-1"></a><span class="fu">author</span><span class="kw">:</span><span class="at"> Jane Doe</span></span>
<span id="cb3-5"><a href="#cb3-5" tabindex="-1"></a><span class="fu">date</span><span class="kw">:</span><span class="at"> March 01, 2020</span></span>
<span id="cb3-6"><a href="#cb3-6" tabindex="-1"></a><span class="fu">output</span><span class="kw">:</span></span>
<span id="cb3-7"><a href="#cb3-7" tabindex="-1"></a><span class="at"> </span><span class="fu">html_document</span><span class="kw">:</span></span>
<span id="cb3-8"><a href="#cb3-8" tabindex="-1"></a><span class="at"> </span><span class="fu">toc</span><span class="kw">:</span><span class="at"> </span><span class="ch">yes</span></span>
<span id="cb3-9"><a href="#cb3-9" tabindex="-1"></a><span class="pp">---</span></span>
<span id="cb3-10"><a href="#cb3-10" tabindex="-1"></a><span class="at"> </span></span></code></pre></div>
<p> </p>
</div>
<div id="formatted-text" class="section level3">
<h3>Formatted text</h3>
<p>As mentioned above, one of the great things about R markdown is that
you don’t need to rely on your word processor to bring your R code,
analysis and writing together. R markdown is able to render (almost) all
of the text formatting that you are likely to need such as italics,
bold, strike-through, super and subscript as well as bulleted and
numbered lists, headers and footers, images, links to other documents or
web pages and also equations. However, in contrast to your familiar
<em>What-You-See-Is-What-You-Get</em> (<a
href="https://en.wikipedia.org/wiki/WYSIWYG">WYSIWYG</a>) word
processing software you don’t see the final formatted text in your R
markdown document (as you would in MS Word), rather you need to ‘markup’
the formatting in your text ready to be rendered in your output
document. At first, this might seem like a right pain in the proverbial
but it’s actually very easy to do and also has many <a
href="https://dev.to/practicalprogramming/advantages-of-document-markup-languages-vs-wysiwyg-editors-9f6">advantages</a>
(do you find yourself spending more time on making your text look pretty
in MS Word rather than writing good content?!).</p>
<p>Here is an example of marking up text formatting in an R markdown
document</p>
<p> </p>
<div class="sourceCode" id="cb4"><pre
class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a></span>
<span id="cb4-2"><a href="#cb4-2" tabindex="-1"></a><span class="fu">#### Benthic Biodiversity experiment</span></span>
<span id="cb4-3"><a href="#cb4-3" tabindex="-1"></a>These data were obtained from a mesocosm experiment which aimed to examine the effect </span>
<span id="cb4-4"><a href="#cb4-4" tabindex="-1"></a>of benthic polychaete (*Nereis diversicolor*) biomass on sediment nutrient </span>
<span id="cb4-5"><a href="#cb4-5" tabindex="-1"></a>(NH~4~, NO~3~ and PO~3~) release. At the start of the experiment 15 replicate mesocosms </span>
<span id="cb4-6"><a href="#cb4-6" tabindex="-1"></a>were filled with 20 cm^2^ of **homogenised** marine sediment and assigned to one of five </span>
<span id="cb4-7"><a href="#cb4-7" tabindex="-1"></a>polychaete biomass treatments (0, 0.5, 1, 1.5, 2 g per mesocosm).</span></code></pre></div>
<p> </p>
<p>which would look like this in the final rendered document (can you
spot the markups?)</p>
<p> </p>
<blockquote>
<p style="font-weight:400; font-size:20px">
Benthic Biodiversity experiment.
</p>
<p>These data were obtained from a mesocosm experiment which aimed to
examine the effect of benthic polychaete (<em>Nereis diversicolor</em>)
biomass on sediment nutrient (NH<sub>4</sub>, NO<sub>3</sub> and
PO<sub>3</sub>) release. At the start of the experiment replicate
mesocosms were filled with 20 cm<sup>2</sup> of
<strong>homogenised</strong> marine sediment and assigned to one of five
polychaete biomass treatments (0, 0.5, 1, 1.5, 2 g per mesocosm).</p>
</blockquote>
<p> </p>
<div id="emphasis" class="section level4">
<h4>Emphasis</h4>
<p>Some of the most common R markdown syntax for providing emphasis and
formatting text is given below.</p>
<p> </p>
<table>
<thead>
<tr class="header">
<th align="center">Goal</th>
<th align="center">R markdown</th>
<th align="center">output</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">bold text</td>
<td align="center"><code>**mytext**</code></td>
<td align="center"><strong>mytext</strong></td>
</tr>
<tr class="even">
<td align="center">italic text</td>
<td align="center"><code>*mytext*</code></td>
<td align="center"><em>mytext</em></td>
</tr>
<tr class="odd">
<td align="center">strikethrough</td>
<td align="center"><code>~~mytext~~</code></td>
<td align="center"><del>mytext</del></td>