forked from UNM-CARC/QuickBytes
-
Notifications
You must be signed in to change notification settings - Fork 0
/
R.html
415 lines (335 loc) · 11.8 KB
/
R.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
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
<title>R_usage</title>
<style type="text/css">
body {
font-family: Helvetica, arial, sans-serif;
font-size: 14px;
line-height: 1.6;
padding-top: 10px;
padding-bottom: 10px;
background-color: white;
padding: 30px; }
body > *:first-child {
margin-top: 0 !important; }
body > *:last-child {
margin-bottom: 0 !important; }
a {
color: #4183C4; }
a.absent {
color: #cc0000; }
a.anchor {
display: block;
padding-left: 30px;
margin-left: -30px;
cursor: pointer;
position: absolute;
top: 0;
left: 0;
bottom: 0; }
h1, h2, h3, h4, h5, h6 {
margin: 20px 0 10px;
padding: 0;
font-weight: bold;
-webkit-font-smoothing: antialiased;
cursor: text;
position: relative; }
h1:hover a.anchor, h2:hover a.anchor, h3:hover a.anchor, h4:hover a.anchor, h5:hover a.anchor, h6:hover a.anchor {
background: url(data:image/png;base64,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) no-repeat 10px center;
text-decoration: none; }
h1 tt, h1 code {
font-size: inherit; }
h2 tt, h2 code {
font-size: inherit; }
h3 tt, h3 code {
font-size: inherit; }
h4 tt, h4 code {
font-size: inherit; }
h5 tt, h5 code {
font-size: inherit; }
h6 tt, h6 code {
font-size: inherit; }
h1 {
font-size: 28px;
color: black; }
h2 {
font-size: 24px;
border-bottom: 1px solid #cccccc;
color: black; }
h3 {
font-size: 18px; }
h4 {
font-size: 16px; }
h5 {
font-size: 14px; }
h6 {
color: #777777;
font-size: 14px; }
p, blockquote, ul, ol, dl, li, table, pre {
margin: 15px 0; }
hr {
background: transparent url(data:image/png;base64,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) repeat-x 0 0;
border: 0 none;
color: #cccccc;
height: 4px;
padding: 0;
}
body > h2:first-child {
margin-top: 0;
padding-top: 0; }
body > h1:first-child {
margin-top: 0;
padding-top: 0; }
body > h1:first-child + h2 {
margin-top: 0;
padding-top: 0; }
body > h3:first-child, body > h4:first-child, body > h5:first-child, body > h6:first-child {
margin-top: 0;
padding-top: 0; }
a:first-child h1, a:first-child h2, a:first-child h3, a:first-child h4, a:first-child h5, a:first-child h6 {
margin-top: 0;
padding-top: 0; }
h1 p, h2 p, h3 p, h4 p, h5 p, h6 p {
margin-top: 0; }
li p.first {
display: inline-block; }
li {
margin: 0; }
ul, ol {
padding-left: 30px; }
ul :first-child, ol :first-child {
margin-top: 0; }
dl {
padding: 0; }
dl dt {
font-size: 14px;
font-weight: bold;
font-style: italic;
padding: 0;
margin: 15px 0 5px; }
dl dt:first-child {
padding: 0; }
dl dt > :first-child {
margin-top: 0; }
dl dt > :last-child {
margin-bottom: 0; }
dl dd {
margin: 0 0 15px;
padding: 0 15px; }
dl dd > :first-child {
margin-top: 0; }
dl dd > :last-child {
margin-bottom: 0; }
blockquote {
border-left: 4px solid #dddddd;
padding: 0 15px;
color: #777777; }
blockquote > :first-child {
margin-top: 0; }
blockquote > :last-child {
margin-bottom: 0; }
table {
padding: 0;border-collapse: collapse; }
table tr {
border-top: 1px solid #cccccc;
background-color: white;
margin: 0;
padding: 0; }
table tr:nth-child(2n) {
background-color: #f8f8f8; }
table tr th {
font-weight: bold;
border: 1px solid #cccccc;
margin: 0;
padding: 6px 13px; }
table tr td {
border: 1px solid #cccccc;
margin: 0;
padding: 6px 13px; }
table tr th :first-child, table tr td :first-child {
margin-top: 0; }
table tr th :last-child, table tr td :last-child {
margin-bottom: 0; }
img {
max-width: 100%; }
span.frame {
display: block;
overflow: hidden; }
span.frame > span {
border: 1px solid #dddddd;
display: block;
float: left;
overflow: hidden;
margin: 13px 0 0;
padding: 7px;
width: auto; }
span.frame span img {
display: block;
float: left; }
span.frame span span {
clear: both;
color: #333333;
display: block;
padding: 5px 0 0; }
span.align-center {
display: block;
overflow: hidden;
clear: both; }
span.align-center > span {
display: block;
overflow: hidden;
margin: 13px auto 0;
text-align: center; }
span.align-center span img {
margin: 0 auto;
text-align: center; }
span.align-right {
display: block;
overflow: hidden;
clear: both; }
span.align-right > span {
display: block;
overflow: hidden;
margin: 13px 0 0;
text-align: right; }
span.align-right span img {
margin: 0;
text-align: right; }
span.float-left {
display: block;
margin-right: 13px;
overflow: hidden;
float: left; }
span.float-left span {
margin: 13px 0 0; }
span.float-right {
display: block;
margin-left: 13px;
overflow: hidden;
float: right; }
span.float-right > span {
display: block;
overflow: hidden;
margin: 13px auto 0;
text-align: right; }
code, tt {
margin: 0 2px;
padding: 0 5px;
white-space: nowrap;
border: 1px solid #eaeaea;
background-color: #f8f8f8;
border-radius: 3px; }
pre code {
margin: 0;
padding: 0;
white-space: pre;
border: none;
background: transparent; }
.highlight pre {
background-color: #f8f8f8;
border: 1px solid #cccccc;
font-size: 13px;
line-height: 19px;
overflow: auto;
padding: 6px 10px;
border-radius: 3px; }
pre {
background-color: #f8f8f8;
border: 1px solid #cccccc;
font-size: 13px;
line-height: 19px;
overflow: auto;
padding: 6px 10px;
border-radius: 3px; }
pre code, pre tt {
background-color: transparent;
border: none; }
sup {
font-size: 0.83em;
vertical-align: super;
line-height: 0;
}
kbd {
display: inline-block;
padding: 3px 5px;
font-size: 11px;
line-height: 10px;
color: #555;
vertical-align: middle;
background-color: #fcfcfc;
border: solid 1px #ccc;
border-bottom-color: #bbb;
border-radius: 3px;
box-shadow: inset 0 -1px 0 #bbb
}
* {
-webkit-print-color-adjust: exact;
}
@media screen and (min-width: 914px) {
body {
width: 854px;
margin:0 auto;
}
}
@media print {
table, pre {
page-break-inside: avoid;
}
pre {
word-wrap: break-word;
}
}
</style>
</head>
<body>
<h1 id="toc_0">R Programming in HPC</h1>
<h2 id="toc_1">What is R?</h2>
<p>R is a programming language and a software environment for statistical computing and graphics techniques. This is widely used now a days by statisticians and data miners for developing software tools required for data analysis. The R language is primarily derived from the S language developed at Bell Laboratories in 1975. R provides various tools and techniques for linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering etc. More history and documentation of R are available at this <a href="https://cran.r-project.org/manuals.html">link</a></p>
<h2 id="toc_2">How to run R?</h2>
<p>First login to one of the CARC machines via SSH.</p>
<p><code>ssh -X user@machine_name.alliance.unm.edu</code></p>
<p>Once logged into the machine, you have to load the module which has R program files. </p>
<p><code>module load r-3.5.0-gcc-4.8.5-python2-khqxja7</code></p>
<p>After loading the R module, begin R programming by typing</p>
<p><code>R</code></p>
<p>This will shows</p>
<div><pre><code class="language-bash">
R version 3.5.0 (2018-04-23) -- "Joy in Playing"
Copyright (C) 2018 The R Foundation for Statistical
Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
</code></pre></div>
<p>This means the R module is loaded and you are ready to use R for your research</p>
<h2 id="toc_3">Running a sample script example.R</h2>
<p>Let us look a sample script, example.R which will print "Hello World"
The script looks like </p>
<div><pre><code class="language-bash"># Program to print Hello World
print('Hello World')</code></pre></div>
<p>In order to execute this script, type</p>
<p><code>Rscript example.R</code></p>
<p>This will give an output of</p>
<p><code>[1] "Hello World"</code></p>
<p>If you want to generate samples from a normal distribution, you can use the <code>rnorm()</code> function. Let's make some change to the example.R script. </p>
<div><pre><code class="language-bash"># Program to print Hello World and to generate normal random numbers
print('Hello World')
#Calling the rnorm() function to generate three random numbers from a
normal distribution with mean 5 and a standard deviation of 5
rnorm(3,mean=5,sd=5)</code></pre></div>
<p>Execute the script again and the look at the new output.</p>
<div><pre><code class="language-bash">[1] "Hello World"
[1] 3.744463 7.954163 3.363275</code></pre></div>
</body>
</html>