forked from RVerse-Tutorials/RWorkflow-NWFSC-2021
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathweek6-more-packages.html
674 lines (575 loc) · 24.8 KB
/
week6-more-packages.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
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<title>Week 6: Advanced package topics</title>
<script src="site_libs/header-attrs-2.9/header-attrs.js"></script>
<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/readable.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>
<link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.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" />
<link rel="shortcut icon" href="favicon.ico" type="image/x-icon">
<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;}</style>
<script type="text/javascript">
if (window.hljs) {
hljs.configure({languages: []});
hljs.initHighlightingOnLoad();
if (document.readyState && document.readyState === "complete") {
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
}
}
</script>
<link rel="stylesheet" href="styles.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;
}
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 it active
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.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 {
content: "";
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: "";
border: none;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.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">
#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-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">RWorkflow</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="set-up.html">
<span class="fa fa-clone"></span>
Set-up
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-calendar"></span>
Workshop Weekly Notes
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="week1.html">
<span class="fa fa-cogs"></span>
Week 1 RStudio + Version Control
</a>
</li>
<li>
<a href="week2.html">
<span class="fa fa-gitalt"></span>
Week 2 More Git/GitHub
</a>
</li>
<li>
<a href="week3.html">
<span class="fab fa-github"></span>
Week 3 GitHub
</a>
</li>
</ul>
</li>
<li>
<a href="https://rverse-tutorials.github.io/RWorkflow/">
<span class="fa fa-folder"></span>
Archive
</a>
</li>
<li>
<a href="https://rverse-tutorials.github.io/RWorkflow-NWFSC-2020">
<span class="fa fa-clock"></span>
2020 website
</a>
</li>
<li>
<a href="links.html">
<span class="fa fa-info"></span>
More resources
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/RVerse-Tutorials/RWorkflow-NWFSC-2021">
<span class="fab fa-github"></span>
Repo
</a>
</li>
<li>
<a href="https://github.com/orgs/RWorkflow-Workshop-2021">Org</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div id="header">
<h1 class="title toc-ignore">Week 6: Advanced package topics</h1>
</div>
<table class="table" style="margin-left: auto; margin-right: auto;">
<tbody>
<tr>
<td style="text-align:left;color: white !important;background-color: blue !important;width: 20%; ">
Compartmentalized
</td>
<td style="text-align:left;color: white !important;background-color: blue !important;width: 20%; ">
Documented
</td>
<td style="text-align:left;color: white !important;background-color: blue !important;width: 20%; ">
Extendible
</td>
<td style="text-align:left;color: white !important;background-color: blue !important;width: 20%; ">
Reproducible
</td>
<td style="text-align:left;color: white !important;background-color: blue !important;width: 20%; ">
Robust
</td>
</tr>
</tbody>
</table>
<p>This week I will cover more advanced topics regarding R packages:</p>
<ul>
<li>How to use the “check” feature to find problems in your package.</li>
<li>How to write a vignette for your package.</li>
<li>How to write print and plot functions for your objects.</li>
<li>Using pkgdown to make a website for your package.</li>
</ul>
<p>If/when you want to go into R packaging in more depth, work through the material from this <a href="https://combine-australia.github.io/r-pkg-dev/">R package workshop material</a>. You’ve seen much of this material so it should be somewhat familiar. See also Hadley Wickham’s book <a href="http://r-pkgs.had.co.nz/">R Packages</a>.</p>
<p>The repository that I used to demo these features is here: <a href="https://github.com/eeholmes/MyNewPackage" class="uri">https://github.com/eeholmes/MyNewPackage</a></p>
<div id="checking-your-package" class="section level2">
<h2>Checking your package</h2>
<p>Just use the RStudio Check in the Build tab. You’ll have many issues (most likely). Plug away at each one until you pass with no errors or warnings. Don’t ignore Notes either. They are sometimes more serious than the errors and warnings.</p>
<p>If R asks you to update packages, and then proceeds to fail at installation because of a warning that a package was built under a later R version than you have on your computer, use</p>
<pre><code>Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS=TRUE)</code></pre>
</div>
<div id="creating-print-and-plot-methods-for-your-objects" class="section level2">
<h2>Creating print and plot methods for your objects</h2>
<div id="make-your-output-an-object" class="section level3">
<h3>Make your output an object</h3>
<pre><code>littleforecast <- function(data, nyears=10){
fit <- forecast::auto.arima(data)
fc <- forecast::forecast(fit, h = nyears)
ggplot2::autoplot(fc)
class(fit) <- c("foo", class(fit))
return(fit)
}</code></pre>
</div>
<div id="print-method" class="section level3">
<h3>print method</h3>
<pre><code>#' Prints foo object
#'
#' prints a foo object returned from littlefunction().
#'
#' @param x foo object
#' @param ... Not used
#' @method print foo
#' @export
print.foo <- function(x, ...) {
cat("Hello there")
}</code></pre>
</div>
<div id="plot-method" class="section level3">
<h3>plot method</h3>
<pre><code>#' Plots foo object
#'
#' Plots foo object.
#'
#' @param x An foo object.
#' @param ... Not used.
#' @method plot foo
#' @export
plot.foo <- function(x, ...) {
plot(1:10)
}</code></pre>
<p>Note, <code>plot()</code> is part of the graphics package so you need to add that to Imports in your DESCRIPTION file. Our Imports line is now:</p>
<pre><code>Imports: forecast, graphics</code></pre>
</div>
<div id="add-your-methods-to-your-namespace" class="section level3">
<h3>Add your methods to your namespace</h3>
<pre><code>S3method(print,foo)
S3method(plot,foo)</code></pre>
</div>
<div id="example" class="section level3">
<h3>Example</h3>
<p>Install and restart MyNewPackage.</p>
<pre><code>fit=littleforecast(WWW2)
fit
plot(fit)</code></pre>
</div>
</div>
<div id="writing-a-vignette" class="section level2">
<h2>Writing a vignette</h2>
<p>Doing this in RStudio is easy. See <a href="https://bookdown.org/yihui/rmarkdown-cookbook/package-vignette.html">rmarkdown vignette chapter</a> and <a href="http://r-pkgs.had.co.nz/vignettes.html">Hadley’s vignette chapter</a> for more info.</p>
<div id="making-the-vignette" class="section level3">
<h3>Making the vignette</h3>
<p>Manually</p>
<ul>
<li>Make a vignettes folder at the base level (same level as the R folder)</li>
<li>Create a new vignette file from a template. RStudio > File > New > R Markdown > From Template > Vignette</li>
<li>Save in vignettes folder</li>
<li>Change the title in the 2 places in the yaml at the top. ‘yaml’ is between the <code>---</code> fences.</li>
<li>Add the following 2 lines to your DESCRIPTION file:</li>
</ul>
<pre><code>Suggests: knitr, rmarkdown
VignetteBuilder: knitr</code></pre>
<p>Or use a helper function:</p>
<pre><code>devtools::use_vignette("my-vignette")</code></pre>
<p>or</p>
<pre><code>usethis::use_vignette("MyNewPackage")</code></pre>
</div>
<div id="testing-your-vignette" class="section level3">
<h3>Testing your vignette</h3>
<p>Open your vignette file and click the Knit button.</p>
</div>
<div id="getting-your-vignette-to-show-up" class="section level3">
<h3>Getting your vignette to show up</h3>
<p>Once you have your vignettes in the <code>vignettes</code> folder, you’l like to be able to build them and have them appear when you type <code>browseVignettes("MyNewPackage")</code>. This will not work. In fact, RStudio seems to actively hinders this workflow.</p>
<p>Vignettes can take a long time to build and by default when R builds a package from source (which is what Install and Restart on the build tab does), it does not re-make your vignettes. You can make RStudio re-make your vignettes in the <code>vignettes</code> folder (if the Rmd file changes) using Tools > Project Options > Build Tools > Generate documentation with Roxygen > Configure and clicking the vignettes check-box. But this will not get your vignettes loaded when you click Install and Restart on the Build tab (<code>browseVignettes()</code> still won’t work).</p>
<p>So how does R know about your vignettes when it is building from source (i.e. from Install and Restart in the Build tab in RStudio)? It needs the vignette files (.Rmd, .R and .html) in the <code>inst/doc</code> folder. How do you get them there? You have to put them there.</p>
<p>That’s easy. I’ll just put them there whenever I change or add vignettes. Unfortunately, the default RStudio default behavior is to delete the whole <code>inst/doc</code> folder whenever you click Check (package) in the Build tab. It’s happening because the default is to use <code>devtools::check()</code> and there is no way to set <code>devtools::check(vignettes=FALSE)</code>. To stop RStudio from deleting <code>inst/doc</code> on package checking, uncheck the <code>use devtools package functions if available</code> box. You may also want to add <code>--no-manual</code> to the R CMD Check options box since that is the default for <code>devtools::check()</code>.</p>
<p>This is my vignette workflow:</p>
<ul>
<li>Create the <code>vignette</code> folder and add vignette Rmds to it using the R Markdown vignette template in RStudio.</li>
<li>Create the <code>inst</code> folder in my package at the base level (same level as the R folder).</li>
<li>Edit my vignette Rmd and use the Knit button to preview.</li>
<li>When I am done, run the following code to update the vignette files and copy to the <code>inst/doc</code> folder.</li>
</ul>
<pre><code>tools::buildVignettes(dir = ".", tangle=TRUE)
dir.create("inst/doc")
file.copy(dir("vignettes", full.names=TRUE), "inst/doc", overwrite=TRUE)</code></pre>
<p>Once your vignette files are in <code>inst/doc</code>, Install and Restart button will add the vignettes to your package and <code>install_github()</code> will have them too.</p>
<p><strong>Careful, RStudio <code>Check</code> in the Build tab will delete the <code>inst/doc</code> folder and not recreate it.</strong> So always check that <code>inst/doc</code> not been trashed and <strong>uncheck</strong> the <code>use devtools package functions</code> checkbox on the Build > More > Configure Build Tools… window. You will most likely also want to add <code>--no-manual</code> to the <code>R CMD check additional options</code> box.</p>
</div>
</div>
<div id="pkgdown" class="section level2">
<h2><strong>pkgdown</strong></h2>
<p><a href="https://pkgdown.r-lib.org/articles/pkgdown.html">pkgdown</a> makes it easy to make nice webpages for your packages.</p>
</div>
<div id="depends-versus-imports" class="section level2">
<h2>Depends versus Imports</h2>
<p><strong><span class="citation">@Depends</span></strong> These packages that will be loaded when your package is loaded. So if you have <strong>gplot2</strong> in <span class="citation">@Depends</span>, like above, then the user automatically can use <strong>ggplot2</strong> functions without issuing the command <code>library(ggplot2)</code>.</p>
<p><strong><span class="citation">@Imports</span></strong> Are required for the package functions, but the user will not have access to the functions without calling <code>library(...)</code>. In your package, you will use <code>::</code> to access the functions from the packages on the <span class="citation">@Imports</span> line. <em>Most of your package dependencies will be here.</em></p>
<p>To limit the number of headaches that users face when trying to install your package, use as few packages on your <span class="citation">@Depends</span> and <span class="citation">@Imports</span> lines in DESCRIPTION file as possible. If your package does not need the package to work, then put the package on <span class="citation">@Suggests</span>.</p>
<p>I have R packages that are mainly for my personal use. I use the package to make sure I have access to the various packages that I’ll be using. So for example, if I am doing work on my sardine papers, I have set of packages that I use. When I issue the command <code>library(SardineForecast)</code> a bunch of packages are loaded. This makes it handy for me, but all those dependencies makes it a huge hassle to install the package from GitHub for my collaborators (and even a hassle for me to install from GitHub). Huge Hassle. Invariable one of the 15 packages that I need will itself have a dependency that won’t load and then I have to debug that. If I need collaborators, who are on different operating systems and various versions of R to install it, it’s a suffer-fest.</p>
<p>For my MARSS package, I have only 3 non-base dependencies in the <span class="citation">@Imports</span> line and nothing on the <span class="citation">@Depends</span> line besides R. The imports are KFAS, mvtnorm, and nlme. Then on the <span class="citation">@Suggests</span> line, I have a bunch of packages that are used in the vignettes. MARSS is easy to install from GitHub (though it is also hosted on CRAN).</p>
<p><strong>What should you put on your Depends and Imports lines?</strong></p>
<p>First off, when you are starting, don’t worry too much about this. Just add packages that are needed as you work on your functions.</p>
<ul>
<li><p>ALWAYS use <code>::</code> to use functions from other packages in your package functions. Seriously. You will save yourself so many headaches down the road by being able to search for <code>xyzpackage::</code> to find all that packages functions. Why? Trust me, one day you will want to swap out packages or remove dependencies. Note, this can be a hassle with functions like <code>ggplot()</code> which use functions within their calls and you have to use <code>::</code> everywhere. Like so</p>
<pre class="r"><code>ggplot2::ggplot(df) +
ggplot2::geom_point(ggplot2::aes(gp, y))</code></pre>
<p>Arg. Another example is say a GAM call:</p>
<pre class="r"><code>mgcv::gam(a ~ mgcv::s(b), data=df)</code></pre>
<p>But this is just for your package functions. In your scripts, you’d probably use a <code>library()</code> call.</p></li>
<li><p>Never ever use <code>library()</code> in a function! Use <code>xyzfunction::function</code>. Sure use <code>library()</code> in your scripts, but never in a package function. When you add a function from a new package to your function, add those packages to <span class="citation">@Depends</span> or <span class="citation">@Imports</span> in your DESCRIPTION file as you go along.</p></li>
<li><p>Every so often check that you don’t have packages on <span class="citation">@Depends</span> and <span class="citation">@Imports</span> that you don’t use. Just do a Edit > Find in Files… search for <code>xyzpackage::</code> to find out if you are still using <code>xyzpackage</code>.</p></li>
<li><p>How do you know if you forgot a dependency or forgot a <code>::</code> somewhere? Two ways:</p>
<ol style="list-style-type: decimal">
<li>Do Session > Restart R to close all your loaded packages. Then load your package with <code>library(yourpackagename)</code> and try your functions. Things will fail if you have a package in <span class="citation">@Imports</span> but forgot a <code>::</code> somewhere.</li>
<li>From the Build tab, use More > Check Package. That should show package dependency errors (plus a whole slew of other problems for you to work through).</li>
</ol></li>
</ul>
</div>
<div id="styling-your-code" class="section level2">
<h2>Styling your code</h2>
<p>You should stick with a uniform style guide to make your code easier to follow. I use the tidyverse style guide with the <a href="https://www.tidyverse.org/blog/2017/12/styler-1.0.0/"><strong>styler</strong> R package</a>. <strong>styler</strong> has an RStudio Addin which does all the work of styling my code for me. Install the package, restart RStudio, and then go to Tools > Addins > Browse Addins. Scroll down to styler, and select the file(s), you want to style.</p>
</div>
<div id="byte-compile" class="section level2">
<h2>Byte Compile</h2>
<p>Adding this line to your DESCRIPTION file can really speed up your code. This is one of the advantages of putting your functions in a package. It can actually make your functions faster.</p>
<pre><code>ByteCompile: TRUE</code></pre>
</div>
<hr>
<div style="text-align: center">
<i class="fas fa-cubes"></i> NWFSC Math Bio Program <i class="fas fa-cubes"></i>
</div>
</div>
</div>
</div>
<script>
// add bootstrap table styles to pandoc tables
function bootstrapStylePandocTables() {
$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
}
$(document).ready(function () {
bootstrapStylePandocTables();
});
</script>
<!-- tabsets -->
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
<!-- code folding -->
<script>
$(document).ready(function () {
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
$('.unlisted.unnumbered').addClass('toc-ignore')
// 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",
theme: "bootstrap3",
context: '.toc-content',
hashGenerator: function (text) {
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
},
ignoreSelector: ".toc-ignore",
scrollTo: 0
};
options.showAndHide = false;
options.smoothScroll = true;
// tocify
var toc = $("#TOC").tocify(options).data("toc-tocify");
});
</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>