-
Notifications
You must be signed in to change notification settings - Fork 0
/
cheatsheet.html
688 lines (658 loc) · 29.8 KB
/
cheatsheet.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
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.555">
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
<meta name="author" content="M. Rolland">
<meta name="dcterms.date" content="2024-06-08">
<title>Reproducible Research in R (and friends)</title>
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
div.columns{display: flex; gap: min(4vw, 1.5em);}
div.column{flex: auto; overflow-x: auto;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
ul.task-list li input[type="checkbox"] {
width: 0.8em;
margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */
vertical-align: middle;
}
/* CSS for citations */
div.csl-bib-body { }
div.csl-entry {
clear: both;
margin-bottom: 0em;
}
.hanging-indent div.csl-entry {
margin-left:2em;
text-indent:-2em;
}
div.csl-left-margin {
min-width:2em;
float:left;
}
div.csl-right-inline {
margin-left:2em;
padding-left:1em;
}
div.csl-indent {
margin-left: 2em;
}</style>
<script src="cheatsheet_files/libs/clipboard/clipboard.min.js"></script>
<script src="cheatsheet_files/libs/quarto-html/quarto.js"></script>
<script src="cheatsheet_files/libs/quarto-html/popper.min.js"></script>
<script src="cheatsheet_files/libs/quarto-html/tippy.umd.min.js"></script>
<script src="cheatsheet_files/libs/quarto-html/anchor.min.js"></script>
<link href="cheatsheet_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="cheatsheet_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
<script src="cheatsheet_files/libs/bootstrap/bootstrap.min.js"></script>
<link href="cheatsheet_files/libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
<link href="cheatsheet_files/libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light">
</head>
<body>
<div id="quarto-content" class="page-columns page-rows-contents page-layout-article">
<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
<nav id="TOC" role="doc-toc" class="toc-active">
<h2 id="toc-title">Table of contents</h2>
<ul>
<li><a href="#project-organization" id="toc-project-organization" class="nav-link active" data-scroll-target="#project-organization"><span class="header-section-number">1</span> Project Organization</a></li>
<li><a href="#version-control" id="toc-version-control" class="nav-link" data-scroll-target="#version-control"><span class="header-section-number">2</span> Version Control</a></li>
<li><a href="#data-management" id="toc-data-management" class="nav-link" data-scroll-target="#data-management"><span class="header-section-number">3</span> Data Management</a></li>
<li><a href="#documentation" id="toc-documentation" class="nav-link" data-scroll-target="#documentation"><span class="header-section-number">4</span> Documentation</a></li>
<li><a href="#environment-management" id="toc-environment-management" class="nav-link" data-scroll-target="#environment-management"><span class="header-section-number">5</span> Environment Management</a></li>
<li><a href="#workflow-automation" id="toc-workflow-automation" class="nav-link" data-scroll-target="#workflow-automation"><span class="header-section-number">6</span> Workflow Automation</a></li>
<li><a href="#analysis-scripts" id="toc-analysis-scripts" class="nav-link" data-scroll-target="#analysis-scripts"><span class="header-section-number">7</span> Analysis Scripts</a></li>
<li><a href="#computational-reproducibility" id="toc-computational-reproducibility" class="nav-link" data-scroll-target="#computational-reproducibility"><span class="header-section-number">8</span> Computational reproducibility</a></li>
<li><a href="#reporting" id="toc-reporting" class="nav-link" data-scroll-target="#reporting"><span class="header-section-number">9</span> Reporting</a></li>
<li><a href="#validation" id="toc-validation" class="nav-link" data-scroll-target="#validation"><span class="header-section-number">10</span> Validation</a></li>
<li><a href="#sharing-code-and-data" id="toc-sharing-code-and-data" class="nav-link" data-scroll-target="#sharing-code-and-data"><span class="header-section-number">11</span> Sharing Code And Data</a></li>
</ul>
</nav>
</div>
<main class="content" id="quarto-document-content">
<header id="title-block-header" class="quarto-title-block default">
<div class="quarto-title">
<h1 class="title">Reproducible Research in R (and friends)</h1>
<p class="subtitle lead">Cheatsheet</p>
</div>
<div class="quarto-title-meta">
<div>
<div class="quarto-title-meta-heading">Author</div>
<div class="quarto-title-meta-contents">
<p>M. Rolland, MSc <a href="mailto:matthieu.rolland@univ-grenoble-alpes.fr" class="quarto-title-author-email"><i class="bi bi-envelope"></i></a> <a href="https://orcid.org/0000-0002-8076-5550" class="quarto-title-author-orcid"> <img src="data:image/png;base64,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"></a></p>
</div>
</div>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">June 8, 2024</p>
</div>
</div>
<div>
<div class="quarto-title-meta-heading">Modified</div>
<div class="quarto-title-meta-contents">
<p class="date-modified">June 14, 2024</p>
</div>
</div>
</div>
</header>
<p>This cheatsheet provides essential guidelines and best practices for conducting reproducible research using R and related tools. It covers project organization, version control, data management, documentation, environment management, workflow automation, and more. For any suggestions or feedback, please feel free to email me.</p>
<section id="project-organization" class="level2" data-number="1">
<h2 data-number="1" class="anchored" data-anchor-id="project-organization"><span class="header-section-number">1</span> Project Organization</h2>
<ul>
<li>Use a consistent folder structure:
<ul>
<li><code>data/</code> - Analysis data files</li>
<li><code>scripts/</code> - Analysis scripts</li>
<li><code>outputs/</code> - Results (figures, tables)</li>
<li><code>docs/</code> - Documentation and reports</li>
</ul></li>
<li>Use RStudio Projects to facilitate project management and environment isolation</li>
<li>Maintain a project log to document progress, changes, and key decisions throughout the analysis</li>
<li>Reference:
<ul>
<li><a href="https://peerj.com/preprints/3192/">The concept of research compendium</a></li>
<li><a href="https://support.posit.co/hc/en-us/articles/200526207-Using-RStudio-Projects">Using RStudio projects</a></li>
</ul></li>
</ul>
</section>
<section id="version-control" class="level2" data-number="2">
<h2 data-number="2" class="anchored" data-anchor-id="version-control"><span class="header-section-number">2</span> Version Control</h2>
<ul>
<li>Use Git to track changes in scripts and documents</li>
<li>Commit regularly with meaningful messages</li>
<li>One repository per analysis</li>
<li>Make sure your <code>data/</code> folder is in the <code>.gitignore</code> file</li>
<li>Make sure there is no sensitive information in your code</li>
<li>Reference:
<ul>
<li><a href="https://happygitwithr.com/">Happy Git with R</a></li>
</ul></li>
</ul>
</section>
<section id="data-management" class="level2" data-number="3">
<h2 data-number="3" class="anchored" data-anchor-id="data-management"><span class="header-section-number">3</span> Data Management</h2>
<ul>
<li>Store raw data in <code>data/raw/</code> and never modify it directly</li>
<li>Produce a README describing the source data</li>
<li>Use scripts to clean and process data, save the cleaned data in <code>data/processed/</code></li>
<li>Document each step of data cleaning</li>
<li>Keep data cleaning separate from analysis</li>
<li>Organize your data in a tidy format: each variable is a column, each observation is a row</li>
<li>Reference:
<ul>
<li><a href="https://www.jstatsoft.org/article/view/v059i10">Principles of tidy data</a></li>
</ul></li>
</ul>
</section>
<section id="documentation" class="level2" data-number="4">
<h2 data-number="4" class="anchored" data-anchor-id="documentation"><span class="header-section-number">4</span> Documentation</h2>
<ul>
<li>Comment code extensively to explain steps and logic</li>
<li>Create README files to explain project structure and instructions for running the analysis</li>
<li>Document all functions clearly, including input parameters, output, and purpose</li>
<li>Reference:
<ul>
<li><a href="https://gricad-gitlab.univ-grenoble-alpes.fr/iab-env-epi/rolland_effects_2022">Example README file</a></li>
<li><a href="https://cran.r-project.org/web/packages/roxygen2/vignettes/roxygen2.html">{roxygen2} for function documentation</a></li>
</ul></li>
</ul>
</section>
<section id="environment-management" class="level2" data-number="5">
<h2 data-number="5" class="anchored" data-anchor-id="environment-management"><span class="header-section-number">5</span> Environment Management</h2>
<ul>
<li>Use <code>sessionInfo()</code> or <code>devtools::session_info()</code> to capture the R session information</li>
<li>Use <code>{renv}</code> to manage package versions</li>
<li>Reference:
<ul>
<li><a href="https://rstudio.github.io/renv/articles/renv.html">Introduction to renv</a></li>
<li><a href="https://gricad-gitlab.univ-grenoble-alpes.fr/iab-env-epi/rolland_effects_2022">Example on how to show the session info (scroll to bottom)</a></li>
</ul></li>
</ul>
</section>
<section id="workflow-automation" class="level2" data-number="6">
<h2 data-number="6" class="anchored" data-anchor-id="workflow-automation"><span class="header-section-number">6</span> Workflow Automation</h2>
<ul>
<li>Organize your analysis into a series of numbered and ordered scripts to create a clear and reproducible workflow (e.g., 01-data-cleaning.R, 02-data-analysis.R, 03-visualization.R)</li>
<li>Create a master script (e.g., run_all.R) that sequentially runs each numbered script</li>
</ul>
<p>OR</p>
<ul>
<li><p>Use Makefile or <code>{targets}</code> package to automate and document the workflow</p></li>
<li><p>Reference:</p>
<ul>
<li><a href="https://books.ropensci.org/targets/">{targets} Package</a><br>
</li>
<li><a href="https://mjrolland.github.io/ed-neuro-hpa/">Example Project using {targets}</a></li>
</ul></li>
</ul>
</section>
<section id="analysis-scripts" class="level2" data-number="7">
<h2 data-number="7" class="anchored" data-anchor-id="analysis-scripts"><span class="header-section-number">7</span> Analysis Scripts</h2>
<ul>
<li>Break analysis into small, reusable functions</li>
<li>Use meaningful and consistent naming conventions such as provided by the <a href="https://style.tidyverse.org/syntax.html#object-names">Tidyverse Naming Conventions</a> for variables and functions and by <a href="https://datacarpentry.org/rr-organization1/01-file-naming/index.html">data carpentry</a> for folders and files</li>
<li>Style your code according to standardized recommendations from the <a href="https://style.tidyverse.org/">Tidyverse Style Guide</a></li>
<li>Reference:
<ul>
<li><a href="https://tidyverse.tidyverse.org/articles/manifesto.html#embrace-functional-programming">Embrace functional programming</a></li>
<li><a href="https://style.tidyverse.org/">Tidyverse Style Guide</a></li>
</ul></li>
</ul>
</section>
<section id="computational-reproducibility" class="level2" data-number="8">
<h2 data-number="8" class="anchored" data-anchor-id="computational-reproducibility"><span class="header-section-number">8</span> Computational reproducibility</h2>
<ul>
<li>Set seeds to ensure reproducibility when using randomness in your analysis</li>
<li>Document all warnings</li>
<li>Reference:
<ul>
<li><a href="https://makemeanalyst.com/r-programming/random-number-seed/">Random number seed in R</a></li>
</ul></li>
</ul>
</section>
<section id="reporting" class="level2" data-number="9">
<h2 data-number="9" class="anchored" data-anchor-id="reporting"><span class="header-section-number">9</span> Reporting</h2>
<ul>
<li>Use RMarkdown (.Rmd) or Quarto (.Qmd) files to combine code, results, and narrative for creating dynamic reports</li>
<li>Reference:
<ul>
<li><a href="https://quarto.org/">Quarto Documentation</a></li>
</ul></li>
</ul>
</section>
<section id="validation" class="level2" data-number="10">
<h2 data-number="10" class="anchored" data-anchor-id="validation"><span class="header-section-number">10</span> Validation</h2>
<ul>
<li>Get your code reviewed prior to publication</li>
<li>Reference:
<ul>
<li><a href="https://mtlynch.io/human-code-reviews-1/">Code Review Practices</a></li>
</ul></li>
</ul>
</section>
<section id="sharing-code-and-data" class="level2" data-number="11">
<h2 data-number="11" class="anchored" data-anchor-id="sharing-code-and-data"><span class="header-section-number">11</span> Sharing Code And Data</h2>
<ul>
<li>Use repositories like <a href="https://github.com/">GitHub</a> or <a href="https://gitlab.com/">GitLab</a> for sharing code</li>
<li>Use repositories like <a href="https://zenodo.org/">Zenodo</a> or <a href="https://www.data.gouv.fr/fr/">data.gouv.fr</a> if you have data sets to share</li>
</ul>
</section>
<div id="quarto-appendix" class="default"><section class="quarto-appendix-contents" role="doc-bibliography" id="quarto-bibliography"><h2 class="anchored quarto-appendix-heading">References</h2><div id="refs" class="references csl-bib-body hanging-indent" data-entry-spacing="0" role="list">
<div id="ref-marwick_packaging_2018" class="csl-entry" role="listitem">
Marwick, Ben, Carl Boettiger, and Lincoln Mullen. 2018. <span>“Packaging Data Analytical Work Reproducibly Using <span>R</span> (and Friends).”</span> Preprint. PeerJ Preprints. <a href="https://doi.org/10.7287/peerj.preprints.3192v2">https://doi.org/10.7287/peerj.preprints.3192v2</a>.
</div>
</div></section></div></main>
<!-- /main column -->
<script id="quarto-html-after-body" type="application/javascript">
window.document.addEventListener("DOMContentLoaded", function (event) {
const toggleBodyColorMode = (bsSheetEl) => {
const mode = bsSheetEl.getAttribute("data-mode");
const bodyEl = window.document.querySelector("body");
if (mode === "dark") {
bodyEl.classList.add("quarto-dark");
bodyEl.classList.remove("quarto-light");
} else {
bodyEl.classList.add("quarto-light");
bodyEl.classList.remove("quarto-dark");
}
}
const toggleBodyColorPrimary = () => {
const bsSheetEl = window.document.querySelector("link#quarto-bootstrap");
if (bsSheetEl) {
toggleBodyColorMode(bsSheetEl);
}
}
toggleBodyColorPrimary();
const icon = "";
const anchorJS = new window.AnchorJS();
anchorJS.options = {
placement: 'right',
icon: icon
};
anchorJS.add('.anchored');
const isCodeAnnotation = (el) => {
for (const clz of el.classList) {
if (clz.startsWith('code-annotation-')) {
return true;
}
}
return false;
}
const clipboard = new window.ClipboardJS('.code-copy-button', {
text: function(trigger) {
const codeEl = trigger.previousElementSibling.cloneNode(true);
for (const childEl of codeEl.children) {
if (isCodeAnnotation(childEl)) {
childEl.remove();
}
}
return codeEl.innerText;
}
});
clipboard.on('success', function(e) {
// button target
const button = e.trigger;
// don't keep focus
button.blur();
// flash "checked"
button.classList.add('code-copy-button-checked');
var currentTitle = button.getAttribute("title");
button.setAttribute("title", "Copied!");
let tooltip;
if (window.bootstrap) {
button.setAttribute("data-bs-toggle", "tooltip");
button.setAttribute("data-bs-placement", "left");
button.setAttribute("data-bs-title", "Copied!");
tooltip = new bootstrap.Tooltip(button,
{ trigger: "manual",
customClass: "code-copy-button-tooltip",
offset: [0, -8]});
tooltip.show();
}
setTimeout(function() {
if (tooltip) {
tooltip.hide();
button.removeAttribute("data-bs-title");
button.removeAttribute("data-bs-toggle");
button.removeAttribute("data-bs-placement");
}
button.setAttribute("title", currentTitle);
button.classList.remove('code-copy-button-checked');
}, 1000);
// clear code selection
e.clearSelection();
});
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp('/' + window.location.host + '/');
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
// Inspect non-navigation links and adorn them if external
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
for (var i=0; i<links.length; i++) {
const link = links[i];
if (!isInternal(link.href)) {
// undo the damage that might have been done by quarto-nav.js in the case of
// links that we want to consider external
if (link.dataset.originalHref !== undefined) {
link.href = link.dataset.originalHref;
}
}
}
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
const config = {
allowHTML: true,
maxWidth: 500,
delay: 100,
arrow: false,
appendTo: function(el) {
return el.parentElement;
},
interactive: true,
interactiveBorder: 10,
theme: 'quarto',
placement: 'bottom-start',
};
if (contentFn) {
config.content = contentFn;
}
if (onTriggerFn) {
config.onTrigger = onTriggerFn;
}
if (onUntriggerFn) {
config.onUntrigger = onUntriggerFn;
}
window.tippy(el, config);
}
const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
for (var i=0; i<noterefs.length; i++) {
const ref = noterefs[i];
tippyHover(ref, function() {
// use id or data attribute instead here
let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href');
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
if (note) {
return note.innerHTML;
} else {
return "";
}
});
}
const xrefs = window.document.querySelectorAll('a.quarto-xref');
const processXRef = (id, note) => {
// Strip column container classes
const stripColumnClz = (el) => {
el.classList.remove("page-full", "page-columns");
if (el.children) {
for (const child of el.children) {
stripColumnClz(child);
}
}
}
stripColumnClz(note)
if (id === null || id.startsWith('sec-')) {
// Special case sections, only their first couple elements
const container = document.createElement("div");
if (note.children && note.children.length > 2) {
container.appendChild(note.children[0].cloneNode(true));
for (let i = 1; i < note.children.length; i++) {
const child = note.children[i];
if (child.tagName === "P" && child.innerText === "") {
continue;
} else {
container.appendChild(child.cloneNode(true));
break;
}
}
if (window.Quarto?.typesetMath) {
window.Quarto.typesetMath(container);
}
return container.innerHTML
} else {
if (window.Quarto?.typesetMath) {
window.Quarto.typesetMath(note);
}
return note.innerHTML;
}
} else {
// Remove any anchor links if they are present
const anchorLink = note.querySelector('a.anchorjs-link');
if (anchorLink) {
anchorLink.remove();
}
if (window.Quarto?.typesetMath) {
window.Quarto.typesetMath(note);
}
// TODO in 1.5, we should make sure this works without a callout special case
if (note.classList.contains("callout")) {
return note.outerHTML;
} else {
return note.innerHTML;
}
}
}
for (var i=0; i<xrefs.length; i++) {
const xref = xrefs[i];
tippyHover(xref, undefined, function(instance) {
instance.disable();
let url = xref.getAttribute('href');
let hash = undefined;
if (url.startsWith('#')) {
hash = url;
} else {
try { hash = new URL(url).hash; } catch {}
}
if (hash) {
const id = hash.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
if (note !== null) {
try {
const html = processXRef(id, note.cloneNode(true));
instance.setContent(html);
} finally {
instance.enable();
instance.show();
}
} else {
// See if we can fetch this
fetch(url.split('#')[0])
.then(res => res.text())
.then(html => {
const parser = new DOMParser();
const htmlDoc = parser.parseFromString(html, "text/html");
const note = htmlDoc.getElementById(id);
if (note !== null) {
const html = processXRef(id, note);
instance.setContent(html);
}
}).finally(() => {
instance.enable();
instance.show();
});
}
} else {
// See if we can fetch a full url (with no hash to target)
// This is a special case and we should probably do some content thinning / targeting
fetch(url)
.then(res => res.text())
.then(html => {
const parser = new DOMParser();
const htmlDoc = parser.parseFromString(html, "text/html");
const note = htmlDoc.querySelector('main.content');
if (note !== null) {
// This should only happen for chapter cross references
// (since there is no id in the URL)
// remove the first header
if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
note.children[0].remove();
}
const html = processXRef(null, note);
instance.setContent(html);
}
}).finally(() => {
instance.enable();
instance.show();
});
}
}, function(instance) {
});
}
let selectedAnnoteEl;
const selectorForAnnotation = ( cell, annotation) => {
let cellAttr = 'data-code-cell="' + cell + '"';
let lineAttr = 'data-code-annotation="' + annotation + '"';
const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
return selector;
}
const selectCodeLines = (annoteEl) => {
const doc = window.document;
const targetCell = annoteEl.getAttribute("data-target-cell");
const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
const lines = annoteSpan.getAttribute("data-code-lines").split(",");
const lineIds = lines.map((line) => {
return targetCell + "-" + line;
})
let top = null;
let height = null;
let parent = null;
if (lineIds.length > 0) {
//compute the position of the single el (top and bottom and make a div)
const el = window.document.getElementById(lineIds[0]);
top = el.offsetTop;
height = el.offsetHeight;
parent = el.parentElement.parentElement;
if (lineIds.length > 1) {
const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
const bottom = lastEl.offsetTop + lastEl.offsetHeight;
height = bottom - top;
}
if (top !== null && height !== null && parent !== null) {
// cook up a div (if necessary) and position it
let div = window.document.getElementById("code-annotation-line-highlight");
if (div === null) {
div = window.document.createElement("div");
div.setAttribute("id", "code-annotation-line-highlight");
div.style.position = 'absolute';
parent.appendChild(div);
}
div.style.top = top - 2 + "px";
div.style.height = height + 4 + "px";
div.style.left = 0;
let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
if (gutterDiv === null) {
gutterDiv = window.document.createElement("div");
gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
gutterDiv.style.position = 'absolute';
const codeCell = window.document.getElementById(targetCell);
const gutter = codeCell.querySelector('.code-annotation-gutter');
gutter.appendChild(gutterDiv);
}
gutterDiv.style.top = top - 2 + "px";
gutterDiv.style.height = height + 4 + "px";
}
selectedAnnoteEl = annoteEl;
}
};
const unselectCodeLines = () => {
const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
elementsIds.forEach((elId) => {
const div = window.document.getElementById(elId);
if (div) {
div.remove();
}
});
selectedAnnoteEl = undefined;
};
// Handle positioning of the toggle
window.addEventListener(
"resize",
throttle(() => {
elRect = undefined;
if (selectedAnnoteEl) {
selectCodeLines(selectedAnnoteEl);
}
}, 10)
);
function throttle(fn, ms) {
let throttle = false;
let timer;
return (...args) => {
if(!throttle) { // first call gets through
fn.apply(this, args);
throttle = true;
} else { // all the others get throttled
if(timer) clearTimeout(timer); // cancel #2
timer = setTimeout(() => {
fn.apply(this, args);
timer = throttle = false;
}, ms);
}
};
}
// Attach click handler to the DT
const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
for (const annoteDlNode of annoteDls) {
annoteDlNode.addEventListener('click', (event) => {
const clickedEl = event.target;
if (clickedEl !== selectedAnnoteEl) {
unselectCodeLines();
const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
if (activeEl) {
activeEl.classList.remove('code-annotation-active');
}
selectCodeLines(clickedEl);
clickedEl.classList.add('code-annotation-active');
} else {
// Unselect the line
unselectCodeLines();
clickedEl.classList.remove('code-annotation-active');
}
});
}
const findCites = (el) => {
const parentEl = el.parentElement;
if (parentEl) {
const cites = parentEl.dataset.cites;
if (cites) {
return {
el,
cites: cites.split(' ')
};
} else {
return findCites(el.parentElement)
}
} else {
return undefined;
}
};
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
for (var i=0; i<bibliorefs.length; i++) {
const ref = bibliorefs[i];
const citeInfo = findCites(ref);
if (citeInfo) {
tippyHover(citeInfo.el, function() {
var popup = window.document.createElement('div');
citeInfo.cites.forEach(function(cite) {
var citeDiv = window.document.createElement('div');
citeDiv.classList.add('hanging-indent');
citeDiv.classList.add('csl-entry');
var biblioDiv = window.document.getElementById('ref-' + cite);
if (biblioDiv) {
citeDiv.innerHTML = biblioDiv.innerHTML;
}
popup.appendChild(citeDiv);
});
return popup.innerHTML;
});
}
}
});
</script>
</div> <!-- /content -->
</body></html>