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<h1 class="title">My Start to R</h1>
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<p class="subtitle lead"></p><p>A short introduction to my blog, and R journey.</p><p></p>
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<div class="quarto-title-meta-heading">Author</div>
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<p><a href="https://kyleb.rbind.io/">Kyle Belanger</a> </p>
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<div class="quarto-title-meta-heading">Published</div>
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<p class="date">January 24, 2020</p>
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<h2 id="toc-title">Table of contents</h2>
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<ul>
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<li><a href="#load-libraries" id="toc-load-libraries" class="nav-link active" data-scroll-target="#load-libraries">Load Libraries</a></li>
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<li><a href="#import-data" id="toc-import-data" class="nav-link" data-scroll-target="#import-data">Import Data</a></li>
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<li><a href="#clean-data-names" id="toc-clean-data-names" class="nav-link" data-scroll-target="#clean-data-names">Clean Data Names</a></li>
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<li><a href="#convert-data-to-long-form" id="toc-convert-data-to-long-form" class="nav-link" data-scroll-target="#convert-data-to-long-form">Convert Data to ‘Long Form’</a></li>
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<li><a href="#graph-5.1" id="toc-graph-5.1" class="nav-link" data-scroll-target="#graph-5.1">Graph 5.1</a></li>
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<p>Today starts my attempt at sharing my R journey with the world! I have been learning R off and on now since late 2019, I have begun to take it much more serious as I work through my Data Analytics class at UCF. My love for all things numbers and graphs has really blossomed, and I am choosing to share that love with anyone who cares to read. I will not claim to be the best at R, or any programming for that matter, but these are my attempts. Each post in this serious will be replicated a graph created in Tableau from the book Tableau for Healthcare. Todays graph is a simple horizontal bar chart, in transferring to both a new blog site and computer I have unfortunately lost the original bar graph, but trust me the one I created looks just like it.</p>
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<section id="load-libraries" class="level1">
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<h1>Load Libraries</h1>
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<div class="cell">
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<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyr)</span>
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<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(magrittr)</span>
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<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggplot2)</span>
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<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(stringr)</span>
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<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(dplyr)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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</div>
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</section>
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<section id="import-data" class="level1">
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<h1>Import Data</h1>
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||
<div class="cell">
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||
<div class="sourceCode cell-code" id="cb2"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>ds <span class="ot"><-</span> readxl<span class="sc">::</span><span class="fu">read_excel</span>(</span>
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<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a> <span class="at">path =</span> <span class="st">"Tableau 10 Training Practice Data.xlsx"</span> </span>
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<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a> ,<span class="at">sheet =</span> <span class="st">"02 - Patient Falls-Single Hosp"</span></span>
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||
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a> )</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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</div>
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</section>
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<section id="clean-data-names" class="level1">
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||
<h1>Clean Data Names</h1>
|
||
<div class="cell">
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||
<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="co">#should make reusable forumla at later time</span></span>
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<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="fu">names</span>(ds) <span class="ot"><-</span> <span class="fu">tolower</span>(<span class="fu">names</span>(ds))</span>
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<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a><span class="fu">names</span>(ds) <span class="ot"><-</span> <span class="fu">str_replace_all</span>(<span class="fu">names</span>(ds),<span class="st">" "</span>, <span class="st">"_"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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</div>
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</section>
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<section id="convert-data-to-long-form" class="level1">
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<h1>Convert Data to ‘Long Form’</h1>
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<div class="cell">
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<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a>ds1 <span class="ot"><-</span> ds <span class="sc">%>%</span> </span>
|
||
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">gather</span>(<span class="st">"patient_falls_no_injury_rate"</span> , <span class="st">"patient_falls_with_injury_rate"</span></span>
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||
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a> ,<span class="at">key =</span> <span class="st">"injury"</span> </span>
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<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a> ,<span class="at">value =</span> <span class="st">"rate"</span> ) <span class="sc">%>%</span> </span>
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<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">injury =</span> (injury <span class="sc">==</span> <span class="st">"patient_falls_with_injury_rate"</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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</div>
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</section>
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<section id="graph-5.1" class="level1">
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<h1>Graph 5.1</h1>
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<div class="cell">
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||
<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>b1 <span class="ot"><-</span> ds <span class="sc">%>%</span> </span>
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<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggplot</span>(<span class="at">mapping =</span> <span class="fu">aes</span>(<span class="at">x =</span> <span class="fu">reorder</span>(type_of_care,total_patient_falls_rate ) , <span class="at">y =</span> total_patient_falls_rate)) <span class="sc">+</span></span>
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||
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_col</span>(<span class="at">fill =</span> <span class="st">"#2b83ba"</span>) <span class="sc">+</span> </span>
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||
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">coord_flip</span>() <span class="sc">+</span></span>
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<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_y_continuous</span>(<span class="at">breaks =</span> <span class="cn">NULL</span>) <span class="sc">+</span></span>
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||
<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(<span class="at">axis.ticks =</span> <span class="fu">element_blank</span>()) <span class="sc">+</span></span>
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||
<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">labs</span>(<span class="at">title =</span> <span class="st">"Rate of Patient Falls (per 1,000 Pateint Days)</span><span class="sc">\n</span><span class="st">by Type of Care for FY2017"</span></span>
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||
<span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a> ,<span class="at">x =</span> <span class="cn">NULL</span></span>
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||
<span id="cb5-9"><a href="#cb5-9" aria-hidden="true" tabindex="-1"></a> ,<span class="at">y =</span> <span class="cn">NULL</span></span>
|
||
<span id="cb5-10"><a href="#cb5-10" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
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<span id="cb5-11"><a href="#cb5-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_classic</span>() <span class="sc">+</span></span>
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||
<span id="cb5-12"><a href="#cb5-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_text</span>(<span class="fu">aes</span>(<span class="at">label =</span> <span class="fu">format</span>(total_patient_falls_rate, <span class="at">digits =</span> <span class="dv">2</span>)), <span class="at">nudge_y =</span> <span class="sc">-</span>.<span class="dv">25</span>, <span class="at">color =</span> <span class="st">"white"</span>)</span>
|
||
<span id="cb5-13"><a href="#cb5-13" aria-hidden="true" tabindex="-1"></a> </span>
|
||
<span id="cb5-14"><a href="#cb5-14" aria-hidden="true" tabindex="-1"></a>b1</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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</section>
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<div id="quarto-appendix" class="default"><section class="quarto-appendix-contents"><h2 class="anchored quarto-appendix-heading">Reuse</h2><div id="quarto-reuse" class="quarto-appendix-contents"><div><a rel="license" href="https://creativecommons.org/licenses/by/4.0/">https://creativecommons.org/licenses/by/4.0/</a></div></div></section><section class="quarto-appendix-contents"><h2 class="anchored quarto-appendix-heading">Citation</h2><div><div class="quarto-appendix-secondary-label">BibTeX citation:</div><pre class="sourceCode code-with-copy quarto-appendix-bibtex"><code class="sourceCode bibtex">@online{belanger2020,
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author = {Belanger, Kyle},
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||
title = {My {Start} to {R}},
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date = {2020-01-24},
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langid = {en}
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}
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</code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre><div class="quarto-appendix-secondary-label">For attribution, please cite this work as:</div><div id="ref-belanger2020" class="csl-entry quarto-appendix-citeas" role="listitem">
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Belanger, Kyle. 2020. <span>“My Start to R.”</span> January 24, 2020.
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}
|
||
}
|
||
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();
|
||
});
|
||
function tippyHover(el, contentFn) {
|
||
const config = {
|
||
allowHTML: true,
|
||
content: contentFn,
|
||
maxWidth: 500,
|
||
delay: 100,
|
||
arrow: false,
|
||
appendTo: function(el) {
|
||
return el.parentElement;
|
||
},
|
||
interactive: true,
|
||
interactiveBorder: 10,
|
||
theme: 'quarto',
|
||
placement: 'bottom-start'
|
||
};
|
||
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);
|
||
return note.innerHTML;
|
||
});
|
||
}
|
||
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";
|
||
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;
|
||
};
|
||
// 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> |