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< title > Kyle Belanger - My Start to R< / title >
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< h1 class = "title" > My Start to R< / h1 >
< 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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< li > < a href = "#import-data" id = "toc-import-data" class = "nav-link" data-scroll-target = "#import-data" > Import Data< / a > < / li >
< 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 >
< 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 ‘ ’ < / a > < / li >
< 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 >
< section id = "load-libraries" class = "level1" >
< h1 > Load Libraries< / h1 >
< div class = "cell" >
< 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 >
< span id = "cb1-2" > < a href = "#cb1-2" aria-hidden = "true" tabindex = "-1" > < / a > < span class = "fu" > library< / span > (magrittr)< / span >
< span id = "cb1-3" > < a href = "#cb1-3" aria-hidden = "true" tabindex = "-1" > < / a > < span class = "fu" > library< / span > (ggplot2)< / span >
< span id = "cb1-4" > < a href = "#cb1-4" aria-hidden = "true" tabindex = "-1" > < / a > < span class = "fu" > library< / span > (stringr)< / span >
< 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 >
< / div >
< / section >
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< h1 > Import Data< / h1 >
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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 >
< 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 >
< 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 >
< / div >
< / section >
< section id = "clean-data-names" class = "level1" >
< h1 > Clean Data Names< / h1 >
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< / div >
< / section >
< section id = "convert-data-to-long-form" class = "level1" >
< h1 > Convert Data to ‘ ’ < / h1 >
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< 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 >
< 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 >
< 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 >
< 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 >
< / div >
< / section >
< section id = "graph-5.1" class = "level1" >
< h1 > Graph 5.1< / h1 >
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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 = "cb5-5" > < 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 = "cb5-7" > < 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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author = {Belanger, Kyle},
title = {My {Start} to {R}},
date = {2020-01-24},
langid = {en}
}
< / 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" >
Belanger, Kyle. 2020. < span > “My Start to R.”< / span > January 24, 2020.
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};
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();
});
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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) {
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const config = {
allowHTML: true,
maxWidth: 500,
delay: 100,
arrow: false,
appendTo: function(el) {
return el.parentElement;
},
interactive: true,
interactiveBorder: 10,
theme: 'quarto',
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placement: 'bottom-start',
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};
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if (contentFn) {
config.content = contentFn;
}
if (onTriggerFn) {
config.onTrigger = onTriggerFn;
}
if (onUntriggerFn) {
config.onUntrigger = onUntriggerFn;
}
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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);
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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) {
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});
}
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";
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div.style.left = 0;
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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;
};
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// 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);
}
};
}
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// 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 -->
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< / body > < / html >
