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<title>Reproducible Research & DIR Workflow</title>
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<h2 id="toc-title">Table of contents</h2>
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<li><a href="#overview" id="toc-overview" class="nav-link active" data-scroll-target="#overview">Overview</a></li>
<li><a href="#readings" id="toc-readings" class="nav-link" data-scroll-target="#readings">Readings</a></li>
<li><a href="#reflection" id="toc-reflection" class="nav-link" data-scroll-target="#reflection">Reflection</a>
<ul>
<li><a href="#reproducible-research-with-r-and-rstudio" id="toc-reproducible-research-with-r-and-rstudio" class="nav-link" data-scroll-target="#reproducible-research-with-r-and-rstudio">Reproducible Research with R and RStudio</a></li>
<li><a href="#learning-analytics-goes-to-school-pp.-28---33" id="toc-learning-analytics-goes-to-school-pp.-28---33" class="nav-link" data-scroll-target="#learning-analytics-goes-to-school-pp.-28---33">Learning Analytics Goes to School (pp. 28 - 33)</a></li>
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<li><a href="#references" id="toc-references" class="nav-link" data-scroll-target="#references">References</a></li>
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<h1 class="title">Reproducible Research & DIR Workflow</h1>
<p class="subtitle lead">Orientation Module: Essential Readings</p>
</div>
<div class="quarto-title-meta">
<div>
<div class="quarto-title-meta-heading">Author</div>
<div class="quarto-title-meta-contents">
<p>LASER Institute </p>
</div>
</div>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">July 14, 2024</p>
</div>
</div>
</div>
</header>
<section id="overview" class="level2">
<h2 class="anchored" data-anchor-id="overview">Overview</h2>
<p>The primary goal of our essential readings in the LASER Orientation module is to introduce learners to foundational concepts and practical tools necessary for conducting reproducible research. Learners will explore the importance of reproducibility in scientific inquiry, understand the benefits it offers to individual researchers and the broader scientific community, and learn about the essential tools and workflows that facilitate reproducible research. The discussion questions aim to deepen students’ comprehension of these topics, encourage critical thinking about the practices and principles of reproducible research, and provide practical insights into implementing these methods in their own research projects.</p>
</section>
<section id="readings" class="level2">
<h2 class="anchored" data-anchor-id="readings">Readings</h2>
<p>Read chapters 1 and 2 of <a href="https://github.com/christophergandrud/Rep-Res-Book">Reproducible Research with R and RStudio</a> by <span class="citation" data-cites="gandrud2021">Gandrud (<a href="#ref-gandrud2021" role="doc-biblioref">2021</a>)</span>, which lay the groundwork for understanding and implementing reproducible research:</p>
<p><strong>Reproducible Research with R and RStudio</strong> <span class="citation" data-cites="gandrud2021">(<a href="#ref-gandrud2021" role="doc-biblioref">Gandrud 2021</a>)</span></p>
<ul>
<li><p><strong>Chapter 1: Introducing Reproducible Research</strong>. Chapter 1 introduces the concept of reproducible research, emphasizing its importance for scientific integrity and personal research efficiency, and outlines the main tools and practices essential for achieving reproducibility in computational and quantitative empirical sciences.</p></li>
<li><p><strong>Chapter 2: Getting Started with Reproducible Research</strong>. Chapter 2 provides a detailed workflow for conducting reproducible research, offering practical tips for documenting and organizing research projects to ensure all steps are transparent and easily replicable by others.</p></li>
</ul>
<p><strong>Learning Analytics Goes to School</strong> <span class="citation" data-cites="krumm2018">(<a href="#ref-krumm2018" role="doc-biblioref">Krumm, Means, and Bienkowski 2018</a>)</span></p>
<ul>
<li><strong>Chapter 2: Data Use in Educational Data-Intensive Research (pp. 28 - 33)</strong>. The Data-Intensive Research Workflow introduced in this chapter provides a high-level overview of preparing, wrangling, exploring, modeling, and communicating data for effective and reproducible research.</li>
</ul>
</section>
<section id="reflection" class="level2">
<h2 class="anchored" data-anchor-id="reflection">Reflection</h2>
<p>To help guide your reflection on the readings, a set of guiding questions are provided below. After you have had a chance to work through one or more of the readings, <strong>we encourage you to contribute to our learning community by creating a new post to our <a href="https://laser-scholars.slack.com/archives/C07CF9HCLFN">laser-orientation channel</a> on <a href="http://laser-scholars.slack.com/">Slack</a></strong>. Your post might contain a response to one or more of the guiding questions, questions you still have about the topics addressed, or insights gained into your own research.</p>
<section id="reproducible-research-with-r-and-rstudio" class="level3">
<h3 class="anchored" data-anchor-id="reproducible-research-with-r-and-rstudio">Reproducible Research with R and RStudio</h3>
<p><strong>Chapter 1: Introducing Reproducible Research</strong></p>
<ol type="1">
<li><p>What is Reproducible Research?</p>
<ul>
<li>How does the author define reproducible research in the context of computational and quantitative empirical sciences?</li>
<li>What are the key differences between replicable and reproducible research as outlined in the book?</li>
</ul></li>
<li><p>Why Should Research Be Reproducible?</p>
<ul>
<li>What are the primary reasons reproducible research is crucial for scientific inquiry?</li>
<li>How can reproducible research enhance your own work and productivity?</li>
</ul></li>
<li><p>Benefits for the Scientific Community and Researchers:</p>
<ul>
<li>How does reproducible research contribute to the cumulative growth of scientific knowledge?</li>
<li>In what ways does making your research reproducible lead to better work habits and more effective teamwork?</li>
</ul></li>
<li><p>Tools of Reproducible Research:</p>
<ul>
<li>What are the main tools of reproducible research introduced in this chapter?</li>
<li>Discuss the benefits of using R, knitr, and RStudio for conducting reproducible research.</li>
</ul></li>
</ol>
<p><strong>Chapter 2: Getting Started with Reproducible Research</strong></p>
<ol type="1">
<li><p>Workflow for Reproducible Research:</p>
<ul>
<li>What some core elements of the workflow for reproducible research proposed by Gandrud?</li>
<li>What are some of the key principles and practices for ensuring research is reproducible?</li>
</ul></li>
<li><p>Practical Tips for Reproducible Research:</p>
<ul>
<li>What does the author mean by “Document everything” and why is it important?</li>
<li>How can organizing your files and ensuring they are human-readable contribute to reproducibility?</li>
</ul></li>
<li><p>File Management:</p>
<ul>
<li>Explain the significance of having a plan to organize, store, and make your files available.</li>
<li>Discuss some best practices for file naming conventions and directory structures to facilitate reproducibility.</li>
</ul></li>
<li><p>Implementing Reproducibility:</p>
<ul>
<li>How does Gandrud suggest you explicitly tie your files together in a research project?</li>
<li>What role do tools like GNU Make play in managing reproducible research projects?</li>
</ul></li>
</ol>
</section>
<section id="learning-analytics-goes-to-school-pp.-28---33" class="level3">
<h3 class="anchored" data-anchor-id="learning-analytics-goes-to-school-pp.-28---33">Learning Analytics Goes to School (pp. 28 - 33)</h3>
<ol type="1">
<li><p>What are the five stages of the <strong>data-intensive research workflow</strong>, and what is the primary goal of each stage?</p></li>
<li><p>Why is the “<strong>prepare</strong>” phase crucial in the data-intensive research workflow, and what key activities are involved in this phase?</p></li>
<li><p>What are some common challenges faced during the “<strong>wrangle</strong>” phase, and how can they be effectively addressed?</p></li>
<li><p>How does the “<strong>explore</strong>” phase contribute to the overall research process, and what techniques are commonly used during this phase?</p></li>
<li><p>What is the significance of the “<strong>model</strong>” phase in the workflow, and what are some best practices for building and evaluating models?</p></li>
<li><p>Why is the “<strong>communicate</strong>” phase essential, and what strategies can be used to present research findings to different audiences effectively?</p></li>
<li><p>How do the stages of the workflow integrate with one another, and why is iteration an important aspect of the data-intensive research process?</p></li>
<li><p>Can you think of a real-world example where this workflow could be applied to solve an educational problem? Describe the steps you would take in each phase.</p></li>
</ol>
</section>
</section>
<section id="references" class="level2 unnumbered">
</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-gandrud2021" class="csl-entry" role="listitem">
Gandrud, Christopher. 2021. <em>Reproducible Research with r and r Studio (3rd Edition)</em>. CRC Press. <a href="http://github.com/christophergandrud/Rep-Res-Book">http://github.com/christophergandrud/Rep-Res-Book</a>.
</div>
<div id="ref-krumm2018" class="csl-entry" role="listitem">
Krumm, Andrew, Barbara Means, and Marie Bienkowski. 2018. <em>Learning Analytics Goes to School</em>. Routledge. <a href="https://doi.org/10.4324/9781315650722">https://doi.org/10.4324/9781315650722</a>.
</div>
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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();
});
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);
return note.innerHTML;
});
}
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>