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<div class="quarto-title">
<h1 class="title">pre-course</h1>
</div>
<div class="quarto-title-meta">
</div>
</header>
<section id="sec-pre-course" class="level1">
<h1>Pre-course tasks</h1>
<p>In order to participate in this course, you must complete the pre-course tasks.</p>
<p>These tasks are designed to make it easier for everyone to start the course with everything ready to go.</p>
<p>Depending on your skills and knowledge, these tasks could take between <strong>30 min to 1 hrs to finish</strong>.</p>
<p>If you have any issues, please write us an email or ask during the registration on the morning of the first day of the course.</p>
<section id="list-of-tasks" class="level2">
<h2 class="anchored" data-anchor-id="list-of-tasks">List of tasks</h2>
<p>Here’s a quick overview of the tasks you need to do. Specific details about them are found as you work through this section.</p>
<ol type="1">
<li>Read the learning objectives in <a href="#sec-learning-objectives" class="quarto-xref">Section 1.2</a></li>
<li>Install the necessary programs in <a href="#sec-intall-r-packages" class="quarto-xref">Section 1.3</a></li>
<li>Read the Code of Conduct <a href="#sec-code-of-conduct" class="quarto-xref">Section 1.5</a></li>
<li>Download the data or the repository in <a href="#sec-download-data" class="quarto-xref">Section 1.4</a></li>
</ol>
<p>Check each section for exact details on completing these tasks.</p>
</section>
<section id="sec-learning-objectives" class="level2">
<h2 class="anchored" data-anchor-id="sec-learning-objectives">Learning objectives</h2>
<div class="callout callout-style-default callout-note callout-titled">
<div class="callout-header d-flex align-content-center">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<div class="callout-title-container flex-fill">
The overall course objective
</div>
</div>
<div class="callout-body-container callout-body">
<p>To provide participants with the knowledge, tools and skills to implement modern mediation analysis for investigation of disease mechanisms.</p>
</div>
</div>
<p>The more specific learning outcomes include:</p>
<ul>
<li>Explain the theoretical concepts and statistical methods regarding traditional and modern mediation analysis applied to basic, clinical and epidemiological research on diabetes and endocrine diseases</li>
<li>Perform traditional, causal and modern mediation analysis using R software</li>
<li>Present results from mediation analysis according to the current mediation analysis reporting guidelines</li>
<li>Interpret results from mediation analysis and suggest relevant sensitivity analyses for mediation analyses</li>
<li>Discuss the strengths, limitations and assumptions of traditional, causal and modern mediation analysis</li>
</ul>
</section>
<section id="sec-intall-r-packages" class="level2">
<h2 class="anchored" data-anchor-id="sec-intall-r-packages">Installing programs</h2>
<section id="installing-r" class="level3">
<h3 class="anchored" data-anchor-id="installing-r">Installing R</h3>
<p>If you have not already done so, please download the latest version of R for <a href="https://cran.r-project.org/bin/windows/base/">Window</a> or <a href="https://cran.r-project.org/bin/macosx/">Mac</a></p>
<p>If you have R, check the version.</p>
<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">R.Version</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>If you have anything from 4.3.1 or later, it should be okay.</p>
</section>
<section id="installing-r-packages" class="level3">
<h3 class="anchored" data-anchor-id="installing-r-packages">Installing R packages</h3>
<div class="cell">
<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><span class="fu">install.packages</span>(<span class="st">"pak"</span>)</span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pkg_install</span>(<span class="st">"tidyverse"</span>)</span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pkg_install</span>(<span class="st">"DiagrammeR"</span>)</span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pkg_install</span>(<span class="st">"downlit"</span>)</span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pkg_install</span>(<span class="st">"furrr"</span>)</span>
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pkg_install</span>(<span class="st">"here"</span>)</span>
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pkg_install</span>(<span class="st">"knitr"</span>)</span>
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pkg_install</span>(<span class="st">"mediation"</span>)</span>
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pkg_install</span>(<span class="st">"NetCoupler"</span>)</span>
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pkg_install</span>(<span class="st">"rmarkdown"</span>)</span>
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pkg_install</span>(<span class="st">"survival"</span>)</span>
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pkg_install</span>(<span class="st">"xml2"</span>)</span>
<span id="cb2-13"><a href="#cb2-13" aria-hidden="true" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pkg_install</span>(<span class="st">"here"</span>)</span>
<span id="cb2-14"><a href="#cb2-14" aria-hidden="true" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pkg_install</span>(<span class="st">"BS1125/CMAverse"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>If installation of a package does not work using the “pak” package, then use:</p>
<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="fu">install.packages</span>(<span class="st">"name-of-package"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>If you have issues with the CMA package, you could also try this:</p>
<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><span class="fu">install.packages</span>(<span class="st">"devtools"</span>)</span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a>devtools<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">"BS1125/CMAverse"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
</section>
<section id="sec-download-data" class="level2">
<h2 class="anchored" data-anchor-id="sec-download-data">Download the data</h2>
<p>You can follow all the teaching material on this website. For the exercises, you will need to use the datasets we have created.</p>
<p>You can either download the entire repository (recommended) or simply download the data from our github.</p>
<p>We recommend that you do not do this before March 31, in the afternoon as we will making updates until then.</p>
<section id="download-repository" class="level3">
<h3 class="anchored" data-anchor-id="download-repository">Download repository</h3>
<ol type="1">
<li>Open a new session of R in RStudio. If you are in a project, go our of that project.</li>
<li>Using RStudio’s New Project menu item: “File -> New Project -> Version control -> Git”</li>
<li>Keeping RStudio open, open your browser and go to our <a href="https://github.com/steno-aarhus/mediation-analysis-course">repository</a></li>
<li>Then, Click on the green “code” icon and copy-paste</li>
<li>Now go back to R and put in what you just copy-pasted under “Repository URL.” You should also select where this project should.</li>
<li>Click “create project” and you should now have all materials there.</li>
</ol>
</section>
<section id="download-the-data" class="level3">
<h3 class="anchored" data-anchor-id="download-the-data">Download the data</h3>
<p>If you want to only download the course data. You can go to #<a href="https://github.com/steno-aarhus/mediation-analysis-course/tree/main/data">here</a> for the Framingham, NHANES and simulated data. Click “download raw file” in the top right corner after you have clicked on the specific file.</p>
</section>
</section>
<section id="sec-code-of-conduct" class="level2">
<h2 class="anchored" data-anchor-id="sec-code-of-conduct">Code of conduct</h2>
<p>We have a <a href="https://guides.rostools.org/conduct.html">Code of Conduct</a>. If you haven’t read it, <strong>read it now</strong>. This course is a supportive and safe environment for learning, so this Code of Conduct is important.</p>
<p>See you at the course!</p>
</section>
</section>
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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>