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Lesson5_rmd.html
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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<title>Using RMarkdown for reproducible and neat documents</title>
<script src="site_libs/jquery-1.12.4/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/lumen.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<script src="site_libs/navigation-1.1/codefolding.js"></script>
<script src="site_libs/htmlwidgets-1.5.2/htmlwidgets.js"></script>
<script src="site_libs/plotly-binding-4.9.2.1/plotly.js"></script>
<script src="site_libs/typedarray-0.1/typedarray.min.js"></script>
<link href="site_libs/crosstalk-1.1.0.1/css/crosstalk.css" rel="stylesheet" />
<script src="site_libs/crosstalk-1.1.0.1/js/crosstalk.min.js"></script>
<link href="site_libs/plotly-htmlwidgets-css-1.52.2/plotly-htmlwidgets.css" rel="stylesheet" />
<script src="site_libs/plotly-main-1.52.2/plotly-latest.min.js"></script>
<link href="site_libs/datatables-css-0.0.0/datatables-crosstalk.css" rel="stylesheet" />
<script src="site_libs/datatables-binding-0.13/datatables.js"></script>
<link href="site_libs/dt-core-1.10.20/css/jquery.dataTables.min.css" rel="stylesheet" />
<link href="site_libs/dt-core-1.10.20/css/jquery.dataTables.extra.css" rel="stylesheet" />
<script src="site_libs/dt-core-1.10.20/js/jquery.dataTables.min.js"></script>
<link href="site_libs/nouislider-7.0.10/jquery.nouislider.min.css" rel="stylesheet" />
<script src="site_libs/nouislider-7.0.10/jquery.nouislider.min.js"></script>
<link href="site_libs/selectize-0.12.0/selectize.bootstrap3.css" rel="stylesheet" />
<script src="site_libs/selectize-0.12.0/selectize.min.js"></script>
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
<style type="text/css">code{white-space: pre;}</style>
<style type="text/css" data-origin="pandoc">
div.sourceCode { overflow-x: auto; }
table.sourceCode, tr.sourceCode, td.lineNumbers, td.sourceCode {
margin: 0; padding: 0; vertical-align: baseline; border: none; }
table.sourceCode { width: 100%; line-height: 100%; background-color: #f8f8f8; }
td.lineNumbers { text-align: right; padding-right: 4px; padding-left: 4px; color: #aaaaaa; border-right: 1px solid #aaaaaa; }
td.sourceCode { padding-left: 5px; }
pre, code { background-color: #f8f8f8; }
code > span.kw { color: #204a87; font-weight: bold; } /* Keyword */
code > span.dt { color: #204a87; } /* DataType */
code > span.dv { color: #0000cf; } /* DecVal */
code > span.bn { color: #0000cf; } /* BaseN */
code > span.fl { color: #0000cf; } /* Float */
code > span.ch { color: #4e9a06; } /* Char */
code > span.st { color: #4e9a06; } /* String */
code > span.co { color: #8f5902; font-style: italic; } /* Comment */
code > span.ot { color: #8f5902; } /* Other */
code > span.al { color: #ef2929; } /* Alert */
code > span.fu { color: #000000; } /* Function */
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code > span.wa { color: #8f5902; font-weight: bold; font-style: italic; } /* Warning */
code > span.cn { color: #000000; } /* Constant */
code > span.sc { color: #000000; } /* SpecialChar */
code > span.vs { color: #4e9a06; } /* VerbatimString */
code > span.ss { color: #4e9a06; } /* SpecialString */
code > span.im { } /* Import */
code > span.va { color: #000000; } /* Variable */
code > span.cf { color: #204a87; font-weight: bold; } /* ControlFlow */
code > span.op { color: #ce5c00; font-weight: bold; } /* Operator */
code > span.pp { color: #8f5902; font-style: italic; } /* Preprocessor */
code > span.ex { } /* Extension */
code > span.at { color: #c4a000; } /* Attribute */
code > span.do { color: #8f5902; font-weight: bold; font-style: italic; } /* Documentation */
code > span.an { color: #8f5902; font-weight: bold; font-style: italic; } /* Annotation */
code > span.cv { color: #8f5902; font-weight: bold; font-style: italic; } /* CommentVar */
code > span.in { color: #8f5902; font-weight: bold; font-style: italic; } /* Information */
.sourceCode .row {
width: 100%;
}
.sourceCode {
overflow-x: auto;
}
.code-folding-btn {
margin-right: -30px;
}
</style>
<script>
// apply pandoc div.sourceCode style to pre.sourceCode instead
(function() {
var sheets = document.styleSheets;
for (var i = 0; i < sheets.length; i++) {
if (sheets[i].ownerNode.dataset["origin"] !== "pandoc") continue;
try { var rules = sheets[i].cssRules; } catch (e) { continue; }
for (var j = 0; j < rules.length; j++) {
var rule = rules[j];
// check if there is a div.sourceCode rule
if (rule.type !== rule.STYLE_RULE || rule.selectorText !== "div.sourceCode") continue;
var style = rule.style.cssText;
// check if color or background-color is set
if (rule.style.color === '' && rule.style.backgroundColor === '') continue;
// replace div.sourceCode by a pre.sourceCode rule
sheets[i].deleteRule(j);
sheets[i].insertRule('pre.sourceCode{' + style + '}', j);
}
}
})();
</script>
<style type="text/css">
pre:not([class]) {
background-color: white;
}
</style>
<style type="text/css">
h1 {
font-size: 34px;
}
h1.title {
font-size: 38px;
}
h2 {
font-size: 30px;
}
h3 {
font-size: 24px;
}
h4 {
font-size: 18px;
}
h5 {
font-size: 16px;
}
h6 {
font-size: 12px;
}
.table th:not([align]) {
text-align: left;
}
</style>
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
.tabbed-pane {
padding-top: 12px;
}
.html-widget {
margin-bottom: 20px;
}
button.code-folding-btn:focus {
outline: none;
}
summary {
display: list-item;
}
</style>
<style type="text/css">
/* padding for bootstrap navbar */
body {
padding-top: 54px;
padding-bottom: 40px;
}
/* offset scroll position for anchor links (for fixed navbar) */
.section h1 {
padding-top: 59px;
margin-top: -59px;
}
.section h2 {
padding-top: 59px;
margin-top: -59px;
}
.section h3 {
padding-top: 59px;
margin-top: -59px;
}
.section h4 {
padding-top: 59px;
margin-top: -59px;
}
.section h5 {
padding-top: 59px;
margin-top: -59px;
}
.section h6 {
padding-top: 59px;
margin-top: -59px;
}
.dropdown-submenu {
position: relative;
}
.dropdown-submenu>.dropdown-menu {
top: 0;
left: 100%;
margin-top: -6px;
margin-left: -1px;
border-radius: 0 6px 6px 6px;
}
.dropdown-submenu:hover>.dropdown-menu {
display: block;
}
.dropdown-submenu>a:after {
display: block;
content: " ";
float: right;
width: 0;
height: 0;
border-color: transparent;
border-style: solid;
border-width: 5px 0 5px 5px;
border-left-color: #cccccc;
margin-top: 5px;
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
}
.dropdown-submenu.pull-left {
float: none;
}
.dropdown-submenu.pull-left>.dropdown-menu {
left: -100%;
margin-left: 10px;
border-radius: 6px 0 6px 6px;
}
</style>
<script>
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
if (href === "")
href = "index.html";
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
});
</script>
<!-- tabsets -->
<style type="text/css">
.tabset-dropdown > .nav-tabs {
display: inline-table;
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs > li.active:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "";
border: none;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs > li.active {
display: block;
}
.tabset-dropdown > .nav-tabs > li > a,
.tabset-dropdown > .nav-tabs > li > a:focus,
.tabset-dropdown > .nav-tabs > li > a:hover {
border: none;
display: inline-block;
border-radius: 4px;
background-color: transparent;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
display: block;
float: none;
}
.tabset-dropdown > .nav-tabs > li {
display: none;
}
</style>
<!-- code folding -->
<style type="text/css">
.code-folding-btn { margin-bottom: 4px; }
</style>
<style type="text/css">
#TOC {
margin: 25px 0px 20px 0px;
}
@media (max-width: 768px) {
#TOC {
position: relative;
width: 100%;
}
}
@media print {
.toc-content {
/* see https://github.com/w3c/csswg-drafts/issues/4434 */
float: right;
}
}
.toc-content {
padding-left: 30px;
padding-right: 40px;
}
div.main-container {
max-width: 1200px;
}
div.tocify {
width: 20%;
max-width: 260px;
max-height: 85%;
}
@media (min-width: 768px) and (max-width: 991px) {
div.tocify {
width: 25%;
}
}
@media (max-width: 767px) {
div.tocify {
width: 100%;
max-width: none;
}
}
.tocify ul, .tocify li {
line-height: 20px;
}
.tocify-subheader .tocify-item {
font-size: 0.90em;
}
.tocify .list-group-item {
border-radius: 0px;
}
</style>
</head>
<body>
<div class="container-fluid main-container">
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
</div>
<div class="toc-content col-xs-12 col-sm-8 col-md-9">
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html">R Coding Club</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">Home</a>
</li>
<li>
<a href="Lesson1.html">Lesson 1</a>
</li>
<li>
<a href="Lesson2.html">Lesson 2</a>
</li>
<li>
<a href="Lesson3.html">Lesson 3</a>
</li>
<li>
<a href="Lesson4.html">Lesson 4</a>
</li>
<li>
<a href="Lesson5.html">Lesson 5</a>
</li>
<li>
<a href="Lesson6.html">Lesson 6</a>
</li>
<li>
<a href="Lesson7.html">Lesson 7</a>
</li>
<li>
<a href="Lesson8.html">Lesson 8</a>
</li>
<li>
<a href="Lesson9.html">Lesson 9</a>
</li>
<li>
<a href="Lesson10.html">Lesson 10</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/darwinanddavis/EmoRyCodingClub">
<span class="fa fa-github"></span>
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div class="btn-group pull-right">
<button type="button" class="btn btn-default btn-xs dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span>Code</span> <span class="caret"></span></button>
<ul class="dropdown-menu" style="min-width: 50px;">
<li><a id="rmd-show-all-code" href="#">Show All Code</a></li>
<li><a id="rmd-hide-all-code" href="#">Hide All Code</a></li>
</ul>
</div>
<h1 class="title toc-ignore">Using RMarkdown for reproducible and neat documents</h1>
<h4 class="author"><div style="white-space: pre-line;">Your name here
Your affiliation here</div></h4>
</div>
<!-- this enables math encoding in the knitted documents -->
<script type="text/x-mathjax-config">
MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "all"} } });
</script>
<p>Date: 2021-12-06<br />
R version: 3.5.0<br />
*Corresponding author: Your email here</p>
<div id="overview" class="section level1">
<h1>Overview</h1>
<p>This document showcases how to create and use <code>RMarkdown</code> documents.</p>
</div>
<div id="you-can-easily-create-headings.-this-is-a-first-order-heading." class="section level1">
<h1>You can easily create headings. This is a first order heading.</h1>
<div id="then-move-down-in-heading-order-size" class="section level2">
<h2>Then move down in heading order size</h2>
<div id="like-this-subheading" class="section level3">
<h3>Like this subheading</h3>
<div id="and-this-fourth-order-heading" class="section level4">
<h4>And this fourth order heading</h4>
<!-- To create a new line of text, insert two spaces after every line in the `Rmd` file, then hit _ENTER_. -->
<p>You can write in <strong>bold</strong> and <em>italicised</em> text (in <strong>two</strong> different <em>ways</em>).</p>
<p>You can write in-line <code>code</code> if you want to differentiate between when you are typing normally or highlighting <code>model parameters</code>, for example.</p>
<p>Equations like this <span class="math inline">\(t' = \gamma(t - vx/c^{2})\)</span>, to appear within text lines.</p>
<p>Create links to your <a href="https://github.com/darwinanddavis">website</a>.</p>
<p>Make footnotes<a href="#fn1" class="footnoteRef" id="fnref1"><sup>1</sup></a>.</p>
<p>Insert line breaks <br> between text like this, which works best in large <br> slabs of text</p>
<p>Insert a horizontal line break using five asterisks ('*****')</p>
<!-- horizontal line -->
<!-- ***** -->
<p>The raw Rmd file also has the code for inserting user comments. <!-- To do this, place the cursor on the text and type 'Cmd/Ctl + Shift + C' --></p>
<p>(There is also a page break here. Best seen in PDF. Check the raw Rmd file to see the code)</p>
<!-- page break -->
</div>
</div>
</div>
<div id="define-equations" class="section level2">
<h2>Define equations</h2>
<p>Accordingly, we write the eigenfunction of a spinless particle as the superposition of plane wave states of momentum (<span class="math inline">\(\pi\)</span>) and energy (<span class="math inline">\(E_{j}\)</span>) having amplitudes <span class="math inline">\(a(\pi,E_{j})\)</span> (from <a href="https://www.academia.edu/33763545/Concise_derivation_of_the_Schr%C3%B6dinger_equation">[1]</a>).</p>
<p><span class="math display">\[
\phi n(r,t) =
\sum_{i, j} a(p_{i},E_{j})
e^{
\frac{i}
{h}
(p_{i} \cdot r - E_{j}t)
}
\]</span> <!-- !!! uncheck the below to include images in HTML and word renders --> <!-- !!! pdf render code is found in the below commmit --> <!-- ## Embed images/gifs: --></p>
<!-- . -->
<!-- code for img in pdf: commit L5 rmd external test final - cmd line pdf/word knit -->
</div>
<div id="create-alter-and-embed-plots" class="section level2">
<h2>Create, alter, and embed plots</h2>
<p><img src="Lesson5_rmd_files/figure-html/unnamed-chunk-1-1.png" width="672" /></p>
<p>Figure 1. Example of a stock plot embedded into a PDF from RMarkdown.</p>
</div>
<div id="show-plots-with-associated-code" class="section level2">
<h2>Show plots with associated code</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">suppressWarnings</span>(<span class="kw">require</span>(viridis))
bm <-<span class="st"> </span><span class="dv">1</span>
<span class="kw">par</span>(<span class="dt">las =</span> <span class="dv">1</span>, <span class="dt">bty =</span> <span class="st">"n"</span>)
xlim <-<span class="st"> </span><span class="kw">c</span>(<span class="op">-</span><span class="dv">5</span>, <span class="dv">5</span>)
ylim <-<span class="st"> </span><span class="kw">c</span>(<span class="dv">0</span>, <span class="fl">0.5</span>)
<span class="kw">set.seed</span>(<span class="dv">12</span>)
N <-<span class="st"> </span><span class="dv">2000</span>
rr <-<span class="st"> </span><span class="kw">rnorm</span>(N)
rr2 <-<span class="st"> </span><span class="kw">rnorm</span>(N<span class="op">^</span><span class="dv">2</span>)
rr3 <-<span class="st"> </span><span class="kw">rnorm</span>(N <span class="op">+</span><span class="st"> </span><span class="fl">0.3</span>)
rrd <-<span class="st"> </span><span class="kw">density</span>(rr)
rrd2 <-<span class="st"> </span><span class="kw">density</span>(rr2)
rrd3 <-<span class="st"> </span><span class="kw">density</span>(rr3)
main <-<span class="st"> </span><span class="kw">paste0</span>(N, <span class="st">" points but plot better"</span>)
xlab <-<span class="st"> "Points in space"</span>
<span class="cf">if</span> (bm <span class="op">==</span><span class="st"> </span><span class="dv">1</span>) {
<span class="kw">layout</span>(<span class="kw">matrix</span>(<span class="kw">c</span>(<span class="kw">rep</span>(<span class="dv">1</span>,
<span class="dv">3</span>), <span class="dv">2</span><span class="op">:</span><span class="dv">4</span>), <span class="dv">2</span>, <span class="dv">3</span>, <span class="dt">byrow =</span> <span class="ot">TRUE</span>))
sc <-<span class="st"> </span><span class="dv">1</span>
<span class="kw">plot</span>(rr, <span class="dt">las =</span> <span class="dv">1</span>, <span class="dt">bty =</span> <span class="st">"n"</span>,
<span class="dt">col =</span> <span class="kw">adjustcolor</span>(<span class="kw">viridis</span>(N),
<span class="fl">0.5</span>), <span class="dt">pch =</span> <span class="dv">20</span>,
<span class="dt">cex =</span> <span class="kw">runif</span>(<span class="dv">10</span>, <span class="dv">1</span>,
<span class="dv">5</span>), <span class="dt">main =</span> main,
<span class="dt">xlab =</span> xlab)
<span class="cf">for</span> (r <span class="cf">in</span> <span class="kw">list</span>(rrd, rrd2,
rrd3)) {
<span class="kw">plot</span>(r, <span class="dt">xlim =</span> xlim,
<span class="dt">ylim =</span> ylim, <span class="dt">main =</span> <span class="st">""</span>)
<span class="kw">polygon</span>(r, <span class="dt">col =</span> <span class="kw">adjustcolor</span>(<span class="kw">viridis</span>(<span class="dv">250</span>)[sc],
<span class="fl">0.5</span>), <span class="dt">border =</span> <span class="kw">viridis</span>(<span class="dv">250</span>)[sc])
sc <-<span class="st"> </span>sc <span class="op">+</span><span class="st"> </span><span class="dv">100</span>
}
} <span class="cf">else</span> {
<span class="kw">par</span>(<span class="dt">mfrow =</span> <span class="kw">c</span>(<span class="dv">1</span>, <span class="dv">1</span>))
<span class="kw">plot</span>(rr, <span class="dt">las =</span> <span class="dv">1</span>, <span class="dt">bty =</span> <span class="st">"n"</span>,
<span class="dt">col =</span> <span class="kw">adjustcolor</span>(<span class="kw">viridis</span>(N),
<span class="fl">0.5</span>), <span class="dt">pch =</span> <span class="dv">20</span>,
<span class="dt">cex =</span> <span class="kw">runif</span>(<span class="dv">10</span>, <span class="dv">1</span>,
<span class="dv">5</span>), <span class="dt">main =</span> main,
<span class="dt">xlab =</span> xlab)
}</code></pre></div>
<p><img src="Lesson5_rmd_files/figure-html/unnamed-chunk-2-1.png" width="672" /></p>
<p>Figure 2. Example of a plot with improved graphics and its associated code embedded into the output document from RMarkdown.</p>
</div>
<div id="and-tables" class="section level2">
<h2>And tables</h2>
<p>Table 1. Definitions of model parameters for individual hosts and <strong>parasites</strong>. Dimensions and units: -, dimensionless; cm, centimetres; J, Joules; L, length.</p>
<table>
<thead>
<tr class="header">
<th align="center">Parameter</th>
<th align="left">Definition</th>
<th align="right">Dimension<br/>(unit)</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center"><em>L</em></td>
<td align="left">structural length</td>
<td align="right">cm</td>
</tr>
<tr class="even">
<td align="center"><em>ee</em></td>
<td align="left">scaled reserve density</td>
<td align="right">J (cm<sup>3</sup>)</td>
</tr>
<tr class="odd">
<td align="center"><em>D</em></td>
<td align="left">host development</td>
<td align="right">---</td>
</tr>
<tr class="even">
<td align="center"><em>RH</em></td>
<td align="left">energy in reproduction buffer</td>
<td align="right">J</td>
</tr>
</tbody>
</table>
</div>
<div id="use-buttons-or-tabs-for-sub-chapters" class="section level2 tabset tabset-fade tabset-pills">
<h2>Use buttons or tabs for sub-chapters</h2>
<div id="chapter-1" class="section level3">
<h3>Chapter 1</h3>
<p>. . . . .</p>
<p><em>Then you can add whatever you want here</em> like you would normally write in the <code>Rmd</code> file.</p>
<p>. . . . .</p>
</div>
<div id="chapter-2-with-new-code" class="section level3">
<h3>Chapter 2 (with new code)</h3>
<p>Here's an Easter egg for you ...</p>
<div id="htmlwidget-1ab56893abd9ca76ccf2" style="width:672px;height:480px;" class="plotly html-widget"></div>
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</div>
<div id="more-tables" class="section level3">
<h3>More tables</h3>
<p>Here's a new way of creating tables using the <code>DT</code> package</p>
<div id="htmlwidget-d303ae407d0d0ffab9ff" style="width:100%;height:auto;" class="datatables html-widget"></div>
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position: absolute; width: 200px;\">\n <div data-min=\"3\" data-max=\"5\"><\/div>\n <span style=\"float: left;\"><\/span>\n <span style=\"float: right;\"><\/span>\n <\/div>\n <\/td>\n <td data-type=\"number\" style=\"vertical-align: top;\">\n <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n <\/div>\n <div style=\"display: none; position: absolute; width: 200px;\">\n <div data-min=\"1\" data-max=\"8\"><\/div>\n <span style=\"float: left;\"><\/span>\n <span style=\"float: right;\"><\/span>\n <\/div>\n <\/td>\n<\/tr>","caption":"<caption>Table 1. The 'mtcars' dataset presented in a datatable. Try editing the columns and cells.<\/caption>","editable":{"target":"cell","disable":{"columns":null}},"data":[["Mazda RX4","Mazda RX4 Wag","Datsun 710","Hornet 4 Drive","Hornet Sportabout","Valiant","Duster 360","Merc 240D","Merc 230","Merc 280","Merc 280C","Merc 450SE","Merc 450SL","Merc 450SLC","Cadillac Fleetwood","Lincoln Continental","Chrysler Imperial","Fiat 128","Honda Civic","Toyota Corolla","Toyota Corona","Dodge Challenger","AMC Javelin","Camaro Z28","Pontiac Firebird","Fiat X1-9","Porsche 914-2","Lotus Europa","Ford Pantera L","Ferrari Dino","Maserati Bora","Volvo 142E"],[21,21,22.8,21.4,18.7,18.1,14.3,24.4,22.8,19.2,17.8,16.4,17.3,15.2,10.4,10.4,14.7,32.4,30.4,33.9,21.5,15.5,15.2,13.3,19.2,27.3,26,30.4,15.8,19.7,15,21.4],[6,6,4,6,8,6,8,4,4,6,6,8,8,8,8,8,8,4,4,4,4,8,8,8,8,4,4,4,8,6,8,4],[160,160,108,258,360,225,360,146.7,140.8,167.6,167.6,275.8,275.8,275.8,472,460,440,78.7,75.7,71.1,120.1,318,304,350,400,79,120.3,95.1,351,145,301,121],[110,110,93,110,175,105,245,62,95,123,123,180,180,180,205,215,230,66,52,65,97,150,150,245,175,66,91,113,264,175,335,109],[3.9,3.9,3.85,3.08,3.15,2.76,3.21,3.69,3.92,3.92,3.92,3.07,3.07,3.07,2.93,3,3.23,4.08,4.93,4.22,3.7,2.76,3.15,3.73,3.08,4.08,4.43,3.77,4.22,3.62,3.54,4.11],[2.62,2.875,2.32,3.215,3.44,3.46,3.57,3.19,3.15,3.44,3.44,4.07,3.73,3.78,5.25,5.424,5.345,2.2,1.615,1.835,2.465,3.52,3.435,3.84,3.845,1.935,2.14,1.513,3.17,2.77,3.57,2.78],[16.46,17.02,18.61,19.44,17.02,20.22,15.84,20,22.9,18.3,18.9,17.4,17.6,18,17.98,17.82,17.42,19.47,18.52,19.9,20.01,16.87,17.3,15.41,17.05,18.9,16.7,16.9,14.5,15.5,14.6,18.6],[0,0,1,1,0,1,0,1,1,1,1,0,0,0,0,0,0,1,1,1,1,0,0,0,0,1,0,1,0,0,0,1],[1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,1,1,1,1,1,1,1],[4,4,4,3,3,3,3,4,4,4,4,3,3,3,3,3,3,4,4,4,3,3,3,3,3,4,5,5,5,5,5,4],[4,4,1,1,2,1,4,2,2,4,4,3,3,3,4,4,4,1,2,1,1,2,2,4,2,1,2,2,4,6,8,2]],"container":"<table class=\"cell-border stripe\">\n <thead>\n <tr>\n <th> <\/th>\n <th>mpg<\/th>\n <th>cyl<\/th>\n <th>disp<\/th>\n <th>hp<\/th>\n <th>drat<\/th>\n <th>wt<\/th>\n <th>qsec<\/th>\n <th>vs<\/th>\n <th>am<\/th>\n <th>gear<\/th>\n <th>carb<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"pageLength":5,"scrollX":true,"columnDefs":[{"className":"dt-right","targets":[1,2,3,4,5,6,7,8,9,10,11]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true,"lengthMenu":[5,10,25,50,100]}},"evals":[],"jsHooks":[]}</script>
<!-- *** -->
</div>
</div>
<div id="embed-code-from-different-languages" class="section level2">
<h2>Embed code from different languages</h2>
<div id="this-is-r-code" class="section level3">
<h3>This is <code>R</code> code</h3>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">pck <-<span class="st"> </span><span class="dv">0</span>
<span class="cf">if</span> (pck <span class="op">==</span><span class="st"> </span><span class="dv">1</span>) {
p <-<span class="st"> </span><span class="kw">c</span>(<span class="st">"rJava"</span>, <span class="st">"RNetLogo"</span>)
<span class="kw">remove.packages</span>(p)
<span class="co"># then install rJava and</span>
<span class="co"># RNetLogo from source</span>
<span class="kw">install.packages</span>(<span class="st">"rJava"</span>,
<span class="dt">repos =</span> <span class="st">"https://cran.r-project.org/"</span>)
<span class="kw">install.packages</span>(<span class="st">"RNetLogo"</span>,
<span class="dt">repos =</span> <span class="st">"https://cran.r-project.org/"</span>)
}</code></pre></div>
</div>
<div id="shellbash" class="section level3">
<h3><code>shell/bash</code></h3>
<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="bu">echo</span> <span class="st">"Hello Bash!"</span>
<span class="bu">pwd</span> <span class="co"># check working dir</span>
<span class="fu">git</span> init <span class="co"># initialise git</span></code></pre></div>
</div>
<div id="octave-and-matlab-from-the-rmatlab-package." class="section level3">
<h3>Octave (and MATLAB from the <code>RMatlab</code> package).</h3>
<p><a href="https://cran.r-project.org/web/packages/R.matlab/index.html"><code>RMatlab documentation</code></a>.</p>
<div class="sourceCode"><pre class="sourceCode octave"><code class="sourceCode octave">b = [<span class="fl">4</span>; <span class="fl">9</span>; <span class="fl">2</span>] <span class="co"># Column vector</span>
A = [ <span class="fl">3</span> <span class="fl">4</span> <span class="fl">5</span>;
<span class="fl">1</span> <span class="fl">3</span> <span class="fl">1</span>;
<span class="fl">3</span> <span class="fl">5</span> <span class="fl">9</span> ]
x = A \ b <span class="co"># Solve the system Ax = b</span></code></pre></div>
</div>
<div id="html" class="section level3">
<h3>HTML</h3>
<div class="sourceCode"><pre class="sourceCode html"><code class="sourceCode html"><span class="co"><!-- links--></span>
<span class="kw"><div</span><span class="ot"> class=</span><span class="st">"footer"</span><span class="kw">></span>
<span class="kw"><a</span><span class="ot"> href=</span><span class="st">"dd_feed.html"</span>
<span class="ot"> class=</span><span class="st">"transition fade_in"</span><span class="kw">></span>
Latest post
<span class="kw"></a></span>
<span class="dv">&nbsp;</span> <span class="dv">&nbsp;</span> <span class="dv">&nbsp;</span>
<span class="kw"><a</span><span class="ot"> href=</span><span class="st">"dd_contact.html"</span>
<span class="ot"> class=</span><span class="st">"transition fade_in"</span><span class="kw">></span>
Contact
<span class="kw"></a></span>
<span class="dv">&nbsp;</span> <span class="dv">&nbsp;</span> <span class="dv">&nbsp;</span>
<span class="kw"><a</span><span class="ot"> href=</span><span class="st">"dd_subscribe.html"</span>
<span class="ot"> class=</span><span class="st">"transition fade_in"</span><span class="kw">></span>
Subscribe
<span class="kw"></a></span>
<span class="kw"></div></span></code></pre></div>
</div>
<div id="css" class="section level3">
<h3>CSS</h3>
<div class="sourceCode"><pre class="sourceCode css"><code class="sourceCode css"># custom code for the tabs in this file
<span class="fl">.btn</span> <span class="kw">{</span>
<span class="kw">border-width:</span> <span class="dt">0</span> <span class="dt">0px</span> <span class="dt">0px</span> <span class="dt">0px</span><span class="kw">;</span>
<span class="kw">font-weight:</span> <span class="dt">normal</span><span class="kw">;</span>
<span class="kw">text-transform:</span> <span class="kw">;</span>
<span class="kw">}</span>
<span class="fl">.btn-default</span> <span class="kw">{</span>
<span class="kw">color:</span> <span class="dt">#f08080</span><span class="kw">;</span>
<span class="kw">background-color:</span> <span class="dt">#ffffff</span><span class="kw">;</span>
<span class="kw">border-color:</span> <span class="dt">#ffffff</span><span class="kw">;</span>
<span class="kw">}</span></code></pre></div>
</div>
<div id="javascript-to-access-html-and-css" class="section level3">
<h3>Javascript to access <code>html</code> and <code>css</code></h3>
<div class="sourceCode"><pre class="sourceCode js"><code class="sourceCode javascript"><span class="at">$</span>(<span class="st">'.title'</span>).<span class="at">css</span>(<span class="st">'color'</span><span class="op">,</span> <span class="st">'red'</span>)</code></pre></div>
</div>
<div id="python" class="section level3">
<h3>Python</h3>
<div class="sourceCode"><pre class="sourceCode python"><code class="sourceCode python">x <span class="op">=</span> <span class="st">'hello, python world!'</span>
<span class="bu">print</span>(x.split(<span class="st">' '</span>))</code></pre></div>
</div>
<div id="heres-a-complete-list-of-available-languages" class="section level3">
<h3>Here's a complete list of available languages</h3>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">names</span>(knitr<span class="op">::</span>knit_engines<span class="op">$</span><span class="kw">get</span>())</code></pre></div>
<pre><code>## [1] "awk"
## [2] "bash"
## [3] "coffee"
## [4] "gawk"
## [5] "groovy"
## [6] "haskell"
## [7] "lein"
## [8] "mysql"
## [9] "node"
## [10] "octave"
## [11] "perl"
## [12] "psql"
## [13] "Rscript"
## [14] "ruby"
## [15] "sas"
## [16] "scala"
## [17] "sed"
## [18] "sh"
## [19] "stata"
## [20] "zsh"
## [21] "highlight"
## [22] "Rcpp"
## [23] "tikz"
## [24] "dot"
## [25] "c"
## [26] "cc"
## [27] "fortran"
## [28] "fortran95"
## [29] "asy"
## [30] "cat"
## [31] "asis"
## [32] "stan"
## [33] "block"
## [34] "block2"
## [35] "js"
## [36] "css"
## [37] "sql"
## [38] "go"
## [39] "python"
## [40] "julia"
## [41] "sass"
## [42] "scss"
## [43] "R"
## [44] "bslib"
## [45] "targets"</code></pre>
</div>
</div>
</div>
<div id="references" class="section level1">
<h1>References</h1>
<p>[1] Efthimiades, S., Physical meaning and derivation of Schrodinger and Dirac equations, Department of Natural Sciences, Fordham University, <a href="https://www.academia.edu/33763545/Concise_derivation_of_the_Schr%C3%B6dinger_equation">doi: d34464566</a>.</p>
</div>
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<hr />
<ol>
<li id="fn1"><p>Here is the footnote you created earlier, automatically formatted<a href="#fnref1">↩</a></p></li>
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