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index.html
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<!DOCTYPE html>
<html lang="en"><head>
<script src="index_files/libs/clipboard/clipboard.min.js"></script>
<script src="index_files/libs/quarto-html/tabby.min.js"></script>
<script src="index_files/libs/quarto-html/popper.min.js"></script>
<script src="index_files/libs/quarto-html/tippy.umd.min.js"></script>
<link href="index_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="index_files/libs/quarto-html/light-border.css" rel="stylesheet">
<link href="index_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
<link href="index_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
<link href="index_files/libs/quarto-contrib/fontawesome6-0.1.0/all.css" rel="stylesheet">
<link href="index_files/libs/quarto-contrib/fontawesome6-0.1.0/latex-fontsize.css" rel="stylesheet"><meta charset="utf-8">
<meta name="generator" content="quarto-1.3.433">
<title>index</title>
<meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui">
<link rel="stylesheet" href="index_files/libs/revealjs/dist/reset.css">
<link rel="stylesheet" href="index_files/libs/revealjs/dist/reveal.css">
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
div.columns{display: flex; gap: min(4vw, 1.5em);}
div.column{flex: auto; overflow-x: auto;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
ul.task-list li input[type="checkbox"] {
width: 0.8em;
margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */
vertical-align: middle;
}
/* CSS for syntax highlighting */
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
div.sourceCode { margin: 1em 0; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
pre > code.sourceCode { white-space: pre-wrap; }
pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
{ counter-reset: source-line 0; }
pre.numberSource code > span
{ position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
{ content: counter(source-line);
position: relative; left: -1em; text-align: right; vertical-align: baseline;
border: none; display: inline-block;
-webkit-touch-callout: none; -webkit-user-select: none;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
color: #aaaaaa;
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode
{ color: #003b4f; background-color: #f1f3f5; }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span { color: #003b4f; } /* Normal */
code span.al { color: #ad0000; } /* Alert */
code span.an { color: #5e5e5e; } /* Annotation */
code span.at { color: #657422; } /* Attribute */
code span.bn { color: #ad0000; } /* BaseN */
code span.bu { } /* BuiltIn */
code span.cf { color: #003b4f; } /* ControlFlow */
code span.ch { color: #20794d; } /* Char */
code span.cn { color: #8f5902; } /* Constant */
code span.co { color: #5e5e5e; } /* Comment */
code span.cv { color: #5e5e5e; font-style: italic; } /* CommentVar */
code span.do { color: #5e5e5e; font-style: italic; } /* Documentation */
code span.dt { color: #ad0000; } /* DataType */
code span.dv { color: #ad0000; } /* DecVal */
code span.er { color: #ad0000; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #ad0000; } /* Float */
code span.fu { color: #4758ab; } /* Function */
code span.im { color: #00769e; } /* Import */
code span.in { color: #5e5e5e; } /* Information */
code span.kw { color: #003b4f; } /* Keyword */
code span.op { color: #5e5e5e; } /* Operator */
code span.ot { color: #003b4f; } /* Other */
code span.pp { color: #ad0000; } /* Preprocessor */
code span.sc { color: #5e5e5e; } /* SpecialChar */
code span.ss { color: #20794d; } /* SpecialString */
code span.st { color: #20794d; } /* String */
code span.va { color: #111111; } /* Variable */
code span.vs { color: #20794d; } /* VerbatimString */
code span.wa { color: #5e5e5e; font-style: italic; } /* Warning */
</style>
<link rel="stylesheet" href="index_files/libs/revealjs/dist/theme/quarto.css">
<link href="index_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/reveal-menu/menu.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/reveal-menu/quarto-menu.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/quarto-support/footer.css" rel="stylesheet">
<style type="text/css">
.callout {
margin-top: 1em;
margin-bottom: 1em;
border-radius: .25rem;
}
.callout.callout-style-simple {
padding: 0em 0.5em;
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
display: flex;
}
.callout.callout-style-default {
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
}
.callout .callout-body-container {
flex-grow: 1;
}
.callout.callout-style-simple .callout-body {
font-size: 1rem;
font-weight: 400;
}
.callout.callout-style-default .callout-body {
font-size: 0.9rem;
font-weight: 400;
}
.callout.callout-titled.callout-style-simple .callout-body {
margin-top: 0.2em;
}
.callout:not(.callout-titled) .callout-body {
display: flex;
}
.callout:not(.no-icon).callout-titled.callout-style-simple .callout-content {
padding-left: 1.6em;
}
.callout.callout-titled .callout-header {
padding-top: 0.2em;
margin-bottom: -0.2em;
}
.callout.callout-titled .callout-title p {
margin-top: 0.5em;
margin-bottom: 0.5em;
}
.callout.callout-titled.callout-style-simple .callout-content p {
margin-top: 0;
}
.callout.callout-titled.callout-style-default .callout-content p {
margin-top: 0.7em;
}
.callout.callout-style-simple div.callout-title {
border-bottom: none;
font-size: .9rem;
font-weight: 600;
opacity: 75%;
}
.callout.callout-style-default div.callout-title {
border-bottom: none;
font-weight: 600;
opacity: 85%;
font-size: 0.9rem;
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-default div.callout-content {
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-simple .callout-icon::before {
height: 1rem;
width: 1rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 1rem 1rem;
}
.callout.callout-style-default .callout-icon::before {
height: 0.9rem;
width: 0.9rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 0.9rem 0.9rem;
}
.callout-title {
display: flex
}
.callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
.callout.no-icon::before {
display: none !important;
}
.callout.callout-titled .callout-body > .callout-content > :last-child {
margin-bottom: 0.5rem;
}
.callout.callout-titled .callout-icon::before {
margin-top: .5rem;
padding-right: .5rem;
}
.callout:not(.callout-titled) .callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
/* Callout Types */
div.callout-note {
border-left-color: #4582ec !important;
}
div.callout-note .callout-icon::before {
background-image: url('data:image/png;base64,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');
}
div.callout-note.callout-style-default .callout-title {
background-color: #dae6fb
}
div.callout-important {
border-left-color: #d9534f !important;
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<body class="quarto-light">
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<div class="title-slide-container">
<div class="title-slide-content">
<div class="columns">
<div class="column logo" style="width:30%;">
<p><img data-src="https://raw.githubusercontent.com/rdatatoolbox/.github/main/profile/logo-rdatatoolbox_150dpi.png"></p>
</div><div class="column" style="width:70%;">
<div class="title">
<p>Reproducible research</p>
</div>
<div class="subtitle">
<p>Good practices</p>
</div>
<div class="date">
<p>December 2023</p>
</div>
<div class="columns">
<div class="column author" style="width:45%;">
<p>Nicolas Casajus<br> <a href="mailto:[email protected]"><i class="fa-solid fa-paper-plane" aria-label="paper-plane"></i></a> <a href="https://github.com/ahasverus"><i class="fa-brands fa-github" aria-label="github"></i></a> <a href="https://nicolascasajus.fr"><i class="fa-solid fa-globe" aria-label="globe"></i></a></p>
<div class="affiliation">
<p><i class="fa-solid fa-house" aria-label="house"></i> <a href="https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/">FRB-CESAB</a></p>
</div>
</div><!--
::: {.column .author width="45%"}
Camille Coux<br/>
[](mailto:[email protected])
[](https://github.com/camillecoux)
[](https://www.fondationbiodiversite.fr/en/membre/camille-coux/)
::: {.affiliation}
[https://github.com/frbcesab](https://github.com/frbcesab)
:::
:::
-->
</div>
</div>
</div>
</div>
</div>
</section>
<section>
<section id="introduction" class="title-slide slide level1 center">
<h1>Introduction</h1>
</section>
<section id="what-is-reproducibility" class="slide level2">
<h2>What is reproducibility?</h2>
<p><br></p>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/reproducible-matrix.jpg" style="width:50.0%"></p>
<figcaption>Source: <a href="https://eliocamp.github.io/reproducibility-with-r/materials/day1/01-introduction/">https://eliocamp.github.io</a></figcaption>
</figure>
</div>
<p><strong>Reproducibility</strong> is about results that can be obtained by someone else (or you in the future) given the <strong>same data</strong> and the <strong>same code</strong>. This is a technical problem.</p>
<p><br></p>
<p><i class="fa-solid fa-hand-point-right" aria-label="hand-point-right"></i> We talk about <strong>Computational reproducibility</strong></p>
</section>
<section id="why-does-it-matter" class="slide level2">
<h2>Why does it matter?</h2>
<blockquote>
<p>An <strong>article</strong> about computational results is advertising, not scholarship. The actual scholarship is the full <strong>software environment</strong>, <strong>code</strong> and <strong>data</strong>, that produced the result.</p>
</blockquote>
<div class="citation">
<p>Claerbout & Karrenbach (1992)<sup>1</sup></p>
</div>
<p><br></p>
<aside><ol class="aside-footnotes"><li id="fn1"><p><a href="https://doi.org/10.1190/1.1822162" class="uri">https://doi.org/10.1190/1.1822162</a></p></li></ol></aside></section>
<section id="why-does-it-matter-1" class="slide level2">
<h2>Why does it matter?</h2>
<blockquote>
<p>An <strong>article</strong> about computational results is advertising, not scholarship. The actual scholarship is the full <strong>software environment</strong>, <strong>code</strong> and <strong>data</strong>, that produced the result.</p>
</blockquote>
<div class="citation">
<p>Claerbout & Karrenbach (1992)<sup>1</sup></p>
</div>
<p><br></p>
<blockquote>
<p>Reproducibility has the potential to serve as a minimum standard for <strong>judging scientific claims</strong> (…).</p>
</blockquote>
<div class="citation">
<p>Peng (2011)<sup>2</sup></p>
</div>
<aside><ol class="aside-footnotes"><li id="fn2"><p><a href="https://doi.org/10.1190/1.1822162" class="uri">https://doi.org/10.1190/1.1822162</a></p></li><li id="fn3"><p><a href="https://doi.org/10.1126/science.1213847" class="uri">https://doi.org/10.1126/science.1213847</a></p></li></ol></aside></section>
<section id="why-does-it-matter-2" class="slide level2">
<h2>Why does it matter?</h2>
<blockquote>
<p>An <strong>article</strong> about computational results is advertising, not scholarship. The actual scholarship is the full <strong>software environment</strong>, <strong>code</strong> and <strong>data</strong>, that produced the result.</p>
</blockquote>
<div class="citation">
<p>Claerbout & Karrenbach (1992)<sup>1</sup></p>
</div>
<p><br></p>
<blockquote>
<p>Reproducibility has the potential to serve as a minimum standard for <strong>judging scientific claims</strong> (…).</p>
</blockquote>
<div class="citation">
<p>Peng (2011)<sup>2</sup></p>
</div>
<p><br></p>
<p><i class="fa-solid fa-hand-point-right" aria-label="hand-point-right"></i> Sharing the code and the data is now a prerequisite for publishing in many journals</p>
<aside><ol class="aside-footnotes"><li id="fn4"><p><a href="https://doi.org/10.1190/1.1822162" class="uri">https://doi.org/10.1190/1.1822162</a></p></li><li id="fn5"><p><a href="https://doi.org/10.1126/science.1213847" class="uri">https://doi.org/10.1126/science.1213847</a></p></li></ol></aside></section>
<section id="reproducibility-spectrum" class="slide level2">
<h2>Reproducibility spectrum</h2>
<p><br></p>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/peng-science.jpg" style="width:75.0%"></p>
<figcaption>Source: Peng (2011)<sup>1</sup></figcaption>
</figure>
</div>
<div class="fragment">
<p><br></p>
<p>Each degree of reproducibility requires additional skills and time. While some of those skills (e.g. literal programming, version control, setting up environments) pay off in the long run, they can require a high up-front investment.</p>
</div>
<aside><ol class="aside-footnotes"><li id="fn6"><p><a href="https://doi.org/10.1126/science.1213847" class="uri">https://doi.org/10.1126/science.1213847</a></p></li></ol></aside></section>
<section id="concepts" class="slide level2">
<h2>Concepts</h2>
<p>According to Wilson <em>et al.</em> (2017)<sup>1</sup>, good practices for a better reproducibility can be organized into the following six topics:</p>
<p><br> <br> <br></p>
<div class="columns">
<div class="column center" style="width:33%;">
<p><i class="fa-solid fa-database" aria-label="database"></i> Data management</p>
</div><div class="column center" style="width:33%;">
<p><i class="fa-solid fa-folder" aria-label="folder"></i> Project organization</p>
</div><div class="column center" style="width:33%;">
<p><i class="fa-solid fa-code-branch" aria-label="code-branch"></i> Tracking changes</p>
</div>
</div>
<p><br></p>
<div class="columns">
<div class="column center" style="width:33%;">
<p><i class="fa-brands fa-github" aria-label="github"></i> Collaboration</p>
</div><div class="column center" style="width:33%;">
<p><i class="fa-brands fa-markdown" aria-label="markdown"></i> Manuscript</p>
</div><div class="column center" style="width:33%;">
<p><i class="fa-brands fa-r-project" aria-label="r-project"></i> Code & Software</p>
</div>
</div>
<aside><ol class="aside-footnotes"><li id="fn7"><p><a href="https://doi.org/10.1371/journal.pcbi.1005510" class="uri">https://doi.org/10.1371/journal.pcbi.1005510</a></p></li></ol></aside></section></section>
<section>
<section id="fa-database-data-management" class="title-slide slide level1 center">
<h1><i class="fa-solid fa-database" aria-label="database"></i> Data management</h1>
</section>
<section id="raw-data" class="slide level2">
<h2>Raw data</h2>
<div class="columns">
<div class="column" style="width:50%;">
<p><strong>General recommendations</strong><sup>1</sup></p>
<ul>
<li>Save and backup the raw data</li>
<li>Do not modify raw data (even for minor changes)</li>
<li>Raw data should be in a read-only mode (🔒)</li>
<li>Any modification produces an output or a derived data</li>
<li>Write code for data acquisition (when possible)
<ul>
<li>database requests</li>
<li>api requests</li>
<li><code>download.file()</code>, <code>wget</code>, <code>curl</code>, etc.</li>
</ul></li>
<li>Describe and document raw data (<code>README</code>, metadata, etc.)</li>
</ul>
</div><div class="column" style="width:15%;">
</div><div class="column" style="width:35%;">
</div>
</div>
<aside><ol class="aside-footnotes"><li id="fn8"><p><a href="https://doi.org/10.1371/journal.pcbi.1005510" class="uri">https://doi.org/10.1371/journal.pcbi.1005510</a></p></li></ol></aside></section>
<section id="raw-data-1" class="slide level2">
<h2>Raw data</h2>
<div class="columns">
<div class="column" style="width:50%;">
<p><strong>General recommendations</strong><sup>1</sup></p>
<ul>
<li>Save and backup the raw data</li>
<li>Do not modify raw data (even for minor changes)</li>
<li>Raw data should be in a read-only mode (🔒)</li>
<li>Any modification produces an output or a derived data</li>
<li>Write code for data acquisition (when possible)
<ul>
<li>database requests</li>
<li>api requests</li>
<li><code>download.file()</code>, <code>wget</code>, <code>curl</code>, etc.</li>
</ul></li>
<li>Describe and document raw data (<code>README</code>, metadata, etc.)</li>
</ul>
</div><div class="column" style="width:15%;">
</div><div class="column" style="width:35%;">
<p><i class="fa-solid fa-lightbulb" aria-label="lightbulb"></i> <strong>Proposed files organization</strong></p>
<pre><code>project/
└─ data/
└─ raw-data/
├─ raw-data-1.csv 🔒
├─ ...
└─ README.md</code></pre>
</div>
</div>
<aside><ol class="aside-footnotes"><li id="fn9"><p><a href="https://doi.org/10.1371/journal.pcbi.1005510" class="uri">https://doi.org/10.1371/journal.pcbi.1005510</a></p></li></ol></aside></section>
<section id="derived-data" class="slide level2">
<h2>Derived data</h2>
<div class="columns">
<div class="column" style="width:50%;">
<p><strong>General recommendations</strong><sup>1</sup></p>
<ul>
<li>Modified raw data become a derived data (or an output)</li>
<li>Record all the steps used to process data (<i class="fa-brands fa-r-project" aria-label="r-project"></i> <code>|</code> <i class="fa-brands fa-python" aria-label="python"></i> <code>|</code> <i class="fa-solid fa-terminal" aria-label="terminal"></i>)</li>
<li>Create the data you wish to see in the world</li>
<li>Create analysis-friendly data: <code>tidy data</code></li>
</ul>
</div><div class="column" style="width:15%;">
</div><div class="column" style="width:35%;">
<p><i class="fa-solid fa-lightbulb" aria-label="lightbulb"></i> <strong>Proposed files organization</strong></p>
<pre><code>project/
└─ data/
└─ raw-data/
├─ raw-data-1.csv 🔒
├─ ...
└─ README.md</code></pre>
</div>
</div>
<aside><ol class="aside-footnotes"><li id="fn10"><p><a href="https://doi.org/10.1371/journal.pcbi.1005510" class="uri">https://doi.org/10.1371/journal.pcbi.1005510</a></p></li></ol></aside></section>
<section id="derived-data-1" class="slide level2">
<h2>Derived data</h2>
<div class="columns">
<div class="column" style="width:50%;">
<p><strong>General recommendations</strong><sup>1</sup></p>
<ul>
<li>Modified raw data become a derived data (or an output)</li>
<li>Record all the steps used to process data (<i class="fa-brands fa-r-project" aria-label="r-project"></i> <code>|</code> <i class="fa-brands fa-python" aria-label="python"></i> <code>|</code> <i class="fa-solid fa-terminal" aria-label="terminal"></i>)</li>
<li>Create the data you wish to see in the world</li>
<li>Create analysis-friendly data: <code>tidy data</code></li>
</ul>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/tidy-data.jpg"></p>
<figcaption>Source: <a href="https://allisonhorst.com/other-r-fun" class="uri">https://allisonhorst.com/other-r-fun</a></figcaption>
</figure>
</div>
</div><div class="column" style="width:15%;">
</div><div class="column" style="width:35%;">
<p><i class="fa-solid fa-lightbulb" aria-label="lightbulb"></i> <strong>Proposed files organization</strong></p>
<pre><code>project/
└─ data/
└─ raw-data/
├─ raw-data-1.csv 🔒
├─ ...
└─ README.md</code></pre>
</div>
</div>
<aside><ol class="aside-footnotes"><li id="fn11"><p><a href="https://doi.org/10.1371/journal.pcbi.1005510" class="uri">https://doi.org/10.1371/journal.pcbi.1005510</a></p></li></ol></aside></section>
<section id="derived-data-2" class="slide level2">
<h2>Derived data</h2>
<div class="columns">
<div class="column" style="width:50%;">
<p><strong>General recommendations</strong><sup>1</sup></p>
<ul>
<li>Modified raw data become a derived data (or an output)</li>
<li>Record all the steps used to process data (<i class="fa-brands fa-r-project" aria-label="r-project"></i> <code>|</code> <i class="fa-brands fa-python" aria-label="python"></i> <code>|</code> <i class="fa-solid fa-terminal" aria-label="terminal"></i>)</li>
<li>Create the data you wish to see in the world</li>
<li>Create analysis-friendly data: <code>tidy data</code></li>
</ul>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/tidy-data.jpg"></p>
<figcaption>Source: <a href="https://allisonhorst.com/other-r-fun" class="uri">https://allisonhorst.com/other-r-fun</a></figcaption>
</figure>
</div>
</div><div class="column" style="width:15%;">
</div><div class="column" style="width:35%;">
<p><i class="fa-solid fa-lightbulb" aria-label="lightbulb"></i> <strong>Proposed files organization</strong></p>
<pre><code>project/
├─ data/
│ ├─ raw-data/
│ │ ├─ raw-data-1.csv 🔒
│ │ ├─ ...
│ │ └─ README.md
│ │
│ └─ derived-data/
│ ├─ derived-data-1.RData
│ └─ ...
│
└─ code/
├─ process-raw-data-1.R
└─ ...</code></pre>
</div>
</div>
<aside><ol class="aside-footnotes"><li id="fn12"><p><a href="https://doi.org/10.1371/journal.pcbi.1005510" class="uri">https://doi.org/10.1371/journal.pcbi.1005510</a></p></li></ol></aside></section>
<section id="derived-data-3" class="slide level2">
<h2>Derived data</h2>
<div class="columns">
<div class="column" style="width:50%;">
<p><strong>General recommendations</strong><sup>1</sup></p>
<ul>
<li>Modified raw data become a derived data (or an output)</li>
<li>Record all the steps used to process data (<i class="fa-brands fa-r-project" aria-label="r-project"></i> <code>|</code> <i class="fa-brands fa-python" aria-label="python"></i> <code>|</code> <i class="fa-solid fa-terminal" aria-label="terminal"></i>)</li>
<li>Create the data you wish to see in the world</li>
<li>Create analysis-friendly data: <code>tidy data</code></li>
</ul>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/tidy-data.jpg"></p>
<figcaption>Source: <a href="https://allisonhorst.com/other-r-fun" class="uri">https://allisonhorst.com/other-r-fun</a></figcaption>
</figure>
</div>
</div><div class="column" style="width:15%;">
</div><div class="column" style="width:35%;">
<p><i class="fa-solid fa-lightbulb" aria-label="lightbulb"></i> <strong>Proposed files organization</strong></p>
<pre><code>project/
├─ data/
│ ├─ raw-data/
│ │ ├─ raw-data-1.csv 🔒
│ │ ├─ ...
│ │ └─ README.md
│ │
│ └─ derived-data/
│ ├─ derived-data-1.RData
│ └─ ...
│
└─ code/
├─ process-raw-data-1.R
└─ ...</code></pre>
<p><br></p>
<p><i class="fa-solid fa-lightbulb" aria-label="lightbulb"></i> <strong>Alternative</strong></p>
<pre><code>project/
├─ data/
│ ├─ raw-data-1.csv 🔒
│ ├─ ...
│ └─ README.md
│
├─ outputs/
│ ├─ output-1.RData
│ └─ ...
│
└─ code/
├─ process-raw-data-1.R
└─ ...</code></pre>
</div>
</div>
<aside><ol class="aside-footnotes"><li id="fn13"><p><a href="https://doi.org/10.1371/journal.pcbi.1005510" class="uri">https://doi.org/10.1371/journal.pcbi.1005510</a></p></li></ol></aside></section>
<section id="data-submission" class="slide level2">
<h2>Data submission</h2>
<ul>
<li>Submit data to a <strong>reputable DOI-issuing repository</strong> so that others can access and cite it</li>
</ul>
<p><br></p>
<div class="columns">
<div class="column" style="width:20%;">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><a href="https://osf.io/"><img data-src="img/osf-logo.png"></a></p>
</figure>
</div>
</div><div class="column" style="width:20%;">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><a href="https://zenodo.org/"><img data-src="img/zenodo-logo.png"></a></p>
</figure>
</div>
</div><div class="column" style="width:60%;">
</div>
</div>
<p><br></p>
<div class="fragment">
<ul>
<li>Write a <strong>data paper</strong>: <a href="https://www.nature.com/sdata/">Scientific Data</a>, <a href="https://www.sciencedirect.com/journal/data-in-brief">Data in Brief</a>, etc.</li>
</ul>
<p><br></p>
</div>
<div class="fragment">
<ul>
<li>Do not forget to write good <strong>metadata</strong> (e.g. <a href="https://eml.ecoinformatics.org/">EML</a>)</li>
</ul>
<p><br></p>
</div>
<div class="fragment">
<ul>
<li>Develop <strong>tools</strong> to access and handle published data (e.g. API, R package, ShinyApp, etc.)</li>
</ul>
</div>
</section></section>
<section>
<section id="fa-folder-project-organization" class="title-slide slide level1 center">
<h1><i class="fa-solid fa-folder" aria-label="folder"></i> Project organization</h1>
</section>
<section id="first-things-first" class="slide level2">
<h2>First things first</h2>
<blockquote>
<p>« There are only two hard things in Computer Science: cache invalidation and <strong>naming things</strong>. »</p>
</blockquote>
<div class="citation">
<p>Phil Karlton</p>
</div>
<div class="fragment">
<p><br></p>
<p><strong>Three principles for naming files</strong><sup>1</sup></p>
<div class="columns">
<div class="column" style="width:50%;">
<ol type="1">
<li><strong>Human readable</strong></li>
</ol>
</div><div class="column" style="width:50%;">
<ul>
<li>Name contains information on the content</li>
<li>Respect concept of <a href="https://en.wikipedia.org/wiki/Clean_URL#Slug">slug</a> from semantic URLs</li>
</ul>
</div>
</div>
</div>
<aside><ol class="aside-footnotes"><li id="fn14"><p><a href="https://annakrystalli.me/rrresearchACCE20/slides/03_filenaming.html" class="uri">https://annakrystalli.me/rrresearchACCE20/slides/03_filenaming.html</a></p></li></ol></aside></section>
<section id="first-things-first-1" class="slide level2">
<h2>First things first</h2>
<blockquote>
<p>« There are only two hard things in Computer Science: cache invalidation and <strong>naming things</strong>. »</p>
</blockquote>
<div class="citation">
<p>Phil Karlton</p>
</div>
<p><br></p>
<p><strong>Three principles for naming files</strong><sup>1</sup></p>
<div class="columns">
<div class="column" style="width:50%;">
<ol type="1">
<li>Human readable</li>
<li><strong>Machine readable</strong></li>
</ol>
</div><div class="column" style="width:50%;">
<ul>
<li>Regular expression and globbing friendly
<ul>
<li>avoid space and accented characters</li>
<li>good use of punctuation and case</li>
</ul></li>
</ul>
</div>
</div>
<aside><ol class="aside-footnotes"><li id="fn15"><p><a href="https://annakrystalli.me/rrresearchACCE20/slides/03_filenaming.html" class="uri">https://annakrystalli.me/rrresearchACCE20/slides/03_filenaming.html</a></p></li></ol></aside></section>
<section id="first-things-first-2" class="slide level2">
<h2>First things first</h2>
<blockquote>
<p>« There are only two hard things in Computer Science: cache invalidation and <strong>naming things</strong>. »</p>
</blockquote>
<div class="citation">
<p>Phil Karlton</p>
</div>
<p><br></p>
<p><strong>Three principles for naming files</strong><sup>1</sup></p>
<div class="columns">
<div class="column" style="width:50%;">
<ol type="1">
<li>Human readable</li>
<li><strong>Machine readable</strong></li>
</ol>
</div><div class="column" style="width:50%;">
<div class="cell">
<div class="sourceCode cell-code" id="cb7"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a><span class="co"># File names ----</span></span>
<span id="cb7-2"><a href="#cb7-2"></a>files <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"2020-survey_A.csv"</span>, <span class="st">"2021-survey_A.csv"</span>, <span class="st">"2021-survey_B.csv"</span>)</span>
<span id="cb7-3"><a href="#cb7-3"></a></span>
<span id="cb7-4"><a href="#cb7-4"></a><span class="co"># Extract years ----</span></span>
<span id="cb7-5"><a href="#cb7-5"></a><span class="fu">strsplit</span>(files, <span class="st">"-"</span>) <span class="sc">|></span> <span class="co"># Split string by '-'</span></span>
<span id="cb7-6"><a href="#cb7-6"></a> <span class="fu">lapply</span>(<span class="cf">function</span>(x) x[<span class="dv">1</span>]) <span class="sc">|></span> <span class="co"># Get the first element</span></span>
<span id="cb7-7"><a href="#cb7-7"></a> <span class="fu">unlist</span>() <span class="sc">|></span> <span class="co"># Convert to vector</span></span>
<span id="cb7-8"><a href="#cb7-8"></a> <span class="fu">as.numeric</span>() <span class="co"># Convert to numeric</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] 2020 2021 2021</code></pre>
</div>
</div>
</div>
</div>
<aside><ol class="aside-footnotes"><li id="fn16"><p><a href="https://annakrystalli.me/rrresearchACCE20/slides/03_filenaming.html" class="uri">https://annakrystalli.me/rrresearchACCE20/slides/03_filenaming.html</a></p></li></ol></aside></section>
<section id="first-things-first-3" class="slide level2">
<h2>First things first</h2>
<blockquote>
<p>« There are only two hard things in Computer Science: cache invalidation and <strong>naming things</strong>. »</p>
</blockquote>
<div class="citation">
<p>Phil Karlton</p>
</div>
<p><br></p>
<p><strong>Three principles for naming files</strong><sup>1</sup></p>
<div class="columns">
<div class="column" style="width:50%;">
<ol type="1">
<li>Human readable</li>
<li><strong>Machine readable</strong></li>
</ol>
</div><div class="column" style="width:50%;">
<div class="cell">
<div class="sourceCode cell-code" id="cb9"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1"></a><span class="co"># File names ----</span></span>
<span id="cb9-2"><a href="#cb9-2"></a>files <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"2020-survey_A.csv"</span>, <span class="st">"2021-survey_A.csv"</span>, <span class="st">"2021-survey_B.csv"</span>)</span>
<span id="cb9-3"><a href="#cb9-3"></a></span>
<span id="cb9-4"><a href="#cb9-4"></a><span class="co"># Extract years ----</span></span>
<span id="cb9-5"><a href="#cb9-5"></a><span class="fu">strsplit</span>(files, <span class="st">"-"</span>) <span class="sc">|></span> <span class="co"># Split string by '-'</span></span>
<span id="cb9-6"><a href="#cb9-6"></a> <span class="fu">lapply</span>(<span class="cf">function</span>(x) x[<span class="dv">1</span>]) <span class="sc">|></span> <span class="co"># Get the first element</span></span>
<span id="cb9-7"><a href="#cb9-7"></a> <span class="fu">unlist</span>() <span class="sc">|></span> <span class="co"># Convert to vector</span></span>
<span id="cb9-8"><a href="#cb9-8"></a> <span class="fu">as.numeric</span>() <span class="co"># Convert to numeric</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] 2020 2021 2021</code></pre>
</div>
</div>
<p><br></p>
<div class="cell">
<div class="sourceCode cell-code" id="cb11"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1"></a><span class="co"># Extract surveys ----</span></span>
<span id="cb11-2"><a href="#cb11-2"></a><span class="fu">strsplit</span>(files, <span class="st">"-"</span>) <span class="sc">|></span> <span class="co"># Split string by '-'</span></span>
<span id="cb11-3"><a href="#cb11-3"></a> <span class="fu">lapply</span>(<span class="cf">function</span>(x) x[<span class="dv">2</span>]) <span class="sc">|></span> <span class="co"># Get the second element</span></span>
<span id="cb11-4"><a href="#cb11-4"></a> <span class="fu">unlist</span>() <span class="sc">|></span> <span class="co"># Convert to vector</span></span>
<span id="cb11-5"><a href="#cb11-5"></a> <span class="fu">gsub</span>(<span class="st">"survey_|</span><span class="sc">\\</span><span class="st">.csv"</span>, <span class="st">""</span>, <span class="at">x =</span> _) <span class="co"># Clean output</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] "A" "A" "B"</code></pre>
</div>
</div>
</div>
</div>
<aside><ol class="aside-footnotes"><li id="fn17"><p><a href="https://annakrystalli.me/rrresearchACCE20/slides/03_filenaming.html" class="uri">https://annakrystalli.me/rrresearchACCE20/slides/03_filenaming.html</a></p></li></ol></aside></section>
<section id="first-things-first-4" class="slide level2">
<h2>First things first</h2>
<blockquote>
<p>« There are only two hard things in Computer Science: cache invalidation and <strong>naming things</strong>. »</p>
</blockquote>
<div class="citation">
<p>Phil Karlton</p>
</div>
<p><br></p>
<p><strong>Three principles for naming files</strong><sup>1</sup></p>
<div class="columns">
<div class="column" style="width:50%;">
<ol type="1">
<li>Human readable</li>
<li>Machine readable</li>
<li><strong>Play well with default ordering</strong></li>
</ol>
</div><div class="column" style="width:50%;">
<div class="cell">
<div class="sourceCode cell-code" id="cb13"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1"></a><span class="co"># File names (bad) ----</span></span>
<span id="cb13-2"><a href="#cb13-2"></a>files <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"1-survey_A.csv"</span>, <span class="st">"2-survey_B.csv"</span>, <span class="st">"10-survey_C.csv"</span>)</span>
<span id="cb13-3"><a href="#cb13-3"></a></span>
<span id="cb13-4"><a href="#cb13-4"></a><span class="co"># Sort file names ----</span></span>
<span id="cb13-5"><a href="#cb13-5"></a><span class="fu">sort</span>(files)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] "1-survey_A.csv" "10-survey_C.csv" "2-survey_B.csv" </code></pre>
</div>
</div>
</div>
</div>
<aside><ol class="aside-footnotes"><li id="fn18"><p><a href="https://annakrystalli.me/rrresearchACCE20/slides/03_filenaming.html" class="uri">https://annakrystalli.me/rrresearchACCE20/slides/03_filenaming.html</a></p></li></ol></aside></section>
<section id="first-things-first-5" class="slide level2">
<h2>First things first</h2>
<blockquote>
<p>« There are only two hard things in Computer Science: cache invalidation and <strong>naming things</strong>. »</p>
</blockquote>
<div class="citation">
<p>Phil Karlton</p>
</div>
<p><br></p>
<p><strong>Three principles for naming files</strong><sup>1</sup></p>
<div class="columns">
<div class="column" style="width:50%;">
<ol type="1">
<li>Human readable</li>
<li>Machine readable</li>
<li><strong>Play well with default ordering</strong></li>
</ol>
</div><div class="column" style="width:50%;">
<div class="cell">
<div class="sourceCode cell-code" id="cb15"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb15-1"><a href="#cb15-1"></a><span class="co"># File names (bad) ----</span></span>
<span id="cb15-2"><a href="#cb15-2"></a>files <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"1-survey_A.csv"</span>, <span class="st">"2-survey_B.csv"</span>, <span class="st">"10-survey_C.csv"</span>)</span>
<span id="cb15-3"><a href="#cb15-3"></a></span>
<span id="cb15-4"><a href="#cb15-4"></a><span class="co"># Sort file names ----</span></span>
<span id="cb15-5"><a href="#cb15-5"></a><span class="fu">sort</span>(files)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] "1-survey_A.csv" "10-survey_C.csv" "2-survey_B.csv" </code></pre>
</div>
</div>
<p><br></p>
<div class="cell">
<div class="sourceCode cell-code" id="cb17"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb17-1"><a href="#cb17-1"></a><span class="co"># File names (better) ----</span></span>
<span id="cb17-2"><a href="#cb17-2"></a>files <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"01-survey_A.csv"</span>, <span class="st">"02-survey_B.csv"</span>, <span class="st">"10-survey_C.csv"</span>)</span>
<span id="cb17-3"><a href="#cb17-3"></a></span>
<span id="cb17-4"><a href="#cb17-4"></a><span class="co"># Sort file names ----</span></span>
<span id="cb17-5"><a href="#cb17-5"></a><span class="fu">sort</span>(files)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] "01-survey_A.csv" "02-survey_B.csv" "10-survey_C.csv"</code></pre>
</div>
</div>
</div>
</div>
<aside><ol class="aside-footnotes"><li id="fn19"><p><a href="https://annakrystalli.me/rrresearchACCE20/slides/03_filenaming.html" class="uri">https://annakrystalli.me/rrresearchACCE20/slides/03_filenaming.html</a></p></li></ol></aside></section>
<section id="first-things-first-6" class="slide level2">
<h2>First things first</h2>
<blockquote>
<p>« There are only two hard things in Computer Science: cache invalidation and <strong>naming things</strong>. »</p>
</blockquote>
<div class="citation">
<p>Phil Karlton</p>
</div>
<p><br></p>
<p><strong>Three principles for naming files</strong><sup>1</sup></p>
<div class="columns">