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ORT_Science.html
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<!DOCTYPE html>
<html lang="en"><head>
<script src="ORT_Science_files/libs/clipboard/clipboard.min.js"></script>
<script src="ORT_Science_files/libs/quarto-html/tabby.min.js"></script>
<script src="ORT_Science_files/libs/quarto-html/popper.min.js"></script>
<script src="ORT_Science_files/libs/quarto-html/tippy.umd.min.js"></script>
<link href="ORT_Science_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="ORT_Science_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
<link href="ORT_Science_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles"><meta charset="utf-8">
<meta name="generator" content="quarto-1.2.269">
<meta name="author" content="I. Bartomeus">
<title>Open Reliable and Transparent Science</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="ORT_Science_files/libs/revealjs/dist/reset.css">
<link rel="stylesheet" href="ORT_Science_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 -1.6em;
vertical-align: middle;
}
</style>
<link rel="stylesheet" href="ORT_Science_files/libs/revealjs/dist/theme/quarto.css" id="theme">
<link href="ORT_Science_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.css" rel="stylesheet">
<link href="ORT_Science_files/libs/revealjs/plugin/reveal-menu/menu.css" rel="stylesheet">
<link href="ORT_Science_files/libs/revealjs/plugin/reveal-menu/quarto-menu.css" rel="stylesheet">
<link href="ORT_Science_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-captioned.callout-style-simple .callout-body {
margin-top: 0.2em;
}
.callout:not(.callout-captioned) .callout-body {
display: flex;
}
.callout:not(.no-icon).callout-captioned.callout-style-simple .callout-content {
padding-left: 1.6em;
}
.callout.callout-captioned .callout-header {
padding-top: 0.2em;
margin-bottom: -0.2em;
}
.callout.callout-captioned .callout-caption p {
margin-top: 0.5em;
margin-bottom: 0.5em;
}
.callout.callout-captioned.callout-style-simple .callout-content p {
margin-top: 0;
}
.callout.callout-captioned.callout-style-default .callout-content p {
margin-top: 0.7em;
}
.callout.callout-style-simple div.callout-caption {
border-bottom: none;
font-size: .9rem;
font-weight: 600;
opacity: 75%;
}
.callout.callout-style-default div.callout-caption {
border-bottom: none;
font-weight: 600;
opacity: 85%;
font-size: 0.9rem;
padding-left: 0.5em;
padding-right: 0.5em;
}
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padding-left: 0.5em;
padding-right: 0.5em;
}
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height: 1rem;
width: 1rem;
display: inline-block;
content: "";
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background-size: 1rem 1rem;
}
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height: 0.9rem;
width: 0.9rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 0.9rem 0.9rem;
}
.callout-caption {
display: flex
}
.callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
.callout.no-icon::before {
display: none !important;
}
.callout.callout-captioned .callout-body > .callout-content > :last-child {
margin-bottom: 0.5rem;
}
.callout.callout-captioned .callout-icon::before {
margin-top: .5rem;
padding-right: .5rem;
}
.callout:not(.callout-captioned) .callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
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/* Callout Types */
div.callout-note {
border-left-color: #4582ec !important;
}
div.callout-note .callout-icon::before {
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}
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}
div.callout-important {
border-left-color: #d9534f !important;
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div.callout-important.callout-style-default .callout-caption {
background-color: #f7dddc
}
div.callout-warning {
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</head>
<body class="quarto-light">
<div class="reveal">
<div class="slides">
<section id="title-slide" class="quarto-title-block center">
<h1 class="title">Open Reliable and Transparent Science</h1>
<div class="quarto-title-authors">
<div class="quarto-title-author">
<div class="quarto-title-author-name">
I. Bartomeus
</div>
</div>
</div>
</section>
<section id="open-science-is-hard" class="slide level2">
<h2>Open Science is hard</h2>
<blockquote>
<p>“Caminante, no hay camino, se hace camino al andar” Machado et al. 1912 probably referring to open science</p>
</blockquote>
<p>Open, reliable and transparent science is a path, not and end point.</p>
</section>
<section id="my-path" class="slide level2">
<h2>My path</h2>
<ul>
<li><p>It took me 10 years to approach something I am comfortable calling Open Reliable Transparent science.</p>
<p><img data-src="Images/Plos_example.png"></p>
<p>My first shared code back in 2013</p></li>
</ul>
</section>
<section id="my-path-1" class="slide level2">
<h2>My path</h2>
<ul>
<li><p>Work iteratively. One step at a time.</p></li>
<li><p>We stand on the shoulders of giants such as <a href="https://ropensci.org/">rOpenSci</a> and <a href="https://github.com/Pakillo">Paco Rodriguez</a> (or you don’t need to walk this path alone, find your community)</p></li>
</ul>
</section>
<section id="open-data" class="slide level2">
<h2>Open Data</h2>
<ul>
<li><p>Data collecting:</p>
<ul>
<li><p>Collect “double-blind” when possible</p></li>
<li><p>Use structured sheets to collect data</p></li>
<li><p>Double labeling of samples when possible</p></li>
<li><p>Standardize coding (4_NitrogenPhosphurous > 4NP > 4)</p></li>
<li><p>Keep the link between physical and digital world</p></li>
<li><p>Remember, Excel is a (dangerous) data entry program, nothing else</p></li>
</ul></li>
</ul>
</section>
<section id="open-data-1" class="slide level2">
<h2>Open Data</h2>
<ul>
<li><p>Data processing:</p>
<ul>
<li><p>Never edit the master file</p></li>
<li><p>Use <a href="http://vita.had.co.nz/papers/tidy-data.pdf">tidy</a> data structures and plain, standard and open formats (e.g. csv)</p></li>
<li><p>Implement checkpoints and sanity checks</p>
<ul>
<li>Check impossible values vs improbable values</li>
</ul></li>
</ul></li>
<li><p>Metadata (<a href="https://cran.r-project.org/web/packages/dataspice/vignettes/overview.html">Dataspice</a>: creates computer (JSON, EML) and human readable (html) metadata)</p></li>
</ul>
</section>
<section id="metadata" class="slide level2">
<h2>Metadata</h2>
<img data-src="Images/Iberian_Bees.png" class="r-stretch"></section>
<section id="open-analysis" class="slide level2">
<h2>Open Analysis</h2>
<ul>
<li><p>Script everything (specially data cleaning - Plan ahead!)</p>
<p><img data-src="Images/plan_accordingly.png" width="996"></p></li>
</ul>
</section>
<section id="open-analysis-1" class="slide level2">
<h2>Open Analysis</h2>
<ul>
<li><p>You can’t reproduce… if you don’t understand where a number came from.</p></li>
<li><p>You can’t reproduce… what you don’t remember. And trust me: you won’t.</p></li>
<li><p>You can’t reproduce… what you’ve lost. What if you need access to a file as it existed 1, 10, or 100, or 1000 days ago? - incremental back up (Git, Dropbox, Time machine…)</p></li>
</ul>
</section>
<section id="open-analysis-2" class="slide level2">
<h2>Open Analysis</h2>
<ul>
<li><p>Use version control (e.g. Github):</p>
<ul>
<li>R and github (https://<a href="https://happygitwithr.com/">happygitwithr</a>.com/)</li>
</ul></li>
<li><p>Use a ReadMe file, and a nice repo structure.</p>
<p><img data-src="Images/Lincx_example.png"></p></li>
</ul>
</section>
<section id="open-analysis-3" class="slide level2">
<h2>Open Analysis</h2>
<ul>
<li><p>Defensive programming (<a href="http://adv-r.had.co.nz/Exceptions-Debugging.html#defensive-programming">examples</a>) and maybe functionalize your code</p></li>
<li><p>Track software versions (<a href="https://rstudio.github.io/renv/articles/renv.html">Renv</a>)</p></li>
<li><p>Code review / Pair programming</p></li>
<li><p>Unit testing (<a href="https://testthat.r-lib.org/">testthat</a>)</p></li>
</ul>
</section>
<section id="writing" class="slide level2">
<h2>Writing</h2>
<ul>
<li>Version control
<ul>
<li><p>Github (Markdown) -> allows executing text and code altogether!</p></li>
<li><p>Overleaf (LATEX)</p></li>
<li><p>G-Docs</p></li>
<li><p>etc…</p></li>
</ul></li>
</ul>
</section>
<section id="publishing" class="slide level2">
<h2>Publishing</h2>
<ul>
<li><p><a href="https://choosealicense.com/">Choose a licence</a></p></li>
<li><p>Get a DOI (e.g. <a href="https://zenodo.org/">Zenodo</a>, but also Figshare, …)</p></li>
<li><p>Think on versions (v.0.1, v.0.2)</p>
<ul>
<li><p>Github Releases preserve DOI via Zenodo</p></li>
<li><p>Think on adding a News.md</p></li>
</ul></li>
<li><p>Explain how to contribute (e.g. Github issues)</p></li>
<li><p>Automate the “Data -> Analysis -> Publication” workflow</p>
<ul>
<li>Github actions e.g. <a href="https://github.com/ibartomeus/CropPollinationModels" class="uri">https://github.com/ibartomeus/CropPollinationModels</a></li>
</ul></li>
</ul>
</section>
<section id="the-perfect-repo" class="slide level2">
<h2>The perfect repo:</h2>
<p><code>Readme.md</code> with DOI, version, file description, relevant info, etc...</p>
<p><code>/Data</code> with raw, clean and the relevant scripts.</p>
<p><code>/Analysis</code></p>
<p><code>/Manuscript</code></p>
<p><code>LICENCE</code></p>
<p><code>testthat</code></p>
<p><code>News.md</code></p>
<p><code>Metadata/</code></p>
<p><code>Renv/</code></p>
</section>
<section id="conclusions" class="slide level2">
<h2>Conclusions</h2>
<ul>
<li><p>It’s hard work -> Ensure to claim the credit you deserve</p></li>
<li><p>You are more exposed -> You faults will be seen as honest</p></li>
<li><p>New tools and standards emerge every day -> Work iteraltively and strive to do better, not to do it perfect.</p></li>
</ul>
<div class="footer footer-default">
</div>
</section>
</div>
</div>
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