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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">
<link href="index_files/libs/quarto-contrib/academicons-1.9.2/all.css" rel="stylesheet">
<link href="index_files/libs/quarto-contrib/academicons-1.9.2/size.css" rel="stylesheet"><meta charset="utf-8">
<meta name="generator" content="quarto-1.4.549">
<title>Presentation title</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 { 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/reveal-chalkboard/font-awesome/css/all.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/reveal-chalkboard/style.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 {
padding-bottom: 0.5rem;
margin-bottom: 0;
}
.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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</head>
<body class="quarto-light">
<div class="reveal">
<div class="slides">
<section class="slide level2">
<!-- Insert section 'Title slide' -->
<div class="title-slide-container">
<div class="title-slide-content">
<div class="columns">
<!-- Title slide logo --><div class="column logo" style="width:32%;">
<p><img data-src="images/logo-title-slide.png"></p>
</div><!-- Title slide content --><div class="column information" style="width:68%;">
<div class="title">
<p>Targets</p>
</div>
<div class="subtitle">
<p>A pipeline toolkit for R</p>
</div>
<div class="date">
<p>December 2024</p>
</div>
<div class="columns authors">
<div class="column author" style="width:32%;">
<p>François Guilhaumon<br> <a href="mailto:francois.guilhaumon@ird.fr"><i class="fa-solid fa-envelope" aria-label="envelope"></i></a> <a href="https://fguyilhaumon.github.io"><i class="fa-solid fa-globe" aria-label="globe"></i></a> <a href="https://orcid.org/0000-0003-4707-8932"><i class="fa-brands fa-orcid" aria-label="orcid"></i></a> <a href="https://scholar.google.fr/citations?user=jJwtZT0AAAAJ"><i class="ai ai-google-scholar"></i></a></p>
</div><!-- Second author --><div class="column author" style="width:32%;">
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[](author-website)
[](author-github)
[](author-orcid)
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<!--
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[](mailto:author-email)
[](author-website)
[](author-github)
[](author-orcid)
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</div><!-- Close {.columns .authors} -->
</div>
<div class="columns affiliations">
<div class="column affiliation" style="width:32%;">
<p>Research scientist <br> <code><span class="citation" data-cites="IRD">@IRD</span></code> <a href="https://ird.fr"><i class="fa-solid fa-globe" aria-label="globe"></i></a></p>
</div><!-- Second affiliation --><div class="column affiliation" style="width:32%;">
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</div><!-- Close {.columns} -->
</div>
<!-- Close {.title-slide-content} -->
</div>
<!-- Close {.title-slide-container} -->
</div>
<!-- Insert section 'Targets' -->
</section>
<section>
<section id="what-is-targets" class="title-slide slide level1 center">
<h1>What is targets?</h1>
</section>
<section id="section" class="slide level2">
<h2></h2>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/tweet.png" class="quarto-figure quarto-figure-center"></p>
</figure>
</div>
</section>
<section id="section-1" class="slide level2" data-auto-animate="true">
<h2 data-id="quarto-animate-title"></h2>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/François_Tomb_Carlo_Ruspi_02.jpg" class="quarto-figure quarto-figure-center" style="width:80.0%"></p>
</figure>
</div>
</section>
<section id="section-2" class="slide level2" data-auto-animate="true">
<h2 data-id="quarto-animate-title"></h2>
<div class="columns">
<div class="column">
<p><br> <br></p>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/François_Tomb_Carlo_Ruspi_02.jpg" class="quarto-figure quarto-figure-center" style="width:80.0%"></p>
</figure>
</div>
</div><div class="column">
<p><br> <br></p>
<p>The Sisyphean workflow:</p>
<ul>
<li class="fragment">Launch the code. <br> <br></li>
<li class="fragment">Wait while it runs <br> <br></li>
<li class="fragment">Discover an issue <br> <br></li>
<li class="fragment">Restart from scratch</li>
</ul>
</div>
</div>
</section>
<section id="targets" class="slide level2">
<h2>Targets</h2>
<p><a href="https://docs.ropensci.org/targets/">Targets</a> is an extension developed by Will Landau that allows you to organize a project in the form of a processing pipeline, made up of different stages, and automatically managing the dependencies between them.</p>
<p>This organization has several advantages:</p>
<ul>
<li class="fragment">it allows all pipeline stages to be described in a dedicated file, and forces the various stages to be separated into separate functions, making the project easier to read and maintain</li>
</ul>
<ul>
<li class="fragment">it facilitates reproducibility of processing, as it guarantees that all steps have been carried out in the right order and in a new environment</li>
</ul>
<ul>
<li class="fragment">it optimizes calculation times, because in the event of modification, only those steps that require it are restarted</li>
</ul>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/logo-targets.svg" class="quarto-figure quarto-figure-center" style="width:20.0%"></p>
</figure>
</div>
</section></section>
<section>
<section id="how-does-it-work" class="title-slide slide level1 center">
<h1>How does it work?</h1>
</section>
<section id="use-functions" class="slide level2">
<h2>Use functions</h2>
<p>Transform blocks of code into functions by wrapping them into <code><- function() { my_code }</code> and setting appropriate parameters.</p>
<p><br></p>
<div class="cell">
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href=""></a>mydata <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"mydata.csv"</span>)</span>
<span id="cb1-2"><a href=""></a></span>
<span id="cb1-3"><a href=""></a>data2 <span class="ot"><-</span> <span class="fu">clean</span>(mydata)</span>
<span id="cb1-4"><a href=""></a>data3 <span class="ot"><-</span> <span class="fu">transform</span>(data2)</span>
<span id="cb1-5"><a href=""></a>data4 <span class="ot"><-</span> <span class="fu">erase_na</span>(data3)</span>
<span id="cb1-6"><a href=""></a>data_clean <span class="ot"><-</span> <span class="fu">transform</span>(data_4)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p><br> <br></p>
<div class="fragment">
<div class="cell">
<div class="sourceCode cell-code" id="cb2"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href=""></a>mydata <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"mydata.csv"</span>)</span>
<span id="cb2-2"><a href=""></a></span>
<span id="cb2-3"><a href=""></a>wrangle <span class="ot"><-</span> <span class="cf">function</span>(data){</span>
<span id="cb2-4"><a href=""></a> data2 <span class="ot"><-</span> <span class="fu">clean</span>(data)</span>
<span id="cb2-5"><a href=""></a> data3 <span class="ot"><-</span> <span class="fu">transform</span>(data2)</span>
<span id="cb2-6"><a href=""></a> data4 <span class="ot"><-</span> <span class="fu">erase_na</span>(data3)</span>
<span id="cb2-7"><a href=""></a> data_clean <span class="ot"><-</span> <span class="fu">transform</span>(data_4)</span>
<span id="cb2-8"><a href=""></a> <span class="fu">return</span>(data_clean)</span>
<span id="cb2-9"><a href=""></a>}</span>
<span id="cb2-10"><a href=""></a></span>
<span id="cb2-11"><a href=""></a>data_clean <span class="ot"><-</span> <span class="fu">wrangle</span>(mydata)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</section>
<section id="targets-1" class="slide level2">
<h2>Targets</h2>
<p>In <strong>targets</strong>, a data analysis pipeline is a collection of target objects that express the individual steps of the workflow</p>
<ul>
<li class="fragment">a target is a step of your pipeline (can also be an input file or a <code>Quarto</code> report)</li>
</ul>
<ul>
<li class="fragment">each target is defined using the function <code>tar_target()</code>, providing the name of the target as first argument and the function to create it as a second argument, there is a third optional argument to specify the ‘type’ of the target</li>
</ul>
<ul>
<li class="fragment">dependencies between targets are exposed because upstream targets are arguments of the functions used to build downstream targets</li>
</ul>
<ul>
<li class="fragment">this allow to visualize the pipeline as a dependency graph</li>
</ul>
<div class="fragment">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/airquality-pipeline.png" class="quarto-figure quarto-figure-center"></p>
</figure>
</div>
</div>
</section>
<section id="creating-the-pipeline" class="slide level2">
<h2>Creating the pipeline</h2>
<p>The pipeline is written in an R file, by default <code>Targets</code> looks for a <code>_targets.R</code> file located at the root of your project.</p>
<p><strong>But</strong> this can be changed and the pipeline can be defined in an <code>R</code> file of your choice, you’ll have to set it up using the following (e.g. in your <code>make.R</code> file):</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href=""></a><span class="co"># ---- project execution</span></span>
<span id="cb3-2"><a href=""></a>targets<span class="sc">::</span><span class="fu">tar_config_set</span>(</span>
<span id="cb3-3"><a href=""></a> <span class="at">store =</span> <span class="st">"outputs/pipeline/"</span>,</span>
<span id="cb3-4"><a href=""></a> <span class="at">script =</span> <span class="st">"analyses/pipeline.R"</span></span>
<span id="cb3-5"><a href=""></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>Note that we also specified a custom location to store the targets.</p>
<p><br></p>
<div class="fragment">
<div class="cell">
<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href=""></a><span class="fu">library</span>(targets)</span>
<span id="cb4-2"><a href=""></a></span>
<span id="cb4-3"><a href=""></a><span class="fu">list</span>(</span>
<span id="cb4-4"><a href=""></a> <span class="co"># Make the workflow depends on the raw data file</span></span>
<span id="cb4-5"><a href=""></a> <span class="fu">tar_target</span>(<span class="at">name =</span> raw_data_file, <span class="at">command =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"airquality.csv"</span>), </span>
<span id="cb4-6"><a href=""></a> <span class="at">format =</span> <span class="st">"file"</span>), </span>
<span id="cb4-7"><a href=""></a> </span>
<span id="cb4-8"><a href=""></a> <span class="co"># Read the data and return a data.frame</span></span>
<span id="cb4-9"><a href=""></a> <span class="fu">tar_target</span>(<span class="at">name =</span> raw_data, <span class="at">command =</span> <span class="fu">read.csv</span>(raw_data_file)),</span>
<span id="cb4-10"><a href=""></a> </span>
<span id="cb4-11"><a href=""></a> <span class="co"># Transform the data</span></span>
<span id="cb4-12"><a href=""></a> <span class="fu">tar_target</span>(data, raw_data <span class="sc">%>%</span> <span class="fu">filter</span>(<span class="sc">!</span><span class="fu">is.na</span>(Ozone))),</span>
<span id="cb4-13"><a href=""></a> </span>
<span id="cb4-14"><a href=""></a> <span class="co"># Explore the data (custom function)</span></span>
<span id="cb4-15"><a href=""></a> <span class="fu">tar_target</span>(hist, <span class="fu">hist</span>(data<span class="sc">$</span>Ozone)), </span>
<span id="cb4-16"><a href=""></a> </span>
<span id="cb4-17"><a href=""></a> <span class="co"># Model the data</span></span>
<span id="cb4-18"><a href=""></a> <span class="fu">tar_target</span>(fit, <span class="fu">lm</span>(Ozone <span class="sc">~</span> Wind <span class="sc">+</span> Temp, data))</span>
<span id="cb4-19"><a href=""></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</section>
<section id="creating-the-pipeline-1" class="slide level2">
<h2>Creating the pipeline</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href=""></a><span class="fu">library</span>(targets)</span>
<span id="cb5-2"><a href=""></a></span>
<span id="cb5-3"><a href=""></a><span class="fu">list</span>(</span>
<span id="cb5-4"><a href=""></a> <span class="co"># Make the workflow depends on the raw data file</span></span>
<span id="cb5-5"><a href=""></a> <span class="fu">tar_target</span>(<span class="at">name =</span> raw_data_file, <span class="at">command =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"airquality.csv"</span>), </span>
<span id="cb5-6"><a href=""></a> <span class="at">format =</span> <span class="st">"file"</span>), </span>
<span id="cb5-7"><a href=""></a> </span>
<span id="cb5-8"><a href=""></a> <span class="co"># Read the data and return a data.frame</span></span>
<span id="cb5-9"><a href=""></a> <span class="fu">tar_target</span>(<span class="at">name =</span> raw_data, <span class="at">command =</span> <span class="fu">read.csv</span>(raw_data_file)),</span>
<span id="cb5-10"><a href=""></a> </span>
<span id="cb5-11"><a href=""></a> <span class="co"># Transform the data</span></span>
<span id="cb5-12"><a href=""></a> <span class="fu">tar_target</span>(data, raw_data <span class="sc">%>%</span> <span class="fu">filter</span>(<span class="sc">!</span><span class="fu">is.na</span>(Ozone))),</span>
<span id="cb5-13"><a href=""></a> </span>
<span id="cb5-14"><a href=""></a> <span class="co"># Explore the data (custom function)</span></span>
<span id="cb5-15"><a href=""></a> <span class="fu">tar_target</span>(hist, <span class="fu">hist</span>(data<span class="sc">$</span>Ozone)), </span>
<span id="cb5-16"><a href=""></a> </span>
<span id="cb5-17"><a href=""></a> <span class="co"># Model the data</span></span>
<span id="cb5-18"><a href=""></a> <span class="fu">tar_target</span>(fit, <span class="fu">lm</span>(Ozone <span class="sc">~</span> Wind <span class="sc">+</span> Temp, data))</span>
<span id="cb5-19"><a href=""></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="fragment">
<p>then visualise it:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href=""></a>targets<span class="sc">::</span><span class="fu">tar_visnetwork</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/airquality-pipeline.png" class="quarto-figure quarto-figure-center"></p>
</figure>
</div>
</div>
</section>
<section id="creating-the-pipeline-2" class="slide level2">
<h2>Creating the pipeline</h2>
<p><br></p>
<p>All target script files have these requirements:</p>
<p><br></p>
<div>
<ol type="1">
<li class="fragment">Load the <a href="https://github.com/ropensci/targets"><code>targets</code></a> package itself.</li>
</ol>
<p><br></p>
<ol start="2" type="1">
<li class="fragment">Load your custom functions and global objects into the R session: <code>targets::tar_source()</code>.</li>
</ol>
<p><br></p>
<ol start="3" type="1">
<li class="fragment">Define individual targets with the <code>tar_target()</code> function. Each target is an intermediate step of the workflow. At minimum, a target must have a <strong>name</strong> and an <strong>R expression</strong> but it’s better if it uses a function that you defined in <code>R/</code>.</li>
</ol>
<p><br></p>
<ol start="4" type="1">
<li class="fragment">Every target script must end with a list of your <code>tar_target()</code> objects.</li>
</ol>
</div>
</section>
<section id="running-the-pipeline" class="slide level2">
<h2>Running the pipeline</h2>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/airquality-pipeline.png" class="quarto-figure quarto-figure-center" style="width:40.0%"></p>
</figure>
</div>
<p>Once the pipeline is ready and inspected via targets::tar_visnetwork(), you can run it with:</p>
<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=""></a>targets<span class="sc">::</span><span class="fu">tar_make</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="fragment">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/targets-tar_make-1.png" class="quarto-figure quarto-figure-center"></p>
</figure>
</div>
</div>
</section>
<section id="running-the-pipeline-1" class="slide level2">
<h2>Running the pipeline</h2>
<p>And inspect it again:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb8"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb8-1"><a href=""></a>targets<span class="sc">::</span><span class="fu">tar_visnetwork</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/targets-tar_vis_2.png" class="quarto-figure quarto-figure-center"></p>
</figure>
</div>
</section>
<section id="retrieving-the-results-the-targets" class="slide level2">
<h2>Retrieving the results (the targets)</h2>
<p>Targets objects are stored in the <code>Targets store</code> but you d’ont need to think about it when retrieving your results.</p>
<p>Just load or read targets with their names:</p>
<ul>
<li><code>Loading</code> a target in the current workspace:</li>
</ul>
<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=""></a>targets<span class="sc">::</span><span class="fu">tar_load</span>(<span class="st">"hist"</span>)</span>
<span id="cb9-2"><a href=""></a></span>
<span id="cb9-3"><a href=""></a><span class="fu">plot</span>(hist)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/hist_Ozone.png" class="quarto-figure quarto-figure-center" style="width:50.0%"></p>
</figure>
</div>
</section>
<section id="retrieving-the-results-the-targets-1" class="slide level2">
<h2>Retrieving the results (the targets)</h2>
<p>Targets objects are stored in the <code>Targets store</code> but you d’ont need to think about it when retrieving your results.</p>
<p>Just load or read targets with their names:</p>
<ul>
<li><code>Reading</code> a target value and assign it to a new object:</li>
</ul>
<div class="cell">
<div class="sourceCode cell-code" id="cb10"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb10-1"><a href=""></a>histo <span class="ot"><-</span> targets<span class="sc">::</span><span class="fu">tar_read</span>(<span class="st">"hist"</span>)</span>
<span id="cb10-2"><a href=""></a></span>
<span id="cb10-3"><a href=""></a><span class="fu">plot</span>(histo)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/hist_Ozone.png" class="quarto-figure quarto-figure-center" style="width:50.0%"></p>
</figure>
</div>
</section></section>
<section>
<section id="targets-loves-changes" class="title-slide slide level1 center">
<h1>Targets loves changes</h1>
</section>
<section id="changing-the-pipeline" class="slide level2">
<h2>Changing the pipeline</h2>
<p>Let’s modidify the target “hist” to use ggplot2 instead of R base graphics.</p>
<p>We will create a function that generate a <code>ggplot2</code> histogram object and write it’s definition in <code>R/functions.R</code>:</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=""></a>R<span class="sc">/</span>functions.R</span>
<span id="cb11-2"><a href=""></a></span>
<span id="cb11-3"><a href=""></a>make_hist <span class="ot"><-</span> <span class="cf">function</span>(dat) {</span>
<span id="cb11-4"><a href=""></a> </span>
<span id="cb11-5"><a href=""></a> <span class="co">#dat = targets::tar_read("data")</span></span>
<span id="cb11-6"><a href=""></a> </span>
<span id="cb11-7"><a href=""></a> ggplot2<span class="sc">::</span><span class="fu">ggplot</span>(<span class="at">data =</span> dat, <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(<span class="at">x =</span> Ozone)) <span class="sc">+</span></span>
<span id="cb11-8"><a href=""></a> ggplot2<span class="sc">::</span><span class="fu">geom_histogram</span>()</span>
<span id="cb11-9"><a href=""></a> </span>
<span id="cb11-10"><a href=""></a>}</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>And modify the pipeline to use it:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb12" data-code-line-numbers="|17"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb12-1"><a href=""></a><span class="fu">library</span>(targets)</span>
<span id="cb12-2"><a href=""></a></span>
<span id="cb12-3"><a href=""></a><span class="fu">tar_source</span>() <span class="co">#load functions in R/</span></span>
<span id="cb12-4"><a href=""></a></span>
<span id="cb12-5"><a href=""></a><span class="fu">list</span>(</span>
<span id="cb12-6"><a href=""></a> <span class="co"># Make the workflow depends on the raw data file</span></span>
<span id="cb12-7"><a href=""></a> <span class="fu">tar_target</span>(<span class="at">name =</span> raw_data_file, <span class="at">command =</span> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"airquality.csv"</span>), </span>
<span id="cb12-8"><a href=""></a> <span class="at">format =</span> <span class="st">"file"</span>), </span>
<span id="cb12-9"><a href=""></a> </span>
<span id="cb12-10"><a href=""></a> <span class="co"># Read the data and return a data.frame</span></span>
<span id="cb12-11"><a href=""></a> <span class="fu">tar_target</span>(<span class="at">name =</span> raw_data, <span class="at">command =</span> <span class="fu">read.csv</span>(raw_data_file)),</span>
<span id="cb12-12"><a href=""></a> </span>
<span id="cb12-13"><a href=""></a> <span class="co"># Transform the data</span></span>
<span id="cb12-14"><a href=""></a> <span class="fu">tar_target</span>(data, raw_data <span class="sc">|></span> dplyr<span class="sc">::</span><span class="fu">filter</span>(<span class="sc">!</span><span class="fu">is.na</span>(Ozone))),</span>
<span id="cb12-15"><a href=""></a> </span>
<span id="cb12-16"><a href=""></a> <span class="co"># Explore the data (custom function)</span></span>
<span id="cb12-17"><a href=""></a> <span class="fu">tar_target</span>(hist, <span class="fu">make_hist</span>(data)), </span>
<span id="cb12-18"><a href=""></a> </span>
<span id="cb12-19"><a href=""></a> <span class="co"># Model the data</span></span>
<span id="cb12-20"><a href=""></a> <span class="fu">tar_target</span>(fit, <span class="fu">lm</span>(Ozone <span class="sc">~</span> Wind <span class="sc">+</span> Temp, data))</span>
<span id="cb12-21"><a href=""></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="changing-the-pipeline-1" class="slide level2">
<h2>Changing the pipeline</h2>
<p>And inspect it again:</p>
<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=""></a>targets<span class="sc">::</span><span class="fu">tar_visnetwork</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/targets-tar_vis_3.png" class="quarto-figure quarto-figure-center" style="width:70.0%"></p>
</figure>
</div>
</section>
<section id="changing-the-pipeline-2" class="slide level2">
<h2>Changing the pipeline</h2>
<p>And run it again:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb14"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb14-1"><a href=""></a>targets<span class="sc">::</span><span class="fu">tar_make</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p><br></p>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/targets-tar_make-2.png" class="quarto-figure quarto-figure-center" style="width:70.0%"></p>
</figure>
</div>
</section>
<section id="targets-workflow" class="slide level2">
<h2>Targets workflow</h2>
<h4 id="workflow">Workflow</h4>
<ol type="1">
<li><p>Write an R function</p></li>
<li><p>Add a target to the pipeline</p></li>
<li><p>Visualize the pipeline</p></li>
<li><p>Make the pipeline</p></li>
<li><p>Check the results</p></li>
<li><p>Write a function</p></li>
</ol>
</section>
<section id="targets-workflow-1" class="slide level2" data-auto-animate="true">
<h2 data-id="quarto-animate-title">Targets workflow</h2>
<h4 id="workflow-1">Workflow</h4>
<ol type="1">
<li><p>Write an R function</p></li>
<li><p>Add a target to the pipeline</p></li>
<li><p>Visualize the pipeline</p></li>
<li><p>Make the pipeline</p></li>
<li><p>Check the results</p></li>
<li><p>Write a function</p></li>
</ol>
<p><img data-src="images/Sisyphe_lol.jpg" class="absolute" style="bottom: 100px; right: 10px; width: 60%; "></p>
</section>
<section id="targets-workflow-2" class="slide level2" data-auto-animate="true">
<h2 data-id="quarto-animate-title">Targets workflow</h2>
<h4 id="workflow-2">Workflow</h4>
<ol type="1">
<li><p>Write an R function</p></li>
<li><p>Add a target to the pipeline</p></li>
<li><p>Visualize the pipeline</p></li>
<li><p>Make the pipeline</p></li>
<li><p>Check the results</p></li>
<li><p>Write a function</p></li>
</ol>
<p><img data-src="images/Sisyphe_lol_cut.jpg" class="absolute" style="bottom: 50px; right: 10px; width: 20%; "></p>
</section>
<section id="targets-workflow-3" class="slide level2" data-auto-animate="true">
<h2 data-id="quarto-animate-title">Targets workflow</h2>
<h4 id="workflow-3">Workflow</h4>
<ol type="1">
<li><p>Write an R function</p></li>
<li><p>Add a target to the pipeline</p></li>
<li><p>Visualize the pipeline</p></li>
<li><p>Make the pipeline</p></li>
<li><p>Check the results</p></li>
<li><p>Write a function</p></li>
</ol>
<p><img data-src="images/Sisyphe_lol_cut.jpg" class="absolute" style="bottom: 700px; right: 300px; width: 20%; "></p>
</section></section>
<section>
<section id="input-output-files" class="title-slide slide level1 center">
<h1>Input / Output Files</h1>
</section>
<section id="external-input-files" class="slide level2">
<h2>External input files</h2>
<p><br></p>
<p>To reproducibly track an external input file, you need to define a new target that has:</p>
<p><br></p>
<div>
<ol type="1">
<li class="fragment"><p>A command that returns the file path as a character vector, and</p></li>
<li class="fragment"><p>specify <code>format = "file"</code> in <code>tar_target()</code>.</p></li>
</ol>
</div>
<div class="fragment">
<p><br> <br></p>
<p>When the target runs in the pipeline, the returned character vector gets recorded, and <code>Targets</code> watches the data file and invalidates the target when that file changes.</p>
</div>
<div class="fragment">
<p><br></p>
<p>To track multiple files this way, simply define a multi-element character vector where each element is a path.</p>
</div>
<div class="fragment">
<p><br></p>
<p>Each element can also be a directory, but this directory must not be empty at the time the target runs.</p>
</div>
</section>
<section id="external-input-files-1" class="slide level2">
<h2>External input files</h2>
<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=""></a><span class="fu">library</span>(targets)</span>
<span id="cb15-2"><a href=""></a></span>
<span id="cb15-3"><a href=""></a>path_to_data <span class="ot"><-</span> <span class="cf">function</span>() {</span>
<span id="cb15-4"><a href=""></a> <span class="st">"data/raw_data.csv"</span></span>
<span id="cb15-5"><a href=""></a>}</span>
<span id="cb15-6"><a href=""></a></span>
<span id="cb15-7"><a href=""></a><span class="fu">list</span>(</span>
<span id="cb15-8"><a href=""></a> <span class="fu">tar_target</span>(raw_data_file, <span class="fu">path_to_data</span>(), <span class="at">format =</span> <span class="st">"file"</span>),</span>
<span id="cb15-9"><a href=""></a> <span class="fu">tar_target</span>(raw_data, <span class="fu">read.csv</span>(raw_data_file))</span>
<span id="cb15-10"><a href=""></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="several-independant-input-files" class="slide level2">
<h2>Several independant input files</h2>
<p>A target with <code>format = "file"</code> treats the entire set of files as an irreducible bundle.</p>
<p>That means in order to “branch” over files, each file should be associated with its own target.</p>
<p>This is not optimal at all. Using the argument <code>pattern</code> solve this by providing a way to dynamically create targets for each input file.</p>
<p>Here is a pipeline that begins with data files and loads each into a different dynamic branch.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb16"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb16-1"><a href=""></a><span class="fu">library</span>(targets)</span>
<span id="cb16-2"><a href=""></a></span>
<span id="cb16-3"><a href=""></a><span class="fu">list</span>(</span>
<span id="cb16-4"><a href=""></a> <span class="fu">tar_target</span>(paths, <span class="fu">c</span>(<span class="st">"data_file_1.csv"</span>, <span class="st">"data_file_2.csv"</span>)),</span>
<span id="cb16-5"><a href=""></a> <span class="fu">tar_target</span>(files, paths, <span class="at">format =</span> <span class="st">"file"</span>, <span class="at">pattern =</span> <span class="fu">map</span>(paths)),</span>
<span id="cb16-6"><a href=""></a> <span class="fu">tar_target</span>(data, <span class="fu">read.csv</span>(files), <span class="at">pattern =</span> <span class="fu">map</span>(files))</span>
<span id="cb16-7"><a href=""></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>The <a href="https://docs.ropensci.org/tarchetypes/reference/tar_files.html"><code>tar_files()</code></a> function from the <a href="https://github.com/ropensci/tarchetypes"><code>tarchetypes</code></a> package is shorthand for the first two targets above.</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=""></a><span class="fu">library</span>(targets)</span>
<span id="cb17-2"><a href=""></a></span>
<span id="cb17-3"><a href=""></a><span class="fu">list</span>(</span>
<span id="cb17-4"><a href=""></a> tarchetypes<span class="sc">::</span><span class="fu">tar_files</span>(files, <span class="fu">c</span>(<span class="st">"data_file_1.csv"</span>, <span class="st">"data_file_2.csv"</span>)),</span>
<span id="cb17-5"><a href=""></a> <span class="fu">tar_target</span>(data, <span class="fu">read.csv</span>(files), <span class="at">pattern =</span> <span class="fu">map</span>(files))</span>
<span id="cb17-6"><a href=""></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="external-output-files" class="slide level2">
<h2>External output files</h2>
<p>Output files have the same mechanics as input files. The target uses <code>format = "file"</code>, and the return value is a vector of paths to generated files.</p>
<p>The only difference here is that the target’s R command writes to storage before it returns a value.</p>
<p>For example, here is an output file target that saves a visualization.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb18"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb18-1"><a href=""></a><span class="fu">tar_target</span>(plot_file, <span class="fu">save_plot_and_return_path</span>(), <span class="at">format =</span> <span class="st">"file"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>Here, our custom <code>save_plot_and_return_path()</code> function does exactly what the name describes.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb19"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb19-1"><a href=""></a>save_plot_and_return_path <span class="ot"><-</span> <span class="cf">function</span>() {</span>
<span id="cb19-2"><a href=""></a> plot <span class="ot"><-</span> <span class="fu">ggplot</span>(mtcars) <span class="sc">+</span></span>
<span id="cb19-3"><a href=""></a> <span class="fu">geom_point</span>(<span class="fu">aes</span>(<span class="at">x =</span> wt, <span class="at">y =</span> mpg))</span>
<span id="cb19-4"><a href=""></a> <span class="fu">ggsave</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"outputs"</span>, <span class="st">"plot_file.png"</span>), plot, </span>
<span id="cb19-5"><a href=""></a> <span class="at">width =</span> <span class="dv">7</span>, <span class="at">height =</span> <span class="dv">7</span>)</span>
<span id="cb19-6"><a href=""></a> <span class="fu">return</span>(<span class="fu">file.path</span>(<span class="st">"outputs"</span>, <span class="st">"plot_file.png"</span>))</span>
<span id="cb19-7"><a href=""></a>}</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section></section>
<section>
<section id="literate-programming" class="title-slide slide level1 center">
<h1>Literate programming</h1>
</section>
<section id="literate-programming-1" class="slide level2">
<h2>Literate programming</h2>
<p><br></p>
<p>If you render a Quarto report as part of a target, the report should be lightweight: mostly prose, minimal code, fast execution, and no output other than the rendered HTML/PDF document.</p>
<p><br> <br></p>
<div class="callout callout-important callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Important</strong></p>
</div>
<div class="callout-content">
<p>In other words, Quarto reports are just targets that document prior results.</p>
<p>The bulk of the computation should have already happened upstream, and the most of the code chunks in the report itself should be terse calls to <code>tar_read()</code> and <code>tar_load()</code>.</p>
</div>
</div>
</div>
</section>
<section id="literate-programming-2" class="slide level2">
<h2>Literate programming</h2>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/qmd-source.png" class="quarto-figure quarto-figure-center" style="width:70.0%"></p>
</figure>
</div>
<p>The report depends on targets <code>fit</code> and <code>hist</code>.</p>
<p>The use of <code>tar_read()</code> and <code>tar_load()</code> allows us to run the report outside the pipeline.</p>
<p>As long as the <code>Targets store</code> folder has data on the required targets from a previous <code>tar_make()</code>, you can open the RStudio IDE, edit the report, and click the Render button like you would for any other Quarto report.</p>
</section>
<section id="literate-programming-3" class="slide level2">
<h2>Literate programming</h2>
<p>The target definition function to render Quarto documents is part of the <a href="https://docs.ropensci.org/tarchetypes/"><code>tarchetypes</code></a> <code>R</code> package and looks like this.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb20"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb20-1"><a href=""></a>tarchetypes<span class="sc">::</span><span class="fu">tar_quarto</span>(report, <span class="st">"report.qmd"</span>) <span class="co"># Just defines a target object.</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="fragment">
<p>Because symbols <code>fit</code> and <code>hist</code> appear in the report via <code>tar_load()</code> and <code>tar_read()</code>, <code>targets</code> knows that <code>report</code> depends on <code>fit</code> and <code>hist</code>.</p>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/qmd-source.png" class="quarto-figure quarto-figure-center" style="width:50.0%"></p>
</figure>
</div>
</div>