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3-1-statistical-computing-with-r-and-python-notebooks-reproducible-code.html
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3-1-statistical-computing-with-r-and-python-notebooks-reproducible-code.html
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<!DOCTYPE html>
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<meta property="og:title" content="The Open Digital Archaeology Textbook Environment" />
<meta property="og:type" content="book" />
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<meta property="og:description" content="The Open Digital Archaeology Textbook Environment combines instructive text with a computational DA laboratory" />
<meta name="github-repo" content="o-date/draft" />
<meta name="author" content="Shawn Graham, Neha Gupta, Michael Carter, & Beth Compton" />
<meta name="date" content="2017-03-08" />
<meta name="description" content="The Open Digital Archaeology Textbook Environment combines instructive text with a computational DA laboratory">
<title>The Open Digital Archaeology Textbook Environment</title>
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<ul>
<li><a href="index.html#notice">notice</a></li>
<li class="has-sub"><a href="about-the-authors.html#about-the-authors">About the Authors</a><ul>
<li><a href="about-the-authors.html#shawn-graham">Shawn Graham</a></li>
<li><a href="about-the-authors.html#neha-gupta">Neha Gupta</a></li>
<li><a href="about-the-authors.html#michael-carter">Michael Carter</a></li>
<li><a href="about-the-authors.html#beth-compton">Beth Compton</a></li>
<li><a href="about-the-authors.html#editorial-board">Editorial Board</a></li>
</ul></li>
<li class="has-sub"><a href="getting-started.html#getting-started">Getting Started</a><ul>
<li><a href="how-to-use-this-text.html#how-to-use-this-text">How to use this text</a></li>
<li><a href="how-to-contribute-changes-or-make-your-own-version.html#how-to-contribute-changes-or-make-your-own-version">How to contribute changes, or make your own version</a></li>
<li><a href="how-to-access-and-use-the-computational-environment.html#how-to-access-and-use-the-computational-environment">How to access and use the computational environment</a></li>
<li class="has-sub"><a href="colophon.html#colophon">Colophon</a><ul>
<li><a href="colophon.html#the-computational-environment">The computational environment</a></li>
</ul></li>
</ul></li>
<li><a href="welcome.html#welcome">Welcome!</a></li>
<li class="has-sub"><a href="1-going-digital.html#going-digital"><span class="toc-section-number">1</span> Going Digital</a><ul>
<li class="has-sub"><a href="1-1-so-what-is-digital-archaeology.html#so-what-is-digital-archaeology"><span class="toc-section-number">1.1</span> So what is Digital Archaeology?</a><ul>
<li><a href="1-1-so-what-is-digital-archaeology.html#is-digital-archaeology-part-of-the-digital-humanities"><span class="toc-section-number">1.1.1</span> Is digital archaeology part of the digital humanities?</a></li>
<li><a href="1-1-so-what-is-digital-archaeology.html#archaeological-glitch-art"><span class="toc-section-number">1.1.2</span> Archaeological Glitch Art</a></li>
<li><a href="1-1-so-what-is-digital-archaeology.html#the-cool-factor"><span class="toc-section-number">1.1.3</span> The ‘cool’ factor</a></li>
<li><a href="1-1-so-what-is-digital-archaeology.html#takeaways"><span class="toc-section-number">1.1.4</span> Takeaways</a></li>
<li><a href="1-1-so-what-is-digital-archaeology.html#exercises"><span class="toc-section-number">1.1.5</span> Exercises</a></li>
</ul></li>
<li class="has-sub"><a href="1-2-project-management-basics.html#project-management-basics"><span class="toc-section-number">1.2</span> Project Management Basics</a><ul>
<li><a href="1-2-project-management-basics.html#take-aways"><span class="toc-section-number">1.2.1</span> Take-aways</a></li>
<li><a href="1-2-project-management-basics.html#exercises-1"><span class="toc-section-number">1.2.2</span> exercises</a></li>
</ul></li>
<li class="has-sub"><a href="1-3-github-version-control.html#github-version-control"><span class="toc-section-number">1.3</span> Github & Version Control</a><ul>
<li><a href="1-3-github-version-control.html#the-core-functions-of-git"><span class="toc-section-number">1.3.1</span> The core functions of Git</a></li>
<li><a href="1-3-github-version-control.html#key-terms"><span class="toc-section-number">1.3.2</span> Key Terms</a></li>
<li><a href="1-3-github-version-control.html#take-aways-1"><span class="toc-section-number">1.3.3</span> Take-aways</a></li>
<li><a href="1-3-github-version-control.html#further-reading"><span class="toc-section-number">1.3.4</span> Further Reading</a></li>
<li><a href="1-3-github-version-control.html#exercises-2"><span class="toc-section-number">1.3.5</span> Exercises</a></li>
<li><a href="1-3-github-version-control.html#warnings"><span class="toc-section-number">1.3.6</span> Warnings</a></li>
</ul></li>
<li class="has-sub"><a href="1-4-open-notebook-research-scholarly-communication.html#open-notebook-research-scholarly-communication"><span class="toc-section-number">1.4</span> Open Notebook Research & Scholarly Communication</a><ul>
<li><a href="1-4-open-notebook-research-scholarly-communication.html#how-to-ask-questions"><span class="toc-section-number">1.4.1</span> How to Ask Questions</a></li>
<li><a href="1-4-open-notebook-research-scholarly-communication.html#discussion"><span class="toc-section-number">1.4.2</span> discussion</a></li>
<li><a href="1-4-open-notebook-research-scholarly-communication.html#take-aways-2"><span class="toc-section-number">1.4.3</span> Take-aways</a></li>
<li><a href="1-4-open-notebook-research-scholarly-communication.html#further-reading-1"><span class="toc-section-number">1.4.4</span> Further Reading</a></li>
<li><a href="1-4-open-notebook-research-scholarly-communication.html#on-privilege-and-open-notebooks"><span class="toc-section-number">1.4.5</span> On Privilege and Open Notebooks</a></li>
<li><a href="1-4-open-notebook-research-scholarly-communication.html#exercises-3"><span class="toc-section-number">1.4.6</span> exercises</a></li>
</ul></li>
<li class="has-sub"><a href="1-5-failing-productively.html#failing-productively"><span class="toc-section-number">1.5</span> Failing Productively</a><ul>
<li><a href="1-5-failing-productively.html#a-taxonomy-of-fails"><span class="toc-section-number">1.5.1</span> A taxonomy of fails</a></li>
<li><a href="1-5-failing-productively.html#exercises-4"><span class="toc-section-number">1.5.2</span> Exercises</a></li>
</ul></li>
<li><a href="1-6-introduction-to-digital-libraries-archives-repositories.html#introduction-to-digital-libraries-archives-repositories"><span class="toc-section-number">1.6</span> Introduction to Digital Libraries, Archives & Repositories</a></li>
<li class="has-sub"><a href="1-7-command-line-methods-for-working-with-apis.html#command-line-methods-for-working-with-apis"><span class="toc-section-number">1.7</span> Command Line Methods for Working with APIs</a><ul>
<li><a href="1-7-command-line-methods-for-working-with-apis.html#working-with-open-context"><span class="toc-section-number">1.7.1</span> Working with Open Context</a></li>
<li><a href="1-7-command-line-methods-for-working-with-apis.html#working-with-omeka"><span class="toc-section-number">1.7.2</span> Working with Omeka</a></li>
<li><a href="1-7-command-line-methods-for-working-with-apis.html#working-with-tdar"><span class="toc-section-number">1.7.3</span> Working with tDAR</a></li>
<li><a href="1-7-command-line-methods-for-working-with-apis.html#working-with-ads"><span class="toc-section-number">1.7.4</span> Working with ADS</a></li>
<li><a href="1-7-command-line-methods-for-working-with-apis.html#exercises-5"><span class="toc-section-number">1.7.5</span> Exercises</a></li>
</ul></li>
<li class="has-sub"><a href="1-8-the-ethics-of-big-data-in-archaeology.html#the-ethics-of-big-data-in-archaeology"><span class="toc-section-number">1.8</span> The Ethics of Big Data in Archaeology</a><ul>
<li><a href="1-8-the-ethics-of-big-data-in-archaeology.html#discussion-1"><span class="toc-section-number">1.8.1</span> discussion</a></li>
<li><a href="1-8-the-ethics-of-big-data-in-archaeology.html#exercises-6"><span class="toc-section-number">1.8.2</span> exercises</a></li>
</ul></li>
</ul></li>
<li class="has-sub"><a href="2-making-data-useful.html#making-data-useful"><span class="toc-section-number">2</span> Making Data Useful</a><ul>
<li class="has-sub"><a href="2-1-designing-data-collection.html#designing-data-collection"><span class="toc-section-number">2.1</span> Designing Data Collection</a><ul>
<li><a href="2-1-designing-data-collection.html#discussion-2"><span class="toc-section-number">2.1.1</span> discussion</a></li>
<li><a href="2-1-designing-data-collection.html#exercises-7"><span class="toc-section-number">2.1.2</span> exercises</a></li>
</ul></li>
<li class="has-sub"><a href="2-2-cleaning-data-with-open-refine.html#cleaning-data-with-open-refine"><span class="toc-section-number">2.2</span> Cleaning Data with Open Refine</a><ul>
<li><a href="2-2-cleaning-data-with-open-refine.html#discussion-3"><span class="toc-section-number">2.2.1</span> discussion</a></li>
<li><a href="2-2-cleaning-data-with-open-refine.html#exercises-8"><span class="toc-section-number">2.2.2</span> exercises</a></li>
</ul></li>
<li class="has-sub"><a href="2-3-linked-open-data-and-data-publishing.html#linked-open-data-and-data-publishing"><span class="toc-section-number">2.3</span> Linked Open Data and Data Publishing</a><ul>
<li><a href="2-3-linked-open-data-and-data-publishing.html#discussion-4"><span class="toc-section-number">2.3.1</span> discussion</a></li>
<li><a href="2-3-linked-open-data-and-data-publishing.html#exercises-9"><span class="toc-section-number">2.3.2</span> exercises</a></li>
</ul></li>
</ul></li>
<li class="has-sub"><a href="3-finding-and-communicating-the-compelling-story.html#finding-and-communicating-the-compelling-story"><span class="toc-section-number">3</span> Finding and Communicating the Compelling Story</a><ul>
<li class="has-sub"><a href="3-1-statistical-computing-with-r-and-python-notebooks-reproducible-code.html#statistical-computing-with-r-and-python-notebooks-reproducible-code"><span class="toc-section-number">3.1</span> Statistical Computing with R and Python Notebooks; Reproducible code</a><ul>
<li><a href="3-1-statistical-computing-with-r-and-python-notebooks-reproducible-code.html#discussion-5"><span class="toc-section-number">3.1.1</span> discussion</a></li>
<li><a href="3-1-statistical-computing-with-r-and-python-notebooks-reproducible-code.html#exercises-10"><span class="toc-section-number">3.1.2</span> exercises</a></li>
</ul></li>
<li class="has-sub"><a href="3-2-d3-processing-and-data-driven-documents.html#d3-processing-and-data-driven-documents"><span class="toc-section-number">3.2</span> D3, Processing, and Data Driven Documents</a><ul>
<li><a href="3-2-d3-processing-and-data-driven-documents.html#discussion-6"><span class="toc-section-number">3.2.1</span> discussion</a></li>
<li><a href="3-2-d3-processing-and-data-driven-documents.html#exercises-11"><span class="toc-section-number">3.2.2</span> exercises</a></li>
</ul></li>
<li><a href="3-3-storytelling-and-the-archaeological-cms-omeka-kora.html#storytelling-and-the-archaeological-cms-omeka-kora"><span class="toc-section-number">3.3</span> Storytelling and the Archaeological CMS: Omeka, Kora</a></li>
<li class="has-sub"><a href="3-4-web-mapping-with-leaflet.html#web-mapping-with-leaflet"><span class="toc-section-number">3.4</span> Web Mapping with Leaflet</a><ul>
<li><a href="3-4-web-mapping-with-leaflet.html#discussion-7"><span class="toc-section-number">3.4.1</span> discussion</a></li>
<li><a href="3-4-web-mapping-with-leaflet.html#exercises-12"><span class="toc-section-number">3.4.2</span> exercises</a></li>
</ul></li>
<li class="has-sub"><a href="3-5-place-based-interpretation-with-locative-augmented-reality.html#place-based-interpretation-with-locative-augmented-reality"><span class="toc-section-number">3.5</span> Place-based Interpretation with Locative Augmented Reality</a><ul>
<li><a href="3-5-place-based-interpretation-with-locative-augmented-reality.html#discussion-8"><span class="toc-section-number">3.5.1</span> discussion</a></li>
<li><a href="3-5-place-based-interpretation-with-locative-augmented-reality.html#exercises-13"><span class="toc-section-number">3.5.2</span> exercises</a></li>
</ul></li>
<li class="has-sub"><a href="3-6-archaeogaming-and-virtual-archaeology.html#archaeogaming-and-virtual-archaeology"><span class="toc-section-number">3.6</span> Archaeogaming and Virtual Archaeology</a><ul>
<li><a href="3-6-archaeogaming-and-virtual-archaeology.html#discussion-9"><span class="toc-section-number">3.6.1</span> discussion</a></li>
<li><a href="3-6-archaeogaming-and-virtual-archaeology.html#exercises-14"><span class="toc-section-number">3.6.2</span> exercises</a></li>
</ul></li>
<li class="has-sub"><a href="3-7-social-media-as-public-engagement-scholarly-communication-in-archaeology.html#social-media-as-public-engagement-scholarly-communication-in-archaeology"><span class="toc-section-number">3.7</span> Social media as Public Engagement & Scholarly Communication in Archaeology</a><ul>
<li><a href="3-7-social-media-as-public-engagement-scholarly-communication-in-archaeology.html#discussion-10"><span class="toc-section-number">3.7.1</span> discussion</a></li>
<li><a href="3-7-social-media-as-public-engagement-scholarly-communication-in-archaeology.html#exercises-15"><span class="toc-section-number">3.7.2</span> exercises</a></li>
</ul></li>
</ul></li>
<li class="has-sub"><a href="4-eliding-the-digital-and-the-physical.html#eliding-the-digital-and-the-physical"><span class="toc-section-number">4</span> Eliding the Digital and the Physical</a><ul>
<li class="has-sub"><a href="4-1-d-photogrammetry-structure-from-motion.html#d-photogrammetry-structure-from-motion"><span class="toc-section-number">4.1</span> 3D Photogrammetry & Structure from Motion</a><ul>
<li><a href="4-1-d-photogrammetry-structure-from-motion.html#discussion-11"><span class="toc-section-number">4.1.1</span> discussion</a></li>
<li><a href="4-1-d-photogrammetry-structure-from-motion.html#exercises-16"><span class="toc-section-number">4.1.2</span> exercises</a></li>
</ul></li>
<li class="has-sub"><a href="4-2-d-printing-the-internet-of-things-and-maker-archaeology.html#d-printing-the-internet-of-things-and-maker-archaeology"><span class="toc-section-number">4.2</span> 3D Printing, the Internet of Things and “Maker” Archaeology</a><ul>
<li><a href="4-2-d-printing-the-internet-of-things-and-maker-archaeology.html#discussion-12"><span class="toc-section-number">4.2.1</span> discussion</a></li>
<li><a href="4-2-d-printing-the-internet-of-things-and-maker-archaeology.html#exercises-17"><span class="toc-section-number">4.2.2</span> exercises</a></li>
</ul></li>
<li class="has-sub"><a href="4-3-artificial-intelligence-in-digital-archaeology.html#artificial-intelligence-in-digital-archaeology"><span class="toc-section-number">4.3</span> Artificial Intelligence in Digital Archaeology</a><ul>
<li><a href="4-3-artificial-intelligence-in-digital-archaeology.html#agent-models"><span class="toc-section-number">4.3.1</span> agent models</a></li>
<li><a href="4-3-artificial-intelligence-in-digital-archaeology.html#discussion-13"><span class="toc-section-number">4.3.2</span> discussion</a></li>
<li><a href="4-3-artificial-intelligence-in-digital-archaeology.html#exercises-18"><span class="toc-section-number">4.3.3</span> exercises</a></li>
<li><a href="4-3-artificial-intelligence-in-digital-archaeology.html#machine-learning-for-image-captioning-and-other-classificatory-tasks"><span class="toc-section-number">4.3.4</span> Machine learning for image captioning and other classificatory tasks</a></li>
<li><a href="4-3-artificial-intelligence-in-digital-archaeology.html#discussion-14"><span class="toc-section-number">4.3.5</span> discussion</a></li>
<li><a href="4-3-artificial-intelligence-in-digital-archaeology.html#exercises-19"><span class="toc-section-number">4.3.6</span> exercises</a></li>
</ul></li>
</ul></li>
<li class="has-sub"><a href="5-digital-archaeologys-place-in-the-world.html#digital-archaeologys-place-in-the-world"><span class="toc-section-number">5</span> Digital Archaeology’s Place in the World</a><ul>
<li class="has-sub"><a href="5-1-marketing-digital-archaeology.html#marketing-digital-archaeology"><span class="toc-section-number">5.1</span> Marketing Digital Archaeology</a><ul>
<li><a href="5-1-marketing-digital-archaeology.html#discussion-15"><span class="toc-section-number">5.1.1</span> discussion</a></li>
<li><a href="5-1-marketing-digital-archaeology.html#exercises-20"><span class="toc-section-number">5.1.2</span> exercises</a></li>
</ul></li>
<li class="has-sub"><a href="5-2-sustainability-power-in-digital-archaeology.html#sustainability-power-in-digital-archaeology"><span class="toc-section-number">5.2</span> Sustainability & Power in Digital Archaeology</a><ul>
<li><a href="5-2-sustainability-power-in-digital-archaeology.html#discussion-16"><span class="toc-section-number">5.2.1</span> discussion</a></li>
<li><a href="5-2-sustainability-power-in-digital-archaeology.html#exercises-21"><span class="toc-section-number">5.2.2</span> exercises</a></li>
</ul></li>
</ul></li>
<li><a href="6-on-the-horizons-where-digital-archaeology-might-go-next.html#on-the-horizons-where-digital-archaeology-might-go-next"><span class="toc-section-number">6</span> On the Horizons: Where Digital Archaeology Might Go Next</a></li>
<li><a href="references.html#references">References</a></li>
</ul>
</div>
</div>
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<div id="statistical-computing-with-r-and-python-notebooks-reproducible-code" class="section level2">
<h2><span class="header-section-number">3.1</span> Statistical Computing with R and Python Notebooks; Reproducible code</h2>
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<h3><span class="header-section-number">3.1.1</span> discussion</h3>
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<h3><span class="header-section-number">3.1.2</span> exercises</h3>
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