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<!DOCTYPE html>
<html>
<head>
<title>Author Carpentry</title>
<link rel="stylesheet" href="css/site.css">
</head>
<body>
<header>
<a href="http://authorcarpentry.github.io"><img src="img/AClogo.jpg" alt="Author Carpentry logo"></a>
</header>
<nav>
<ul>
<li>
<a href=".">Lesson</a>
</li>
<li>
<a href="00-getting-started.html">Getting Started</a>
</li>
<li>
<a href="01-markdown.html">Intro to Markdown</a>
</li>
<li>
<a href="02-modifying-appearance.html">Document Appearance</a>
</li>
<li>
<a href="03-dynamic.html">Dynamic Documents</a>
</li>
<li>
<a href="04-publishing.html">Publishing</a>
</li>
<li>
<a href="mailto:authorcarpentry@library.caltech.edu">Contact Us</a>
</li>
</ul>
</nav>
<section>
<h1 id="reproducible-research-reporting-with-r-and-rstudio">
Reproducible Research Reporting with R and RStudio
</h1>
<ul>
<li>
<em>Maintainers: Tom Morrell</em>
</li>
<li>
<em>Lesson Content: Gail Clement, Tom Morrell, Donna Wrublewski, Robert Doiel, Yuvi Panda</em>
</li>
</ul>
<p>
<strong>Lesson status: In Development</strong>
</p>
<h3 id="what-you-will-learn">
What you will learn:
</h3>
<ul>
<li>
Identify the features of a reproducible and dynamic research report that is fit to enter the scholarly record.
</li>
<li>
Describe the benefits of composing research reports with open authoring tools in RStudio.
</li>
<li>
Apply an open, text-based workflow for creating a paper that combines dynamic text, code and software.
</li>
<li>
Use the Rmarkdown-Knitr-Pandoc workflow to convert openly authored documents for publication, online posting and professional presentation.
</li>
<li>
Demonstrate use of the RStudio GUI platform for authoring and producing professional-quality research reports.
</li>
</ul>
<h3 id="topics">
Topics:
</h3>
<ol type="1">
<li>
<a href="00-getting-started.html">Introduction</a>
</li>
<li>
<a href="01-markdown.html">Basic Markdown</a>
</li>
<li>
<a href="02-modifying-appearance.html">Document Appearance</a>
</li>
<li>
<a href="03-dynamic.html">Dynamic Documents</a>
</li>
<li>
<a href="04-publishing.html">Publishing</a>
</li>
</ol>
<h3 id="requirements">
Requirements
</h3>
<p>
Author Carpentry’s teaching is hands-on, so participants are encouraged to use their own computers to insure the proper setup of tools for an efficient workflow. <em>These lessons assume no prior knowledge of the skills or tools</em>, but working through this lesson requires working copies of R and Rstudio.
</p>
<p>
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio. For this workshop you’ll need to install both R (version 3.4.3 or newer) and RStudio on your computer. Please follow these installation instructions before coming to the workshop
</p>
<h4 id="windows">
Windows
</h4>
<p>
Install R by downloading and running this <a href="https://cran.r-project.org/bin/windows/base/release.htm">.exe</a> file from CRAN. Also, please install the <a href="https://www.rstudio.com/products/rstudio/download/#download">RStudio IDE</a>. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select “Run as administrator” instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.
</p>
<h4 id="macos">
macOS
</h4>
<p>
Install R by downloading and running this <a href="https://cran.r-project.org/bin/macosx/R-latest.pkg">.pkg</a> file from CRAN. Also, please install the <a href="https://www.rstudio.com/products/rstudio/download/#download">RStudio IDE</a>.
</p>
<h4 id="linux">
Linux
</h4>
<p>
You can download the binary files for your distribution from <a href="https://cran.r-project.org/index.html">CRAN</a>. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R). Also, please install the <a href="https://www.rstudio.com/products/rstudio/download/#download">RStudio IDE</a>.
</p>
<h3 id="workshop-files">
Workshop Files
</h3>
<p>
You also need to <a href="data.zip">download some files</a> for this workshop. Extract this folder and put it on your desktop. This is where we will be working throughout the workshop.
</p>
</section>
<footer>
<span>© Author Carpentry</span>
<span><a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img
alt="Creative Commons License" style="vertical-align: middle;"
src="https://i.creativecommons.org/l/by/4.0/80x15.png" /></a></span>
<span>This work is licensed under a <a rel="license"
href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution
4.0 International License</a></span>
</footer>
</body>
</html>