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<h1 class="title toc-ignore">Practical R Workflow for Scientists June-July 2021</h1>
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<p><img style="float: right;" src="images/tools-logo-transparent.png" width=30%></p>
<p>These short sessions (45min to 1hr) will be focused on tools and practices for NMFS scientists to help you be <strong>faster, more efficient and organized</strong> in your coding and in merging reports with code. The focus of these workshops is practical skills and tools. Each session will be stand-alone. While the sessions will be introductory, I will give you links to my GitHub repositories that illustrate more complex examples (and that you can copy and build on).</p>
<p><strong>Target audience</strong>: You already code in R, maybe use RStudio too, but want to learn some tips about being more efficient from a seasoned R programmer who does the kind of coding and work that you do.</p>
<p><strong>About me</strong>: I am a modeler/applied mathematician and I am immersed in R. I develop R packages for public use. I teach time-series analysis at the University of Washington (using R) and I teach workshops on R and reproducible research.</p>
<div id="set-up-for-the-workshop" class="section level2">
<h2>Set-up for the workshop</h2>
<p>Before the workshops, go to <a href="set-up.html">Set-up</a> for instructions. Unless you will only be listening, you’ll need a <a href="https://github.com/">GitHub</a> account. To actively participate in the activities, you’ll want either R, RStudio and GitHub Desktop installed on your computer or you can use <a href="https://rstudio.cloud/">RStudio Cloud</a>. If you do the latter, you don’t need to install any software.</p>
</div>
<div id="video-and-github-organization-links-for-the-sessions" class="section level2">
<h2>Video and GitHub Organization links for the sessions</h2>
<p>Please email Eli (<a href="mailto:[email protected]" class="email">[email protected]</a>) from your NOAA email, and I will send you the WebEx links and link to the GitHub Classroom. It is the same link for each session.</p>
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<div id="topics" class="section level2">
<h2>Topics</h2>
<ul>
<li><p><a href="week1.html">Week 1</a> Introduction to workflow using RStudio and Git/GitHub. The session video will be posted June 2nd but the link has my lectures notes and short videos of the skills. <a href="week1.html">Lecture notes and video links</a></p></li>
<li><p><a href="week2.html">Week 2</a>. More Git skills. The 3 key Git skills. These 3 basic skills are all you need for 95% of your work with Git repositories. <a href="week2.html">The lecture notes, discussion and videos</a></p></li>
<li><p><a href="week3.html">Week 3</a>. GitHub skills. We’ll learn how to use issues and releases on GitHub to be more efficient either working alone or in a team. I’ll show you how I use organizations to organize my repositories and some of the nice ‘landing page’ features of GitHub. For those curious about GitHub Actions, I give you a short demo on that too. <a href="week3.html">The lecture notes and discussion</a></p></li>
<li><p><a href="week4.html">Week 4</a>. Rmarkdown for reports. Let’s make a report that updates when our data change and post that to GitHub.</p></li>
<li><p>Week 5. Making plots with ggplot2. Learning ggplot2 will make it much easier to make plots from the big and complex datasets that you deal with on a daily basis.</p></li>
<li><p>Week 6. Creating a R package. I show you how to make basic data and code packages that allows you to version and document your data and code.</p></li>
<li><p>Week 7. Documentation for R packages using Roxygen.</p></li>
<li><p>Week 8. Creating landing pages using RStudio/R Markdown/GitHub and R packages landing pages using pkgdown.</p></li>
</ul>
</div>
<div id="video-only" class="section level2">
<h2>Video only</h2>
<p>I will make videos of this material.</p>
<ul>
<li><p>Handy clustering tools in R</p></li>
<li><p>Making raster plots with the raster and tmap packages. Working with spatial data is a huge area. We are going to start gently by making raster plots and using the tmap package. You’ll see how easy it easy to make maps of data on a grid.</p></li>
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<p><i class="fas fa-cubes"></i> NWFSC Math Bio Program <i class="fas fa-cubes"></i></p>
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