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Week 2 More Git/GitHub
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Week 3 GitHub
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Archive
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2020 website
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More resources
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<a href="https://github.com/orgs/RWorkflow-Workshop-2021">Org</a>
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<div id="header">
<h1 class="title toc-ignore">Resources</h1>
</div>
<div id="never-worked-with-r" class="section level2">
<h2>Never worked with R?</h2>
<p>If you have never worked with R, you can get a basic familiarity by going through <a href="https://www.datacamp.com/courses/free-introduction-to-r">this free tutorial</a>. Takes about 4 hours.</p>
<p>You can also learn R straight from within R using the <a href="https://swirlstats.com/">swirl package</a>. This doesn’t require internet access except to install the package.</p>
<p>Here is another basic R introduction from <a href="https://www.computerworld.com/article/2497143/business-intelligence/business-intelligence-beginner-s-guide-to-r-introduction.html">ComputerWorld</a>.</p>
<p>The book that I recommend for scientists who have never worked with R is <a href="https://www.amazon.com/R-Student-Companion-Brian-Dennis-ebook/dp/B009AIU07G">The R Student Companion</a> by Brian Dennis. It’ll get you up to speed with the type of programming that scientists do with R. I think you’d be fine just renting it for a month and getting through as much as you can in a month. After a few chapters, you’ll know your way around R and, more importantly, how to program with functions. Then you’ll be ready for something else.</p>
<p>Once you work through that, <a href="https://r4ds.had.co.nz/">R for Data Science</a> by Garrett Grolemund and Hadley Wickham is very good for what the sort of work we do.</p>
</div>
<div id="r-markdown" class="section level1">
<h1>R Markdown</h1>
<ul>
<li><a href="https://rmarkdown.rstudio.com/lesson-1.html">RStudio’s lessons</a></li>
</ul>
</div>
<div id="git-and-github" class="section level1">
<h1>Git and GitHub</h1>
<ul>
<li><a href="https://happygitwithr.com/">Happy Git with R</a> Detail on Git and GitHub, but accessible.</li>
</ul>
</div>
<div id="r-packages-that-i-use-all-the-time" class="section level1">
<h1>R packages that I use all the time</h1>
<p>These are some basic packages that I use all the time. This does not include the analysis packages that I use.</p>
<ul>
<li><a href="https://www.tidyverse.org/">Tidyverse</a> packages. I am not a fan of all the tidyverse package and I dislike piping (because it is horribly slow and I need fast for simulation work), but I try to keep up with the ideas in the “tidyverse” and I try to adopt tidyverse style. In particular, I try to format all my data into tidy format.</li>
<li>ggplot2: I find ggplot to be hard to learn and too confining, but I use it all the time because it makes plots with many layers so much easier and it makes plot layout easier. I don’t like it for my publication quality plots (just too much hassle to get the look I want) but I use it constantly for mock-ups.</li>
<li>stringr: I work with strings all the time so I always need this.</li>
<li>dplyr: When I need to go from wide-form to short-form layout, I like it. Definitely I think it is good to inform yourself as to what it does.</li>
<li>XML: I use it to scrape data from online tables using the <code>readHTMLTable()</code> function. I think xml2 in the tidyverse might do the same thing.</li>
<li>here: This is a handy utility package, along with <code>file.path()</code> allows you to make file paths to the base of the project. If you find yourself doing <code>setwd()</code> anywhere in your code, you’ll want to use <code>here()</code> to avoid that because doing that breaks your code for anyone else.</li>
<li>xtable: Handy for making complex tables.</li>
</ul>
</div>
<div id="other-reproducible-research-short-courses" class="section level1">
<h1>Other Reproducible Research Short-Courses</h1>
<ul>
<li><a href="https://eriqande.github.io/rep-res-eeb-2017/index.html">Reproductible Research 2017</a> Source for some of the introductory material.</li>
</ul>
</div>
<div id="making-simple-websites" class="section level1">
<h1>Making simple websites</h1>
<ul>
<li>[Another tutorial] (<a href="https://jules32.github.io/rmarkdown-website-tutorial/index.html" class="uri">https://jules32.github.io/rmarkdown-website-tutorial/index.html</a>) with more examples and slightly more complicated websites.</li>
</ul>
</div>
<div id="jekyll" class="section level1">
<h1>Jekyll</h1>
<ul>
<li><a href="https://learn.cloudcannon.com/jekyll/install-jekyll-on-os-x/">Installing Jekyll on Mac OS</a></li>
<li><a href="https://learn.cloudcannon.com/jekyll/running-jekyll/">Jekyll build</a></li>
</ul>
</div>
<div id="jekyll-templates" class="section level1">
<h1>Jekyll Templates</h1>
<ul>
<li><a href="https://sourcethemes.com/academic/">Hugo Academic</a> Popular Jekyll template in academia.</li>
</ul>
</div>
<div id="travis-ci-continuous-integration" class="section level1">
<h1>Travis CI (continuous integration)</h1>
<ul>
<li><a href="https://juliasilge.com/blog/beginners-guide-to-travis/" class="uri">https://juliasilge.com/blog/beginners-guide-to-travis/</a></li>
</ul>
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