Lessons & Readings

Lesson 2: Single Page R Markdown 📃 Document

Tue, 21 Apr 2020 21:13:14 -0500

Here is the link to the Practicals Page for Lesson 2. I will add new assignments every day or so to help you create a single page document. For now you can find the raw .Rmd file on GitHub. The link is in the title of the Practicals Page.

R Markdown is a versatile framework for creating a range of high-quality documents including HTML, PDF, presentations, books, websites, and more. Markdown allows documents to be simple and portable while R integration gives you the benefit of creating dynamic documents that contain your results (e.g., tables, graphics, and inline values). Results can be computed and rendered dynamically from R code and are more likely to be reproducible.

Course Topics

Sat, 04 Apr 2020 02:13:50 +0000

This page contains an outline of topics we will cover in this course and will updated often. As always, suggestions are welcome.

Please continue to work on your skills in CSS, HTML, and CLI. See the Self-Paced Tutorials for more information.

Lesson	Topic	Skills
L0	R Markdown example
L1	Setup	IDE, Dev Tools, GitHub, RStudio
L1	Problem Solving	Web search, GitHub, StackOverflow
L2	R Markdown Page	YAML, Markdown, R Code chunks, inline R Code
L2	R Markdown Page	Tables, Figures
L3	GitHub	Submitting Issues & Requests, Pull Requests
L3	Git & GitHub	Git from the CLI, Creating & cloning a Repo, Push changes
L4	Customization	CSS style sheets, inline HTML code
L4	R Markdown Site	Take what you’ve learned and make a site
	Archiving Data	Figshare

Edit this page

Lesson 1A: Problem Solving

Fri, 03 Apr 2020 02:13:50 +0000

To make a successful coding project or website you need to know where and how to get help. In future posts, I will cover approaches specific to certain tools. In this post, I want to share some general tips and tricks about getting and asking for help. I touch on the idea of best practices to use so that your question is answered in the most efficient and effective way possible.

Lesson 1: Building Your Working 🧱️ Environment

Wed, 01 Apr 2020 21:13:14 -0500

We have a wide range of experience levels in this course, so the first lesson is devoted to setting up your working environment and laying down a good foundation for your projects. I would like to give everyone a chance to get everything installed and to get comfortable with these new tools before we dive in. I realize that some of you may have a lot of this done already. If you are interested in developing your skills in HTML and CSS, you can check a fantastic tutorial I linked on the Tutorials. You can access that page up top in the navigation bar. Let’s begin.

Self-Paced Tutorials

Wed, 01 Apr 2020 02:13:50 +0000

Jump to: CLI Tutorials, HTML/CSS Tutorials, & Additional Tutorials.

As advertised, this course is about using R Markdown and GitHub. I appreciate that some of you may not want to spend time learning new skills that you don’t think you need. Originally I considered everything on this page to be optional, however I changed my mind. As I thought more about the structure of the course, I concluded that I would be doing you all a disservice if I made tools like HTML and CSS optional. So, I am now flip flopping and making Command Line Interface and HTML/CSS mandatory, self-paced tutorials. These tools are integral to our learning objectives and your work going forward, so please try to forget what I said before.

The Importance of Open Science

Tue, 31 Mar 2020 02:13:50 +0000

I wanted to share a few thoughts on what I see as key benefits to the community in creating data driven, open source, web products that capture and communicate your science. Bear with me for a minute. Well technically 4 minutes.

Accessibility & Inclusivity

Many journals and journal articles sit behind pay walls that a lot of people can’t access. That sucks, and while people are revolting against this paradigm, for now this is the reality. We do our best to publish open access articles but sometimes this is not possible. A webpage allows you to share your science with a wider audience. By and large, journal articles are technical documents. There is nothing wrong with this; it is just the nature of the medium. But this can make the information inaccessible to non-experts. By also presenting your work as a web product you have the opportunity to tell the story behind the science, which can have important outreach implications.

About the Course

Sun, 29 Mar 2020 02:13:50 +0000

Estimated reading time: 5 minutes, 12 seconds.

Welcome

Welcome to the LockDown 2020 Continuing Education course on Data Curation. This site (written mainly in R Markdown) will be our guidebook as we make our way through the topics. Our main goals with the course are to a) create interactive, data-driven web products in R Markdown, b) host those products on GitHub, and c) use tools like figshare for hosting data and data products. Along the way, we will learn about version control in GitHub and how to use Slack for collaborating and interacting. We will also come up with other ideas for topics to explore. At times, this may be a little frustrating, but I promise with some hard work (and probably a few tears) you will have the tools to create a range of useful and beautiful documents including single HTML or PDF files, multi-page web sites, books, and presentations.

Lesson 0: An Example R Markdown Document

Sat, 28 Mar 2020 21:13:14 -0500

In this mini lesson I’d like to demonstrate a) some Markdown syntax, b) how you run and format R code, and c) how to render R figures. If you read the Course Description you have already seen examples of embedded tables. Remember, our primary goal is to create R Markdown documents that capture code, data, and data products.

R Markdown integrates the concepts of literate programming and reproducible research, which, in addition to explaining or documenting itself, also allows others (including an original investigator) to reproduce a data analysis or other research result.

Resources

Sat, 28 Mar 2020 02:13:50 +0000

This page is a work in progress and will be updated on the fly.

Pictoral Table of Contents.

R Markdown

R Markdown: The Definitive Guide. Title says it all. You should use this. A lot.

R Markdown Cookbook. Another must have.
RStudio IDE Cheatsheet. An overview of the RStudio IDE.
R Markdown Cheatsheet. A general R Markdown reference.
Another R Markdown Cheatsheet. One more? There are a lot of cheatsheets.
R Markdown Reference Guide. Good section on Chunk Options.

R

Run R in your browser. Write, run, and test R code.

Markdown

There are many similarities with the R Markdown references above.