Authoring Scientific Publications with R Markdown

University of California, Santa Barbara


Dec 16-17, 2020

9:00 am - 11:50 am

Instructors: Torin White, Renata Curty, Greg Janee, Kristi Liu

Helpers: Jon Jablonski, Ian Lessing

Registration for this workshop opens on Wednesday, Nov 25 at 8:00 am PST

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General Information

Ever wondered how you can create more dynamic and reproducible academic reports?

Join us for a carpentry-style R Markdown workshop for scientific authoring. Participants will build on using their R data analysis skills in R Studio by learning how to create R Markdown documents that combine analysis and narrative. R Markdown makes it possible to work on a whole research project from within R Studio in an easily reproducible manner: from data upload, cleaning, and analysis, to writing your paper, adding figures, citations and bibliography with proper formatting. R markdown allows you to output your work as .html, .pdf, .docx (among many other formats) to publish your work as a website, paper, etc. This workshop will involve lecture and demos alternating with hands-on exercises, so by the end of the workshop you will have “authored” a short paper of your own with data and narrative we provide.

Who: The course is aimed at graduate students, faculty, and other researchers.

We recommend that you have previous knowledge or familiarity of R and Rstudio for this workshop. We will have a demo using Github during the workshop so while not necessary, it may be beneficial to create a Github account and Rpubs account prior to attending the workshop.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: Dec 16-17, 2020. Add to your Google Calendar.

Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Day 1: Dec 16

08:30 am Zoom opens, R installation help
09:00 am Zoom Carpentry Intro
09:15 am Why R Markdown?
09:35 am Starting with R Markdown
10:00 am Break
10:10 am Markdown Syntax:Headings and Lists
10:35 am Markdown Syntax:Hyperlinks, Images, and Tables
10:55 am Markdown Syntax: Emphases, Formulas, and Footnotes
11:15 am Break
11:25 am Markdown Syntax: Citations and Bibliography
12:00 pm End of Day 1
Scripts Lesson 4:Extra Scripts/Notes

Day 2: Dec 17

09:00 am Review
09:15 am Finding and Applying Existing Templates
09:25 am Knitr Syntax: Inline Code and Code Chunks
10:15 am Break
10:25 am Knitr Syntax: Styling Code Outputs
maybe Break
11:05 am Publishing a Report
12:00 pm End of Workshop


To participate in a Data Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

Here is the Data Folder for our workshop. Download and unzip this file to your desktop before the workshop.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

The setup instructions for the Data Carpentry Social Sciences workshops (with R) can be found below


R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. 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.

Video Tutorial

You can download the binary files for your distribution from CRAN. 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 RStudio IDE.