Updated R Markdown thesis template

In October of 2015, I released an R Markdown senior thesis template R package and discussed it in the blogpost here. It was well-received by students and faculty that worked with it and this past summer I worked on updating it to make it even nicer for students. The big addition is the ability for students to export their senior thesis to a webpage (example here) and also label and cross-reference figures and tables more easily. These additions and future revisions will be in the new thesisdown package in the spirit of the bookdown package developed and released by RStudio in summer 2016.

I encourage you to look over my blog post last year to get an idea of why R Markdown is such a friendly environment to work in. Markdown specifically allows for typesetting of the finished document to be transparent inside the actual document. Down the road, it is my hope that students will be able to write generating R Markdown files that will then export into many formats. These currently include the LaTeX format to produce a PDF following Reed's senior thesis guidelines and the HTML version in gitbook style. Eventually, this will include a Word document following Reed's guidelines and also an ePub (electronic book) version. These last two are available at the moment but are not fully functional.

By allowing senior theses in a variety of formats, seniors will be more easily able to display their work to potential employers, other students, faculty members, and potential graduate schools. This will allow them to get the word out about their studies and research while still encouraging reproducibility in their computations and in their analyses.

Install the template generating package

To check out the package yourself, make sure you have RStudio and LaTeX installed and then direct your browser to the GitHub page for the template: http://github.com/ismayc/thesisdown. The README.md file near the bottom of the page below the files gives directions on installing the template package and getting the template running. As you see there, you'll want to install the thesisdown package via the following commands in the RStudio console:


If you have any questions, feedback, or would like to report any issues, please email me.

(The generating R Markdown file for this HTML document—saved in the .Rmd extension—is available here.)

About chesterismay

I am an Instructional Technologist at Reed College. I work on statistical projects with members of the Reed community and specialize in data visualization and analysis with the R programming language. I have a PhD in Statistics from Arizona State University and my dissertation was in the field of statistical computing. I very much enjoy helping others realize the power and flexibility of R in producing reports, statistical analysis, and excellent visualizations.
This entry was posted in R, Reproducible research. Bookmark the permalink.

11 Responses to Updated R Markdown thesis template

  1. Mario says:

    Does it support page numbers?

  2. I love this blog post! Nice and simple. I’ll be passing this along to my children and my interns.

    • chesterismay says:

      Awesome! I’ll be working over this coming year on putting a repository together for the different LaTeX templates that exist throughout the US and how to integrate them into a thesis template like this. It isn’t necessarily the easiest thing to try to get working with YAML and R so I’m hoping to put a tutorial together for that as well.

  3. Pingback: Updated R Markdown thesis template | A bunch of data

  4. Is it possible to easily publish the thesis to one’s website (like it is done with bookdown)?

  5. nselem84 says:

    Can I use your template even if I’m not a Reed student?

    • chesterismay says:

      Yes, please do! You may need to tweak your LaTeX template file a bit to meet the standards of your school but others have done just this pretty easily. Feel free to post any issues you have on the GitHub page.

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