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An updated R Markdown PhD thesis template using the bookdown package

lgaborini/thesisdownUNIL

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Thesisdownunil.

This is a version of R package thesisdown , customized for UNIL (Université de Lausanne).

It will support LaTeX output, and HTML is a bonus.

Experimental !

This project was inspired by the bookdown package and is an updated version of my Senior Thesis template in the reedtemplates package here . It was originally designed to only work with the Reed College LaTeX template, but has since been adapted to work with many different institutions by many different individuals. Check out the Customizing thesisdown to your institution section below for examples.

Currently, the PDF and gitbook versions are fully-functional. The word and epub versions are developmental, have no templates behind them, and are essentially calls to the appropriate functions in bookdown.

If you are new to working with bookdown / rmarkdown , please read over the documentation available in the gitbook template at https://thesisdown.netlify.com/ . This is also available below at https://ismayc.github.io/thesisdown_book .

The current output for the four versions is here:

• PDF (Generating LaTeX file is available here with other files at in the book directory .)

Under the hood, the Reed College LaTeX template is used to ensure that documents conform precisely to submission standards. At the same time, composition and formatting can be done using lightweight markdown syntax, and R code and its output can be seamlessly included using rmarkdown .

Customizing thesisdown to your institution

In an ideal world, this package would support a variety of different LaTeX templates from a wide range of institutions and we'd love to get it there at some point. Until that time, realize that this was designed to only work with the Reed College LaTeX template but others have adapted it to work with their institutions. Here are some that have customized it to fit their needs. It is recommended you review how they changed the files by comparing their repositories to this one and then make tweaks to yours as needed. Feel free to file an issue on this repo if you have questions/troubles.

Have you created a thesisdown template for your institution and would like to have it included here? Make a PR similar to the commit done to include jayhawkdown . I'll review it and merge it in. Let's keep the list going!

Using thesisdown from Chester's GitHub

Special thanks to Ben Marwick for helping to add a lot more clarity to the directions below from the README of his spin-off huskydown package .

Using thesisdown has some prerequisites which are described below. To compile PDF documents using R , you are going to need to have LaTeX installed. By far the easiest way to install LaTeX on any platform is with the tinytex R package:

You may need to install a few extra LaTeX packages on your first attempt to knit as well.

To use thesisdown from RStudio :

Ensure that you have already installed LaTeX and the fonts described above, and are using the latest version of RStudio . You can use thesisdown without RStudio. For example, you can write the Rmd files in your favourite text editor (e.g. Atom , Notepad++ ). But RStudio is probably the easiest tool for writing both R code and text in your thesis. It also provides a nice way to build your thesis while editing. We'll proceed assuming that you have decided to use the RStudio workflow.

Install the bookdown and thesisdown packages:

Use the New R Markdown dialog to select Thesis :

Note that this will currently only Knit if you name the directory index as shown above. This guarantees that index.html is generated correctly for the Gitbook version of the thesis.

After choosing which type of output you'd like in the YAML at the top of index.Rmd, Knit the index.Rmd file to get the book in PDF or HTML formats.

Day-to-day writing of your thesis

You need to edit the individual chapter R Markdown files to write your thesis. It's recommended that you version control your thesis using GitHub if possible. RStudio can also easily sync up with GitHub to make the process easier. While writing, you should git commit your work frequently, after every major activity on your thesis. For example, every few paragraphs or section of text, and after major step of analysis development. You should git push at the end of each work session before you leave your computer or change task. For gentle novice-friendly guide to getting starting with using Git with R and RStudio, see http://happygitwithr.com/ .

To render your thesis into a PDF, open index.Rmd in RStudio and then click the "knit" button. To change the output formats between PDF, gitbook and Word , look at the output: field in index.Rmd and comment-out the formats you don't want.

The PDF file of your thesis will be deposited in the _book/ directory, by default.

The following components are ones you should edit to customize your thesis:

_bookdown.yml

This is the main configuration file for your thesis. It determines what Rmd files are included in the output, and in what order. Arrange the order of your chapters in this file and ensure that the names match the names in your folders.

This file contains all the meta information that goes at the beginning of your document. You'll need to edit this to put your name on the first page, the title of your thesis, etc.

01-chap1.Rmd , 02-chap2.Rmd , etc.

These are the Rmd files for each chapter in your dissertation. Write your thesis in these. If you're writing in RStudio, you may find the wordcount addin useful for getting word counts and readability statistics in R Markdown documents.

Store your bibliography (as bibtex files) here. We recommend using the citr addin and Zotero to efficiently manage and insert citations.

Specific style files for bibliographies should be stored here. A good source for citation styles is https://github.com/citation-style-language/styles#readme

figure/ and data/

Store your figures and data here and reference them in your R Markdown files. See the bookdown book for details on cross-referencing items using R Markdown.

The Annual Thesis Survey 2022 is open!

Are you a doctoral candidate (PhD or MD) or do you supervise theses at UNIL? On Monday May 16, you must have received an email from the Graduate Campus inviting you to participate in the annual thesis survey.

But what is the annual thesis survey?

It is a one-question questionnaire sent to all persons supervising or doing a PhD/MD thesis at UNIL.

UNIL is committed to ensuring the good management of theses within its university and wishes to allow each person to express themselves in an environment of confidence.

The annual thesis survey is therefore done in a logic of support, advice and listening, and is managed by the Graduate Campus, which acts as the institutional contact for all faculties.

For 2022, an FAQ has been added to the dedicated web page, which itself has been revised in the interests of clarity and transparency. We encourage you to review it!

UNIL already thanks you for your participation, which contributes to maintaining and improving the quality of thesis supervision, and allows us to better meet the needs of our doctoral candidates.

More information here .

Contact  : Dr Pauline Fritsch and Dr Mélanie Bosson, [email protected].

• Actualités formations
• Recherche doctorale
• Annual thesis survey
• Graduate Campus

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Lemanic Neuroscience Doctoral School (LNDS)

PHD PROGRAM IN NEUROSCIENCE OF THE UNIVERSITIES OF GENEVA AND LAUSANNE

Admission to the LNDS

If you are interested in enrolling in the LN Doctoral School, please follow these steps:

• Find a laboratory associated with the LNDS or part of the NeuroLéman Network (*).
• Define a thesis project with your thesis director.
• Register as a doctoral student at the university where your project will take place.
• The Scientific Committee of the Doctoral School will review your application and let you know if you have been accepted into the program.

(*) Students working in laboratories at the EPFL must enroll at the EPFL Doctoral School in Neuroscience ( EPFL-EDNE School ).

Note: MD-PhD candidates or PhD candidates with a medical study background who also want to obtain an MD title please contact the LNDS coordinator for guidance before enrolling to your host university!

Details on the university admission and doctoral school enrollment can be found in the linked documents below. In most cases, the PhD candidate will apply for admission in the faculty of attachment of her/his thesis director. Please make that your thesis director is indeed eligible as such within her/his particular faculty (e.g. holds a position as professor or MER) ***

• UNIGE: Admission and enrollment procedures
• UNIL: Admission and enrollment procedures
• UNIFR: Please follow point 1 of the UNIGE or UNIL procedure above, but follow the UNIFR admission procedure for your faculty of attachment. The UNIFR is a bit apart .. please contact the LNDS coordinator for questions ….

*** For prospective FPSE students @ UNIG E: Please fill and submit the “Thesis attestation” ( Encadrement de thèse ) with the FPSE header during the application process. Should a co-direction be foreseen, please use the co-direction for m to indicate both supervisors. *** For prospective MED or SCI students @ UNIGE : Please fill and submit the “Thesis attestation” ( Encadrement de thèse ), with the logo of the respective faculty of attachment during the application process

Your prospective faculty of attachment will be communicated in the LNDS acceptance letter you will receive (by default, this is the host faculty of your thesis director).

Theses and Dissertations at University of Maryland Libraries

• Online Theses and Dissertations
• Print Theses and Dissertations
• Additional Resources

Associate Director for Engagement, Inclusion, & Reparative Archiving

• Full text of University of Maryland, College Park, theses and dissertations from December 2003 to the present is available online at DRUM: Digital Repository at the University of Maryland .
• In instances where the student has restricted access to his/her electronic thesis or dissertation in DRUM for a specific period, any physical copies are also restricted. As of the Fall 2013 semester, physical copies are no longer created. Written permission from the author is required to make a restricted thesis or dissertation available before the restriction period expires.
• University of Maryland doctoral dissertations from 1997 to the present and master's theses from December 2003 to the present are available through Proquest Dissertations & Theses Global . Because of licensing agreements, this database can be used only by current faculty, staff, and students of the University of Maryland, College Park, and authorized users from other subscribing institutions.
• Permanent, non-circulating copies of University of Maryland, College Park, master's theses and doctoral dissertations are maintained by the University Archives  and stored offsite at Severn Library. They are available for researcher use in the Maryland Room of Hornbake Library.  Requests should be placed at least 2 business days prior to your visit to guarantee that they will be available in the Maryland Room for your use. Please see steps to request Special Collections and University Archives materials from Severn Library .
• In some cases, a second, circulating copy of a thesis or dissertation is available in one of our branch libraries. Researchers should check the UMD Libraries Catalog for the exact location of circulating copies.
• In some cases, you may be able to order the full-text electronically. See the Print Theses and Dissertations page for more details.
• Email the University Archives at [email protected] for more information.
• Next: Online Theses and Dissertations >>
• Last Updated: Apr 2, 2024 3:10 PM
• URL: https://lib.guides.umd.edu/MDdissertations