vivekbhr / doctorRbite

An updated R Markdown thesis template using the bookdown package, for University of Freiburg

doctorRbite

Easy way to write your thesis using Rmarkdown, for doctoral students at the Max Planck Institute of Immunobiology and Epigenetics, Freiburg.

This project was inspired by the bookdown and thesisdown packages. 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 http://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.)
• Word
• ePub
• gitbook

Under the hood, the a custom LaTeX template is used to ensure that documents conform precisely to the University of Freiburg, faculty of biology 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.

Using doctorRbite from Vivek's GitHub

Using doctorRbite has some prerequisites which are described below. To compile PDF documents using R, you are going to need to have LaTeX installed. It can be downloaded for Windows at http://http://miktex.org/download and for Mac at http://tug.org/mactex/mactex-download.html. Follow the instructions to install the necessary packages after downloading the (somewhat large) installer files. You may need to install a few extra LaTeX packages on your first attempt to knit as well.

To use doctorRbite from RStudio:

1. Install the latest RStudio. Only the version as of Oct 2017 has a recent enough Pandoc included so you may need to upgrade this separately or install a newer RStudio.

   rmarkdown::pandoc_available("1.2")
   #> [1] TRUE

2. Install the bookdown and doctorRbite packages:

install.packages("devtools")
devtools::install_github("rstudio/bookdown")
devtools::install_github("vivekbhr/doctorRbite")

3. Use the New R Markdown dialog to select MPIthesis:

   

   Note that this will currently only Knit if you name the directory index as shown above.

4. 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.

5. Edit the individual chapter R Markdown files as you wish and then re-run step (4) again.

Can I write my thesis in word instead?

YES you can write your thesis in MS word/google docs and still format it at the end using doctorRbite. For this you need to first convert your word document into markdown, using pandoc. Contact me for additional details.