johnWilshire/thesis_guide

Very Rough template / Guide to using RMarkdown for writing your thesis!

Rmarkdown preamble:

output:
  #word_document
  pdf_document:
    fig_caption: yes
fontsize: 12pt
bibliography: bibliography.bib
linkcolor: blue
csl: journal-of-ecology.csl

Bibliography

• Rstudio’s guide: authoring_bibliographies_and_citations

My workflow:

0. Install the Google Scholar browser extension

1. Open a paper you want to cite, for example this paper

2. Click on the extensions icon, click the quote symbol, then click bibtex

3. You should then be on a page that looks like this:

% comments are preceded by a % sign
@article{nakagawa2013general, % the documents id
  title={A general and simple method for obtaining R2 from generalized linear mixed-effects models},
  author={Nakagawa, Shinichi and Schielzeth, Holger},
  journal={Methods in Ecology and Evolution},
  volume={4},
  number={2},
  pages={133--142},
  year={2013},
  publisher={Wiley Online Library}
}

4. Copy this into your bibliography.bib

5. You can then cite it from within your document by writing: [@nakagawa2013general] (Nakagawa and Schielzeth 2013)

or unquoted @nakagawa2013general Nakagawa and Schielzeth (2013)

Cite mulitple authours by typing [@nakagawa2013general; nakagawa2013general], seperating them with a ;

Title page

Title pages can be included from other files, different chapters can be included in a similar way

\```{r child = 'title_page.Rmd'}
\```

Useful links

• combining several .Rmds into one document
• Rmarkdown guide
• [Writing your thesis with R Markdown] (https://rosannavanhespenresearch.wordpress.com/2016/02/03/writing-your-thesis-with-r-markdown-1-getting-started/)
• (thesisdown)[https://github.com/ismayc/thesisdown]

Nakagawa, Shinichi, and Holger Schielzeth. 2013. “A General and Simple Method for Obtaining R2 from Generalized Linear Mixed-Effects Models.” Methods in Ecology and Evolution 4 (2). Wiley Online Library: 133–42.