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R - Bibliography in RMD
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  Specifying a bibliography and cite authors

The most important part of your RMD file is the YAML header. For writing an academic paper, I suggest to use PDF output, numbered sections and a table of content (toc).

---
title: "Writing an academic paper in R"
author: "Author"
date: "Date"
output:
  pdf_document:
    number_sections: yes
toc: yes
bibliography: bibliography.bib
---

In this example, our file bibliography.bib looks like this:

@ARTICLE{Meyer2000,  
  AUTHOR="Bernd Meyer",  
  TITLE="A constraint-based framework for diagrammatic reasoning",  
  JOURNAL="Applied Artificial Intelligence",  
  VOLUME= "14",  
  ISSUE = "4",  
  PAGES= "327--344",  
  YEAR=2000  
}

To cite an author mentioned in your .bib file write @ and the bibkey, e.g. Meyer2000.

# Introduction

`@Meyer2000` results in @Meyer2000.

`@Meyer2000 [p. 328]` results in @Meyer2000 [p. 328]

`[@Meyer2000]` results in [@Meyer2000]

`[-@Meyer2000]` results in [-@Meyer2000]

# Summary

# References

Rendering the RMD file via RStudio (Ctrl+Shift+K) or via console rmarkdown::render("<path-to-your-RMD-file">) results in the following output:

enter image description here (opens new window)
  Inline references

If you have no *.bib file, you can use a references field in the document’s YAML metadata. This should include an array of YAML-encoded references, for example:

---
title: "Writing an academic paper in R"
author: "Author"
date: "Date"
output:
  pdf_document:
    number_sections: yes
toc: yes
references:
  - id: Meyer2000
    title: A Constraint-Based Framework for Diagrammatic Reasoning
    author:
    - family: Meyer
      given: Bernd
    volume: 14
    issue: 4
    publisher: Applied Artificial Intelligence
    page: 327-344
    type: article-journal
    issued:
      year: 2000
---

# Introduction

`@Meyer2000` results in @Meyer2000.

`@Meyer2000 [p. 328]` results in @Meyer2000 [p. 328]

`[@Meyer2000]` results in [@Meyer2000]

`[-@Meyer2000]` results in [-@Meyer2000]

# Summary

# References

Rendering this file results in the same output as in example "Specifying a bibliography".
  Citation styles

By default, pandoc will use a Chicago author-date format for citations and references. To use another style, you will need to specify a CSL 1.0 style file in the csl metadata field. In the following a often used citation style, the elsevier style, is presented (download at https://github.com/citation-style-language/styles (opens new window) ). The style-file has to be stored in the same directory as the RMD file OR the absolute path to the file has to be submitted.

To use another style then the default one, the following code is used:

---
title: "Writing an academic paper in R"
author: "Author"
date: "Date"
output:
  pdf_document:
    number_sections: yes
toc: yes
bibliography: bibliography.bib
csl: elsevier-harvard.csl
---

# Introduction

`@Meyer2000` results in @Meyer2000.

`@Meyer2000 [p. 328]` results in @Meyer2000 [p. 328]

`[@Meyer2000]` results in [@Meyer2000]

`[-@Meyer2000]` results in [-@Meyer2000]

# Summary

# Reference

enter image description here (opens new window)

Notice the differences to the output of example "Specifying a bibliography and cite authors"

Parameters

Parameter in YAML header Detail
toc table of contents
number_sections numbering the sections automatically
bibliography path to the bibliography file
csl path to the style file

Remarks

  • The purpose of this documentation is integrating an academic bibliography in a RMD file.
  • To use the documentation given above, you have to install `rmarkdown` in R via `install.packages("rmarkdown")`.

  • Sometimes Rmarkdown removes the hyperlinks of the citations. The solution for this is adding the following code to your YAML header: `link-citations: true`

  • The bibliography may have any of these formats:
    • Format File extension
    MODS .mods
    BibLaTeX .bib
    BibTeX .bibtex
    RIS .ris
    EndNote .enl
    EndNote XML .xml
    ISI .wos
    MEDLINE .medline
    Copac .copac
    JSON citeproc .json
    		 

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