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