knitr-template
This template for an academic journal article uses knitr, R Markdown, and pandoc. It is similar in spirit to project-template, but relies more heavily on Yihui Xie's knitr package to compile the main document, rather than GNU Make.
The main document that contains the article text and analysis is knitr-template.Rmd. The file conversion.R converts knitr-template.Rmd to .md, .html, .pdf, and .doc.
The bibliography and in text citations rely on Carl Boettiger's knitcitations package. The reference information is contained in the file refs.bib, which you could create with any population citation management program (e.g. Mendeley).