This is the source repository for the paper "Viral niche construction alters hosts and ecosystems at multiple scales" by Hamblin et al. (2014).
The article source is written in R Markdown, and can be compiled to other formats; the makefile contains targets for PDF via LaTeX and Microsoft Word (docx). To compile the source, clone the repo and use 'make pdf' or 'make docx' respectively; the paper should also be (mostly) compatible with any of other formats that Pandoc supports. To compile properly will require the following dependencies:
- A recent version of R and knitr.
- A recent version of pandoc.
- A recent version of LaTeX and a copy of elsarticle.cls for PDF output. For example, on Ubuntu 'sudo-apt-get install texlive-full' will install both at once.
I am greatly indebted to the awesome Carl Boettiger, from whom I lifted the Makefile, knit script, and the basis for the elsarticle.latex file (in the rfishbase repo here. The trends.csl style file comes from CitationStyles; the specific file is the trends-journals.csl file in their GitHub repo.
If you have any questions, please feel free to contact me by email or Twitter.