Manuscript describing rotl

rotl is an R package that can be used to query and download subsets of the synthetic Open Tree of Life directly in R. This repository contains a manuscript describing this package and how to get started with it.

A pre-print is available at the PeerJ PrePrints and can be cited as:

Michonneau F, Brown JW, Winter D. (2016) rotl, an R package to interact with the Open Tree of Life data. PeerJ PrePrints 3:e1834 https://dx.doi.org/10.7287/peerj.preprints.1471v3

The peer-reviewed paper is now published in Methods in Ecology & Evolution

Michonneau, F., Brown, J. W. and Winter, D. J. (2016), rotl: an R package to interact with the Open Tree of Life data. Methods in Ecology and Evolution. doi:10.1111/2041-210X.12593

How to build the manuscript?

The manuscript is reproducible but you might need to install tools and packages to make it work. In short, you will need (for more details look at the list of Ubuntu packages that are needed in the .travis.yml file):

• R packages

  • Stable versions of rgbif, ggplot2, maps, and knitr.
  • The development version of rotl

• LaTeX installation

• pdftk

• Fonts

  • Crimson text
  • Source Sans Pro