Information

This repository contains code and workflow data for an ongoing project titled "Sequencing historical RNA: unrealized potential to increase understanding of the plant tree of life". The aim of this repository is to produce publication-quality figures summarizing large amounts of coordinate data from green plants, using RBIEN.

Maitner BS, Boyle B, Casler N, et al. The bien r package: A tool to access the Botanical Information and Ecology Network (BIEN) Database. Methods Ecol Evol. 2018; 9: 373–379. https://doi.org/10.1111/2041-210X.12861

My hope is that this repository can also serve as a tutorial for downloading data from the BIEN database, working with coordinate data in R, and creating figures that display species ranges.

Outline of files included

1. Obtaining a list of species of interest from the NCBI SRA
2. Downloading species occurrences using RBIEN
3. Compiling occurrence data into a larger file, cross-referencing names using GBIF backbone
4. Range map creation using square grids
5. Range map creation using Uber's H3 hexagon mapping

Acknowledgements

This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. 2236870.