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.
- Obtaining a list of species of interest from the NCBI SRA
- Downloading species occurrences using RBIEN
- Compiling occurrence data into a larger file, cross-referencing names using GBIF backbone
- Range map creation using square grids
- Range map creation using Uber's H3 hexagon mapping
This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. 2236870.