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.
Citations for all packages and software used to collect and analyze data
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
R Core Team (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
Brian Maitner (2023). BIEN: Tools for Accessing the Botanical Information and Ecology Network Database. R package version 1.2.6. https://CRAN.R-project.org/package=BIEN
Hadley Wickham, Romain François, Lionel Henry, Kirill Müller and Davis Vaughan (2023). dplyr: A Grammar of Data Manipulation. R package version 1.1.4. https://CRAN.R-project.org/package=dplyr
Chamberlain S, Barve V, Mcglinn D, Oldoni D, Desmet P, Geffert L, Ram K (2024). rgbif: Interface to the Global Biodiversity Information Facility API. R package version 3.8.1, <URL: https://CRAN.R-project.org/package=rgbif>.