Code to run biogeographic analyses for Chen et al. "Systematics and biogeography of the Old World fern genus Antrophyum".
All code is in R. Workflow is maintained with the targets package.
You must have R and Quarto installed.
This code was developed with R v4.2.1 and Quarto v1.3.14. Other versions may work but are not guaranteed.
Place the data files (Antrophyum.newick, Antrophyum_geodata.data, manual_dispersal_multipliers.txt) into _targets/user/data.
Start R and run renv::restore() to install all needed packages.
Within R, run targets::tar_make(). You will see the workflow start running. It may take around 1 hr depending on your computer. When everything is done, a report (bgb.docx) and supplemental figures (PDF files) will be output to reports.
All code except for cladistics.csl is under the MIT license.
cladistics.csl by Steven Vidovic is licensed under a Creative Commons Attribution-ShareAlike 3.0 License. No changes were made to the file.