A set of software tools for EvoHeritage calculations in R
The root directory contains a set of functions for calculating EvoHeritage that can be sourced and then used in analyses The root directory also contains a test file that can be sourced to confirm these functions are working correctly The working directory for running the unit tests should be the root
Sub directories contain individual example applications of the main functions Each example application has a directory called Data which is excluded (gitignored) from the GitHub repository The working directory for running any of the example applications should be the directory of that application
Calculated living fossilness for mammals using various methods based on ED and EvoHeritage Graphs the results and provides a comparison between the methods
Compares species richness, PD and EvoHeritage as descriptors of primary productivity in the Cedar Creek grassland experiments graphs the results comparing the methods
- The EvoHeritage tools and living fossil applications are written by James Rosindell
- The primary productivity application was written by James Rosindell and William D Pearse, based on code to perform the calculation for the PD case provided by William D Pearse.
- These tools and the two applications are as described in "Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage" 2023 authored by James Rosindell, Kerry Manson, Rikki Gumbs, William D Pearse and Mike Steel https://doi.org/10.1101/2022.07.16.499419
For any questions about using this code please write to [email protected]