IQSS / EvoPhylo

A package to perform automated morphological character partitioning for phylogenetic analyses and analyze macroevolutionary parameter outputs from clock (time-calibrated) Bayesian inference analyses.

EvoPhylo: Pre- and Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics

A package to perform automated morphological character partitioning for phylogenetic analyses and analyze macroevolutionary parameter outputs from clock (time-calibrated) Bayesian inference analyses. EvoPhylo is currently designed to pre- and postprocess morphological data for relaxed clock Bayesian phylogenetic analyses using the software Mr. Bayes. Subsequent releases will also implement functions to postprocess output data produced by the software package BEAST2.

The ideas and rationale behind the functionality and objectives of the analyses available in this package were first presented and can be referenced to Simões, T. R. & Pierce, S. E. 2021. Sustained High Rates of Morphological Evolution During the Rise of Tetrapods. Nature Ecology & Evolution.

Installing package EvoPhylo

Install the release version directly from CRAN:

install.packages("EvoPhylo")

or from Github (check this for the latest updates):

# install.packages("devtools")
devtools::install_github("tiago-simoes/EvoPhylo")

Tutorials

See vignette("char-part"), vignette("fbd-params"), vignette("rates-selection"), and vignette("theory") for step-by-step guides on using EvoPhylo to perform these analyses, also available on the EvoPhylo website.

Authors

• Tiago R. Simões: Conceptualization and code development - Github Profile
• Noah Greifer: Code development
• Stephanie E. Pierce: Project supervision

License

This project is licensed under General Public License, version 2.