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 was initially released for pre- and postprocess data using the software Mr. Bayes, but since version 0.3 it also handles data pre- and post-processing for the software package BEAST2.

The ideas and rationale behind the original functionality and objectives of the analyses available in this package were first presented by Simões & Pierce (2021). It’s current functionality is described in detail by Simões, Grifer, Barido-Sottani & Pierce (2023).

Installing package EvoPhylo

Install the latest release version directly from CRAN:

install.packages("EvoPhylo")

or developers version from Github:

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

Tutorials

See vignette("char-part"),vignette("data_treatment"), vignette("rates-selection_MrBayes"), vignette("rates-selection_BEAST2"), vignette("fbd-params"), and vignette("offset_handling"), for step-by-step guides on using EvoPhylo to perform these analyses, also available on the EvoPhylo website.

Authors

Authors (including current developers)

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

License

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