Trait Evolution on Phylogenies Using the Cauchy Process

The Cauchy Process can model pulsed continuous trait evolution on phylogenies. The likelihood is tractable, and is used for parameter inference and ancestral trait reconstruction. See Bastide and Didier (2023) .

cauphy

The Cauchy Process to model trait evolution on phylogenies.

Installation

Stable version on the CRAN

The development version can be installed from GitHub using the remotes package:

install.packages("remotes")
remotes::install_github(repo = "gilles-didier/cauphy", ref = "dev")

Documentation

See package documentation (references and vignettes) here: https://gilles-didier.github.io/cauphy/.

(Built with pkgdown).

Reference

Bastide, P. and Didier, G. (2023), The Cauchy Process on Phylogenies: a Tractable Model for Pulsed Evolution. Systematic Biology. doi:10.1093/sysbio/syad053. [bioRxiv].