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BBMV : phylogenetic comparative methods
The R package BBMV implements models for the evolution of continuous traits on macroevolutionary landscapes.
It uses the Fokker-Planck-Kolmogorov model, in which a continuous trait evolves along the branches of a phylogeny under random diffusion but is also subject to a force that pulls it towards specific values - this force can be of any shape. The package contains functions for both inference, using either maximum-likelihood or MCMC estimation, or simulation of traits evolving on phylogenies.
This tool enables testing complex hypothesis-driven scenarios regarding trait evolution, but it also offers the possibility to estimate the shape of the adaptive landscapes in which traits evolved. Ultimately, this will provide a way to infer how ecological processes have influenced phenotypic evolution over long timescales.
The package is described in the following publication :
Boucher, F.C. (2019) BBMV : an R package for the estimation of macroevolutionary landscapes. Ecography. 42(3) : 558-564.