Implementation of the EM algorithm for the detection of shifts in a phylogeny.

Installation

Stable version on the CRAN.

To get the latest (and possibly unstable) version, you can use the devtools package:

install.packages("devtools")
devtools::install_github(repo = "pbastide/PhylogeneticEM", ref = "develop")

Documentation

See package documentation (references and vignettes) here: http://pbastide.github.io/PhylogeneticEM/

(Built with pkgdown).

References:

Bastide, P., Mariadassou, M. and Robin, S. (2017), Detection of adaptive shifts on phylogenies by using shifted stochastic processes on a tree. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 79(4):1067-1093, doi:10.1111/rssb.12206.

Bastide, P., Ané, C., Robin, S. and Mariadassou, M. (2018), Inference of Adaptive Shifts for Multivariate Correlated Traits. 67(4), 662–680. doi:10.1093/sysbio/syy005.