Automatic Shift Detection using a Phylogenetic EM

Implementation of the automatic shift detection method for Brownian Motion (BM) or Ornstein–Uhlenbeck (OU) models of trait evolution on phylogenies. Some tools to handle equivalent shifts configurations are also available. See Bastide et al. (2017) and Bastide et al. (2018) .

Reference manual

install.packages("PhylogeneticEM")

1.8.1 by Paul Bastide, a year ago

https://github.com/pbastide/PhylogeneticEM, https://pbastide.github.io/PhylogeneticEM/

Report a bug at https://github.com/pbastide/PhylogeneticEM/issues

Browse source code at https://github.com/cran/PhylogeneticEM

Authors: Paul Bastide [aut, cre] , Mahendra Mariadassou [ctb]

Documentation: PDF Manual

GPL (>= 2) | file LICENSE license

Imports capushe, foreach, gglasso, glmnet, graphics, grDevices, LINselect, MASS, methods, plyr, Rcpp, robustbase, stats, utils

Depends on ape, Matrix

Suggests combinat, doParallel, phytools, testthat, TreeSim, knitr, rmarkdown

Linking to Rcpp, RcppArmadillo

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