Automatic Shift Detection using a Phylogenetic EM R package PhylogeneticEM version 1.8.1 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) <doi:10.1111/rssb.12206> and Bastide et al. (2018) <doi:10.1093/sysbio/syy005>. Software Depends: ape (>= 5.3), Matrix (>= 1.2.18), R (>= 3.6.0), Imports: capushe (>= 1.1.1), foreach (>= 1.4.3), gglasso (>= 1.4), glmnet (>= 2.0.5), graphics (>= 3.6.0), grDevices (>= 3.6.0), LINselect (>= 1.1.1), MASS (>= 7.3.45), methods (>= 3.6.0), plyr (>= 1.8.4), Rcpp (>= 1.0.2), robustbase (>= 0.92.6), stats (>= 3.6.0), utils (>= 3.6.0) LinkingTo: Rcpp, RcppArmadillo Suggests: combinat (>= 0.0.8), doParallel (>= 1.0.10), phytools (>= 0.5.38), testthat (>= 1.0.2), TreeSim (>= 2.2), knitr, rmarkdown Paul Bastide <paul.bastide@m4x.org> Comprehensive R Archive Network (CRAN) Paul Bastide [aut, cre], Mahendra Mariadassou [ctb] GPL (>= 2) file LICENSE (https://CRAN.R-project.org/package=PhylogeneticEM/LICENSE) 2025-09-23 application/tgz https://CRAN.R-project.org/package=PhylogeneticEM doi:10.32614/CRAN.package.PhylogeneticEM