Package: PhylogeneticEM
Title: Automatic Shift Detection using a Phylogenetic EM
Version: 1.8.1
Authors@R: c(
    person("Paul", "Bastide", email = "paul.bastide@m4x.org", role = c("aut", "cre")),
    person("Mahendra", "Mariadassou", role = "ctb"))
Description: 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>.
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)
Suggests: combinat (>= 0.0.8), doParallel (>= 1.0.10), phytools (>=
        0.5.38), testthat (>= 1.0.2), TreeSim (>= 2.2), knitr,
        rmarkdown
LinkingTo: Rcpp, RcppArmadillo
License: GPL (>= 2) | file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
URL: https://github.com/pbastide/PhylogeneticEM,
        https://pbastide.github.io/PhylogeneticEM/
BugReports: https://github.com/pbastide/PhylogeneticEM/issues
VignetteBuilder: knitr
Repository: https://pbastide.r-universe.dev
Date/Publication: 2025-09-23 13:48:06 UTC
RemoteUrl: https://github.com/pbastide/phylogeneticem
RemoteRef: HEAD
RemoteSha: 1a098255280e63072dc5be8b25df43a38eb08188
NeedsCompilation: yes
Packaged: 2026-06-21 08:09:12 UTC; root
Author: Paul Bastide [aut, cre],
  Mahendra Mariadassou [ctb]
Maintainer: Paul Bastide <paul.bastide@m4x.org>