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
NeedsCompilation: yes
Packaged: 2025-09-23 15:18:56 UTC; bastidep
Author: Paul Bastide [aut, cre],
  Mahendra Mariadassou [ctb]
Maintainer: Paul Bastide <paul.bastide@m4x.org>
Repository: CRAN
Date/Publication: 2025-09-23 15:40:09 UTC
Built: R 4.4.3; x86_64-w64-mingw32; 2026-02-16 03:47:05 UTC; windows
Archs: x64
