PhylogeneticEM: 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) <doi:10.1111/rssb.12206> and Bastide et al. (2018) <doi:10.1093/sysbio/syy005>.

Version: 1.7.0
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
Published: 2024-01-31
DOI: 10.32614/CRAN.package.PhylogeneticEM
Author: Paul Bastide [aut, cre], Mahendra Mariadassou [ctb]
Maintainer: Paul Bastide <paul.bastide at m4x.org>
BugReports: https://github.com/pbastide/PhylogeneticEM/issues
License: GPL-2 | GPL-3 | file LICENSE [expanded from: GPL (≥ 2) | file LICENSE]
URL: https://github.com/pbastide/PhylogeneticEM
NeedsCompilation: yes
Citation: PhylogeneticEM citation info
Materials: NEWS
CRAN checks: PhylogeneticEM results

Documentation:

Reference manual: PhylogeneticEM.pdf
Vignettes: New World Monkeys
Tutorial

Downloads:

Package source: PhylogeneticEM_1.7.0.tar.gz
Windows binaries: r-devel: PhylogeneticEM_1.7.0.zip, r-release: PhylogeneticEM_1.7.0.zip, r-oldrel: PhylogeneticEM_1.7.0.zip
macOS binaries: r-release (arm64): PhylogeneticEM_1.7.0.tgz, r-oldrel (arm64): PhylogeneticEM_1.7.0.tgz, r-release (x86_64): PhylogeneticEM_1.7.0.tgz, r-oldrel (x86_64): PhylogeneticEM_1.7.0.tgz
Old sources: PhylogeneticEM archive

Linking:

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