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: | 1.8.1 |
| 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: | 2025-09-23 |
| 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 | fileLICENSE [expanded from: GPL (≥ 2) | file LICENSE] |
| URL: | https://github.com/pbastide/PhylogeneticEM,https://pbastide.github.io/PhylogeneticEM/ |
| NeedsCompilation: | yes |
| Citation: | PhylogeneticEM citation info |
| Materials: | NEWS |
| CRAN checks: | PhylogeneticEM results |
| Reference manual: | PhylogeneticEM.html ,PhylogeneticEM.pdf |
| Vignettes: | Analysis of the New World Monkeys dataset (source,R code) An Introduction to the PhylogeneticEM Package (source,R code) |
| Package source: | PhylogeneticEM_1.8.1.tar.gz |
| Windows binaries: | r-devel:PhylogeneticEM_1.8.1.zip, r-release:PhylogeneticEM_1.8.1.zip, r-oldrel:PhylogeneticEM_1.8.1.zip |
| macOS binaries: | r-release (arm64):PhylogeneticEM_1.8.1.tgz, r-oldrel (arm64):PhylogeneticEM_1.8.1.tgz, r-release (x86_64):PhylogeneticEM_1.8.1.tgz, r-oldrel (x86_64):PhylogeneticEM_1.8.1.tgz |
| Old sources: | PhylogeneticEM archive |
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