Package: PhylogeneticEM 1.8.0
Paul Bastide
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>.
Authors:
PhylogeneticEM_1.8.0.tar.gz
PhylogeneticEM_1.8.0.tar.gz(r-4.5-noble)PhylogeneticEM_1.8.0.tar.gz(r-4.4-noble)
PhylogeneticEM_1.8.0.tgz(r-4.4-emscripten)PhylogeneticEM_1.8.0.tgz(r-4.3-emscripten)
PhylogeneticEM.pdf |PhylogeneticEM.html✨
PhylogeneticEM/json (API)
NEWS
| # Install 'PhylogeneticEM' in R: |
| install.packages('PhylogeneticEM', repos = 'https://cloud.r-project.org') |
Bug tracker:https://github.com/pbastide/phylogeneticem/issues
Pkgdown site:https://pbastide.github.io
- monkeys - New World Monkeys dataset
Last updated 1 months agofrom:2c50928342. Checks:3 OK. Indexed: no.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 17 2025 |
| R-4.5-linux-x86_64 | OK | Mar 17 2025 |
| R-4.4-linux-x86_64 | OK | Mar 17 2025 |
Exports:allocate_regimes_from_shiftsallocate_shifts_from_regimescheck_parsimonyclusters_from_shiftscompute_betas_from_shiftscompute_dist_phycompute_shifts_from_betascompute_stationary_variancecompute_times_cacorrespondenceEdgesenlightenumerate_parsimonyenumerate_tips_under_edgesequivalent_shiftsestimateEMextractfind_grid_alphafind_rotationget_criterionimputed_traitsincidence.matrixincidence.matrix.fulllog_likelihoodmerge_alpha_gridsmerge_rotationsmodel_selectionnode_optimal_valuesparams_BMparams_OUparams_processparsimonyCostparsimonyNumberpartitionsNumberPhyloEMplot_criterionshifts_to_simmapshifts.list_to_matrixshifts.matrix_to_listsimul_processtransform_branch_length
Dependencies:apecapushecodetoolsDEoptimRdigestelasticnetforeachgglassoglmnetgtoolsiteratorslarslatticeLINselectMASSMatrixmvtnormnlmeplsplyrrandomForestRcppRcppArmadilloRcppEigenrobustbaseshapesurvival
Citation
To cite PhylogeneticEM in publications use:
Paul Bastide, Mahendra Mariadassou & Stephane Robin (2017). Detection of adaptive shifts on phylogenies by using shifted stochastic processes on a tree. Journal of the Royal Statistical Society: Series B (Statistical Methodology). 79(4):1067-1093<doi:10.1111/rssb.12206>.
Corresponding BibTeX entry:
@Article{,
title = {{Detection of adaptive shifts on phylogenies by using
shifted stochastic processes on a tree}},
author = {Paul Bastide and Mahendra Mariadassou and Stephane
Robin},
journal = {Journal of the Royal Statistical Society: Series B
(Statistical Methodology)},
month = {sep},
year = {2017},
volume = {79},
number = {4},
issn = {1467-9868},
pages = {1067--1093},
doi = {10.1111/rssb.12206},
url = {https://doi.org/10.1111/rssb.12206},
}
