Package: PhylogeneticEM 1.7.0
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_1.7.0.tar.gz
PhylogeneticEM_1.7.0.tar.gz(r-4.5-noble)PhylogeneticEM_1.7.0.tar.gz(r-4.4-noble)
PhylogeneticEM_1.7.0.tgz(r-4.4-emscripten)PhylogeneticEM_1.7.0.tgz(r-4.3-emscripten)
PhylogeneticEM.pdf |PhylogeneticEM.html✨
PhylogeneticEM/json (API)
NEWS
# Install 'PhylogeneticEM' in R: |
install.packages('PhylogeneticEM', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/pbastide/phylogeneticem/issues
- monkeys - New World Monkeys dataset
Last updated 9 months agofrom:29207c14fc. Checks:OK: 1 NOTE: 1. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 01 2024 |
R-4.5-linux-x86_64 | NOTE | Oct 01 2024 |
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_rotationsmodel_selectionnode_optimal_valuesparams_BMparams_OUparams_processparsimonyCostparsimonyNumberpartitionsNumberPhyloEMplot_criterionshifts_to_simmapshifts.list_to_matrixshifts.matrix_to_listsimul_processtransform_branch_length
Dependencies:apecapushecodetoolsDEoptimRdigestelasticnetforeachgglassoglmnetgtoolsiteratorslarslatticeLINselectMASSMatrixmvtnormnlmeplsplyrrandomForestRcppRcppArmadilloRcppEigenrobustbaseshapesurvival