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:Paul Bastide [aut, cre], Mahendra Mariadassou [ctb]

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PhylogeneticEM.pdf |PhylogeneticEM.html✨
PhylogeneticEM/json (API)
NEWS

# Install 'PhylogeneticEM' in R:
install.packages('PhylogeneticEM', repos = c('https://pbastide.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/pbastide/phylogeneticem/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • monkeys - New World Monkeys dataset

On CRAN:

6.18 score 16 stars 47 scripts 264 downloads 2 mentions 39 exports 27 dependencies

Last updated 10 months agofrom:c92c9054ea. Checks:OK: 7 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-win-x86_64NOTEOct 27 2024
R-4.5-linux-x86_64NOTEOct 27 2024
R-4.4-win-x86_64OKOct 27 2024
R-4.4-mac-x86_64OKOct 27 2024
R-4.4-mac-aarch64OKOct 27 2024
R-4.3-win-x86_64OKOct 27 2024
R-4.3-mac-x86_64OKOct 27 2024
R-4.3-mac-aarch64OKOct 27 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

Analysis of the New World Monkeys dataset

Paul Bastide

Rendered frommonkeys.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2024-01-31
Started: 2018-08-07

An Introduction to the PhylogeneticEM Package

Paul Bastide

Rendered fromtutorial.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2024-01-31
Started: 2016-10-21

Readme and manuals

Help Manual

Help pageTopics
Allocation of regimes to nodes.allocate_regimes_from_shifts
Allocation of shifts to edgesallocate_shifts_from_regimes
Check Parsimony, assuming no homoplasycheck_parsimony
Clustering associated to a shift allocation, assuming no homoplasy.clusters_from_shifts
Computation of the optimal values at nodes and tips.compute_betas_from_shifts
Phylogenetic Distancescompute_dist_phy
Computation of shifts from the vector of optimal valuescompute_shifts_from_betas
Compute the stationary variance matrixcompute_stationary_variance
Common Ancestors Timescompute_times_ca
Correspondence between edges numberscorrespondenceEdges
Make the result lighterenlight enlight.PhyloEM
Enumerate all the possible regime allocations, given a clustering of the tips.enumerate_parsimony
Tips descendants of nodes.enumerate_tips_under_edges
Find all equivalent shifts allocations and values.equivalent_shifts
Perform One EMestimateEM
Extraction functionextract
Extract the result of 'enumerate_parsimony' at a node.extract.enumerate_parsimony
Extract the shifts values for one trait.extract.equivalent_shifts
Extraction of the actual number of solutions.extract.parsimonyCost
Extraction of the actual number of solutions.extract.parsimonyNumber
Extract from object 'partitionsNumber'extract.partitionsNumber
Extraction of simulated traitsextract.simul_process
Find a reasonable grid for alphafind_grid_alpha
Test for rotation invariant datasetsfind_rotation
Get Model Selection Criterionget_criterion
Ancestral State Reconstructionimputed_traits imputed_traits.PhyloEM
Incidence matrix of a tree.incidence.matrix
Incidence matrix of a tree.incidence.matrix.full
Log Likelihood of a fitted objectlog_likelihood log_likelihood.params_process log_likelihood.PhyloEM
Merge fits from independent runs of PhyloEM.merge_rotations
Model Selection of a fitted objectmodel_selection model_selection.PhyloEM
New World Monkeys datasetmonkeys
Computation of the optimal values at nodes and tips.node_optimal_values
Create an object 'params_process' for a BMparams_BM
Create an object 'params_process' for an OUparams_OU
Create an object params_processparams_process
Create an object 'params_process'params_process.character
Parameter estimatesparams_process.PhyloEM
Minimal number of shifts needed to get a clustering.parsimonyCost
Number of equivalent parsimonious allocations.parsimonyNumber
Number of different modelspartitionsNumber
Model Estimation with Detection of ShiftsPhyloEM
Plot Model Selection Criterionplot_criterion
Plot all the equivalent solutions.plot.enumerate_parsimony
Plot all the equivalent solutions.plot.equivalent_shifts
Plot for class 'simul_process'plot.params_process
Plot for class 'PhyloEM'plot.PhyloEM
Residuals of a fitted objectresiduals.PhyloEM
Simmap format mapping from list of edgesshifts_to_simmap
Compute the matrix of shifts.shifts.list_to_matrix
Compute the list of shifts.shifts.matrix_to_list
Simulate a Stochastic Process on a treesimul_process simul_process.params_process simul_process.PhyloEM
Transform branch length for a re-scaled BMtransform_branch_length