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PhylogeneticEM (version 1.8.1)

Automatic Shift Detection using a Phylogenetic EM

Description

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) and Bastide et al. (2018) .

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install.packages('PhylogeneticEM')

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602

Version

1.8.1

License

GPL (>= 2) | file LICENSE

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Repository

https://github.com/pbastide/PhylogeneticEM

Homepage

https://pbastide.github.io/PhylogeneticEM/

Maintainer

Paul Bastide

Last Published

September 23rd, 2025

Functions in PhylogeneticEM (1.8.1)

clusters_from_shifts

Clustering associated to a shift allocation, assuming no homoplasy.

compute_expectations.BM

Compute the expected states of a BM

compute_betas_from_shifts

Computation of the optimal values at nodes and tips.

compute_dist_phy

Phylogenetic Distances

check_range_alpha

Check range of alpha

compute_fixed_moments

Compute fixed moments for E step.

compute_E.simple

compute_expectations.scOU

Compute the expected states of a scOU

compute_actualization_matrix_ultrametric

Compute Matrix W of actualization (Ultrametric case)

compute_diff_exp.BM

Compute differences of expectations between node and parent.

compute_sum_var_diff

Compute weighted sum of var_diff

compute_gauss_lasso

Do a lm on top of a lasso regression.

compute_shifts_from_betas

Computation of shifts from the vector of optimal values

compute_residuals.simple

compute_mean_variance.simple

Compute moments of params_old

compute_variance_covariance.OU.nonsym

Complete variance covariance matrix for OU

compute_mahalanobis_distance.simple

Squared Mahalanobis Distance

compute_variance_covariance.OU

Complete variance covariance matrix for OU

compute_variance_covariance.BM

Complete variance covariance matrix for BM

compute_state_filter

List of potential daughter states when parent is in state k.

enumerate_tips_under_edges

Tips descendants of nodes.

compute_times_ca

Common Ancestors Times

compute_stationary_variance

Compute the stationary variance matrix

correspondenceEdges

Correspondence between edges numbers

enumerate_parsimony

Enumerate all the possible regime allocations, given a clustering of the tips.

compute_variance_block_diagonal.OU

Tips Variances for the OU

compute_variance_block_diagonal.BM

Tips Variances for the BM

equivalent_shifts_values

Find values given edges. OU stationary case. Ultrametric tree.

compute_var_M.BM

Computation of the variance.

compute_variance_covariance.scOU

Complete variance covariance matrix for scOU

equivalent_shifts

Find all equivalent shifts allocations and values.

Make the result lighter

compute_tree_correlations_matrix.scOU

Matrix of tree-induced correlations for the scOU

Function to estimate alpha

compute_log_likelihood.simple

compute_tree_correlations_matrix.BM

Matrix of tree-induced correlations for the BM

extract.partitionsNumber

Extract from object partitionsNumber

extract.parsimonyCost

Extraction of the actual number of solutions.

compute_var_diff.BM

Compute variances of differences between nodes and parents.

incidence.matrix.full

Incidence matrix of a tree.

find_grid_alpha

Find a reasonable grid for alpha

incidence.matrix

Incidence matrix of a tree.

equivalent_shifts_edges

Find all the equivalent shift edges allocations.

find_independent_regression_vectors.glmnet_multivariate

Given a regularization path, find K selected independent variables.

extract_variance_covariance

Extract sub-matrices of variance.

Test for rotation invariant datasets

init.alpha.gamma.estimation

Initialization the selection strength alpha using robust estimation

incidence_matrix_actualization_factors

Compute the actualization factors to apply to the incidence matrix.

Initialization of the shifts using Lasso.

init.allocate_regimes_from_shifts

Initialization for the allocation of shifts.

go_back_to_original_process

Scale the parameters back to the original process

extract.parsimonyNumber

Extraction of the actual number of solutions.

init.simulate.OU

Initialize state and expectation matrices

Log Likelihood of a fitted object

merge_rotations

Merge fits from independent runs of PhyloEM.

init.simulate.BM

lasso_regression_K_fixed.glmnet_multivariate

Do a lasso regression with the number of non-zero variables fixed.

extract.equivalent_shifts

Extract the shifts values for one trait.

extract.enumerate_parsimony

Extract the result of enumerate_parsimony at a node.

Extraction function

extract.simul_process

Extraction of simulated traits

model_selection

Model Selection of a fitted object

init.parsimonyNumber

Initialization for parsimonyNumber.

merge_complementary_vectors

Merge several complementary vectors into one.

Run the EM for several values of K

find_shift_values

Find values given edges. OU stationary case. Ultrametric tree.

params_process.PhyloEM

Parameter estimates

params_process.character

Create an object params_process

Minimal number of shifts needed to get a clustering.

Create an object params_process

Create an object params_process for a BM

Get Model Selection Criterion

merge_alpha_grids

Merge PhyloEM fits on various grids of alpha values

merge_params_independent

Merge a list of independent parameters into into one parameter

Create an object params_process for an OU

matrix_of_possibles

Compute parent matrix from possibles daughter matrices.

init.incidence.matrix

Initialization for incidence matrix

init.parsimonyCost

Initialization for parsimonyCost.

get_variance_node

Get variance matrix of a node

init.incidence.matrix.full

Initialization for incidence matrix (full tree)

Ancestral State Reconstruction

init.compute_betas_from_shifts

Initialization for the computation of the optimal values

Plot Model Selection Criterion

Product of elements of a matrix

plot.enumerate_parsimony

Plot all the equivalent solutions.

Scale variance and selection strength from a linear transform

Plot for class PhyloEM

segmentation.OU.specialCase.lasso

Segmentation in the OU special case, using lasso regression

sample_shifts_edges

Sample shifts edges in a parsimonious way.

segmentation.BM

Segmentation in the BM case

residuals.PhyloEM

Residuals of a fitted object

sample_edges_intervals

Sample equally spaced edges.

shifts.matrix_to_list

Compute the list of shifts.

shifts_to_simmap

Simmap format mapping from list of edges

Penalty function type pBIC

penalty_BirgeMassart_shape2

Penalty function type Birgé-Massart 2

shifts.vector_to_list

Compute the list of shifts.

shifts.list_to_vector

Compute the vector of shifts.

parsimonyNumber

Number of equivalent parsimonious allocations.

partitionsNumber

Number of different models

Check whether parameters are in ranges.

init.simulate.StateAndExp

Initialize state and expectation matrices

init.enumerate_parsimony

Initialization for the enumeration of parsimonious solutions.

sum_partitions.cardFixed

Sum on subsets of a given cardinal.

transform_branch_length

Transform branch length for a re-scaled BM

transform_shifts_values

Transform the shift values

penalty_BirgeMassart_shape1

Penalty function type Birgé-Massart 1

Sum on all subsets.

penalty_BaraudGiraudHuet_likelihood

Penalty function type Baraud Giraud Huet.

Generic recursion down the tree.

split_params_independent

Split independent parameters into a list of parameters

Wrapper for E step in EM

Sum on a simplex

node_optimal_values

Computation of the optimal values at nodes and tips.

plot.equivalent_shifts

Plot all the equivalent solutions.

update.partitionsNumber.gen

Update formula in the general case

update.parsimonyNumber

Actualization for parsimonyNumber.

New World Monkeys dataset

test.root.state

Test state of root.

shifts.list_to_matrix

Compute the matrix of shifts.

Simulate a Stochastic Process on a tree

simulate_internal

Simulate a Stochastic Process on a tree

segmentation.OU.specialCase.same_shifts

Segmentation in the OU special case, conserving the same shifts position.

update.incidence.matrix.full

Update function for incidence matrix

plot.params_process

Plot for class simul_process

update.enumerate_parsimony

Actualization of the enumeration.

update.incidence.matrix

Update function for incidence matrix

update.parsimonyCost

Actualization for parsimonyCost.

Sum on a simplex

update.compute_betas_from_shifts

Update function for optimal value computation

update.allocate_regimes_from_shifts

Update function for regime allocation.

check.selection.strength

Check selection strength

allocate_shifts_from_regimes

Allocation of shifts to edges

check_parsimony

Check Parsimony, assuming no homoplasy

allocate_regimes_from_shifts

Allocation of regimes to nodes.

Model Estimation with Detection of Shifts

add_complementary

Add several entries, when only one is not NA.

allocate_subset_node.simulate

Iteration allocation

Test the format of data entry.

check_dimensions

Check dimensions of the parameters

check_parsimony_clusters

Check whether an allocation of the shifts is parsimonious, in the "infinite site model".