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PhylogeneticEM (version 1.8.0)

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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271

Version

1.8.0

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

February 14th, 2025

Functions in PhylogeneticEM (1.8.0)

compute_dist_phy

Phylogenetic Distances

compute_expectations.BM

Compute the expected states of a BM

compute_fixed_moments

Compute fixed moments for E step.

compute_actualization_matrix_ultrametric

Compute Matrix W of actualization (Ultrametric case)

compute_expectations.scOU

Compute the expected states of a scOU

compute_E.simple

compute_times_ca

Common Ancestors Times

compute_log_likelihood.simple

compute_sum_var_diff

Compute weighted sum of var_diff

compute_gauss_lasso

Do a lm on top of a lasso regression.

compute_tree_correlations_matrix.BM

Matrix of tree-induced correlations for the BM

compute_shifts_from_betas

Computation of shifts from the vector of optimal values

compute_tree_correlations_matrix.scOU

Matrix of tree-induced correlations for the scOU

compute_residuals.simple

compute_stationary_variance

Compute the stationary variance matrix

compute_var_M.BM

Computation of the variance.

compute_var_diff.BM

Compute variances of differences between nodes and parents.

compute_state_filter

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

clusters_from_shifts

Clustering associated to a shift allocation, assuming no homoplasy.

correspondenceEdges

Correspondence between edges numbers

Make the result lighter

compute_mean_variance.simple

Compute moments of params_old

compute_diff_exp.BM

Compute differences of expectations between node and parent.

compute_variance_covariance.OU

Complete variance covariance matrix for OU

equivalent_shifts_edges

Find all the equivalent shift edges allocations.

compute_variance_covariance.BM

Complete variance covariance matrix for BM

compute_variance_block_diagonal.BM

Tips Variances for the BM

check_range_alpha

Check range of alpha

compute_variance_block_diagonal.OU

Tips Variances for the OU

equivalent_shifts

Find all equivalent shifts allocations and values.

compute_betas_from_shifts

Computation of the optimal values at nodes and tips.

extract.parsimonyCost

Extraction of the actual number of solutions.

extract.parsimonyNumber

Extraction of the actual number of solutions.

Test for rotation invariant datasets

compute_variance_covariance.OU.nonsym

Complete variance covariance matrix for OU

compute_mahalanobis_distance.simple

Squared Mahalanobis Distance

find_independent_regression_vectors.glmnet_multivariate

Given a regularization path, find K selected independent variables.

incidence.matrix

Incidence matrix of a tree.

incidence.matrix.full

Incidence matrix of a tree.

init.incidence.matrix

Initialization for incidence matrix

compute_variance_covariance.scOU

Complete variance covariance matrix for scOU

equivalent_shifts_values

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

find_grid_alpha

Find a reasonable grid for alpha

extract_variance_covariance

Extract sub-matrices of variance.

extract.equivalent_shifts

Extract the shifts values for one trait.

extract.enumerate_parsimony

Extract the result of enumerate_parsimony at a node.

enumerate_parsimony

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

enumerate_tips_under_edges

Tips descendants of nodes.

init.simulate.BM

Extraction function

Ancestral State Reconstruction

extract.partitionsNumber

Extract from object partitionsNumber

extract.simul_process

Extraction of simulated traits

Function to estimate alpha

go_back_to_original_process

Scale the parameters back to the original process

find_shift_values

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

init.simulate.OU

Initialize state and expectation matrices

init.incidence.matrix.full

Initialization for incidence matrix (full tree)

init.parsimonyCost

Initialization for parsimonyCost.

init.parsimonyNumber

Initialization for parsimonyNumber.

Check whether parameters are in ranges.

init.simulate.StateAndExp

Initialize state and expectation matrices

params_process.PhyloEM

Parameter estimates

Run the EM for several values of K

Get Model Selection Criterion

incidence_matrix_actualization_factors

Compute the actualization factors to apply to the incidence matrix.

merge_complementary_vectors

Merge several complementary vectors into one.

Initialization of the shifts using Lasso.

merge_params_independent

Merge a list of independent parameters into into one parameter

Log Likelihood of a fitted object

merge_rotations

Merge fits from independent runs of PhyloEM.

init.alpha.gamma.estimation

Initialization the selection strength alpha using robust estimation

init.allocate_regimes_from_shifts

Initialization for the allocation of shifts.

lasso_regression_K_fixed.glmnet_multivariate

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

matrix_of_possibles

Compute parent matrix from possibles daughter matrices.

Create an object params_process

Generic recursion down the tree.

New World Monkeys dataset

Create an object params_process for an OU

Create an object params_process for a BM

Plot for class PhyloEM

init.compute_betas_from_shifts

Initialization for the computation of the optimal values

Penalty function type pBIC

init.enumerate_parsimony

Initialization for the enumeration of parsimonious solutions.

penalty_BirgeMassart_shape2

Penalty function type Birgé-Massart 2

get_variance_node

Get variance matrix of a node

model_selection

Model Selection of a fitted object

merge_alpha_grids

Merge PhyloEM fits on various grids of alpha values

params_process.character

Create an object params_process

plot.enumerate_parsimony

Plot all the equivalent solutions.

Minimal number of shifts needed to get a clustering.

parsimonyNumber

Number of equivalent parsimonious allocations.

partitionsNumber

Number of different models

penalty_BaraudGiraudHuet_likelihood

Penalty function type Baraud Giraud Huet.

update.enumerate_parsimony

Actualization of the enumeration.

plot.equivalent_shifts

Plot all the equivalent solutions.

update.incidence.matrix

Update function for incidence matrix

residuals.PhyloEM

Residuals of a fitted object

sample_edges_intervals

Sample equally spaced edges.

shifts.vector_to_list

Compute the list of shifts.

shifts_to_simmap

Simmap format mapping from list of edges

shifts.list_to_matrix

Compute the matrix of shifts.

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

sum_partitions.cardFixed

Sum on subsets of a given cardinal.

penalty_BirgeMassart_shape1

Penalty function type Birgé-Massart 1

shifts.matrix_to_list

Compute the list of shifts.

shifts.list_to_vector

Compute the vector of shifts.

Sum on a simplex

update.allocate_regimes_from_shifts

Update function for regime allocation.

Sum on a simplex

update.compute_betas_from_shifts

Update function for optimal value computation

node_optimal_values

Computation of the optimal values at nodes and tips.

update.parsimonyNumber

Actualization for parsimonyNumber.

update.parsimonyCost

Actualization for parsimonyCost.

Simulate a Stochastic Process on a tree

plot.params_process

Plot for class simul_process

segmentation.OU.specialCase.lasso

Segmentation in the OU special case, using lasso regression

segmentation.BM

Segmentation in the BM case

Wrapper for E step in EM

simulate_internal

Simulate a Stochastic Process on a tree

update.partitionsNumber.gen

Update formula in the general case

Plot Model Selection Criterion

split_params_independent

Split independent parameters into a list of parameters

Product of elements of a matrix

Sum on all subsets.

Scale variance and selection strength from a linear transform

sample_shifts_edges

Sample shifts edges in a parsimonious way.

transform_branch_length

Transform branch length for a re-scaled BM

transform_shifts_values

Transform the shift values

test.root.state

Test state of root.

Model Estimation with Detection of Shifts

check_parsimony

Check Parsimony, assuming no homoplasy

allocate_subset_node.simulate

Iteration allocation

allocate_shifts_from_regimes

Allocation of shifts to edges

allocate_regimes_from_shifts

Allocation of regimes to nodes.

check.selection.strength

Check selection strength

check_parsimony_clusters

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

check_dimensions

Check dimensions of the parameters

add_complementary

Add several entries, when only one is not NA.

Test the format of data entry.