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PhylogeneticEM (version 1.2.1)

Automatic Shift Detection using a Phylogenetic EM

Description

Implementation of the automatic shift detection method for Brownian Motion (BM) or Ornstein<80><93>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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Version

1.2.1

License

GPL (>= 2) | file LICENSE

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Repository

https://github.com/pbastide/PhylogeneticEM

Maintainer

Paul Bastide

Last Published

September 11th, 2018

Functions in PhylogeneticEM (1.2.1)

allocate_subset_node.simulate

Iteration allocation

compute_dist_phy

Phylogenetic Distances

compute_expectations.BM

Compute the expected states of a BM

Test the format of data entry.

check_dimensions

Check dimensions of the parameters

compute_state_filter

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

compute_stationary_variance

Compute the stationary variance matrix

compute_tree_correlations_matrix.BM

Matrix of tree-induced correlations for the BM

compute_tree_correlations_matrix.scOU

Matrix of tree-induced correlations for the scOU

compute_gauss_lasso

Do a lm on top of a lasso regression.

compute_log_likelihood.simple

compute_variance_covariance.OU.nonsym

Complete variance covariance matrix for OU

compute_variance_covariance.scOU

Complete variance covariance matrix for scOU

check_parsimony

Check Parsimony, assuming no homoplasy

extract.parsimonyCost

Extraction of the actual number of solutions.

extract.parsimonyNumber

Extraction of the actual number of solutions.

check_parsimony_clusters

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

compute_betas_from_shifts

Computation of the optimal values at nodes and tips.

compute_diff_exp.BM

Compute differences of expectations between node and parent.

compute_sum_var_diff

Compute weighted sum of var_diff

compute_times_ca

Common Ancestors Times

check_range_alpha

Check range of alpha

clusters_from_shifts

Clustering associated to a shift allocation, assuming no homoplasy.

equivalent_shifts_values

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

init.parsimonyNumber

Initialization for parsimonyNumber.

init.simulate.BM

Create an object params_process for an OU

params_process.PhyloEM

Parameter estimates

Function to estimate alpha

Product of elements of a matrix

extract.partitionsNumber

Extract from object partitionsNumber

compute_var_M.BM

Computation of the variance.

extract.simul_process

Extraction of simulated traits

compute_var_diff.BM

Compute variances of differences between nodes and parents.

shifts.list_to_vector

Compute the vector of shifts.

shifts.list_to_matrix

Compute the matrix of shifts.

Sum on a simplex

go_back_to_original_process

Scale the parameters back to the original process

impute.data.Rphylopars

Initial imputation of missing data for lasso

merge_complementary_vectors

Merge several complementary vectors into one.

Sum on a simplex

merge_params_independent

Merge a list of independent parameters into into one parameter

update.incidence.matrix

Update function for incidence matrix

Extraction function

update.incidence.matrix.full

Update function for incidence matrix

partitionsNumber

Number of different models

find_independent_regression_vectors.glmnet_multivariate

Given a regularization path, find K selected independent variables.

Test for rotation invariant datasets

penalty_BaraudGiraudHuet_likelihood

Penalty function type Baraud Giraud Huet.

Plot for class PhyloEM

Penalty function type pBIC

shifts.matrix_to_list

Compute the list of shifts.

extract.enumerate_parsimony

Extract the result of enumerate_parsimony at a node.

Ancestral State Reconstruction

incidence.matrix

Incidence matrix of a tree.

shifts.vector_to_list

Compute the list of shifts.

simulate_internal

Simulate a Stochastic Process on a tree

init.simulate.OU

Initialize state and expectation matrices

extract.equivalent_shifts

Extract the shifts values for one trait.

split_params_independent

Split independent parameters into a list of parameters

init.simulate.StateAndExp

Initialize state and expectation matrices

find_shift_values

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

merge_rotations

Merge fits from independent runs of PhyloEM.

Model Estimation with Detection of Shifts

Run the EM for several values of K

allocate_regimes_from_shifts

Allocation of regimes to nodes.

add_complementary

Add several entries, when only one is not NA.

model_selection

Model Selection of a fitted object

update.partitionsNumber.gen

Update formula in the general case

Create an object params_process

allocate_shifts_from_regimes

Allocation of shifts to edges

Wrapper for E step in EM

params_process.character

Create an object params_process

compute_E.simple

compute_actualization_matrix_ultrametric

Compute Matrix W of actualization (Ultrametric case)

compute_expectations.scOU

Compute the expected states of a scOU

Generic recursion down the tree.

compute_mahalanobis_distance.simple

Squared Mahalanobis Distance

compute_mean_variance.simple

Compute moments of params_old

residuals.PhyloEM

Residuals of a fitted object

incidence.matrix.full

Incidence matrix of a tree.

incidence_matrix_actualization_factors

Compute the actualizations factors to apply to the incidence matrix.

init.alpha.gamma.estimation

Initialization the selection strength alpha using robust estimation

compute_variance_covariance.BM

Complete variance covariance matrix for BM

compute_fixed_moments

Compute fixed moments for E step.

init.compute_betas_from_shifts

Initialization for the computation of the optimal values

sample_edges_intervals

Sample equally spaced edges.

Check whether parameters are in ranges.

lasso_regression_K_fixed.glmnet_multivariate

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

sample_shifts_edges

Sample shifts edges in a parsimonious way.

Minimal number of shifts needed to get a clustering.

parsimonyNumber

Number of equivalent parsimonious allocations.

compute_variance_covariance.OU

Complete variance covariance matrix for OU

plot.params_process

Plot for class simul_process

Sum on all subsets.

Plot Model Selection Criterion

Scale variance and selection strength from a linear transform

segmentation.BM

Segmentation in the BM case

update.enumerate_parsimony

Actualization of the enumeration.

update.compute_betas_from_shifts

Update function for optimal value computation

sum.partitions.cardFixed

Sum on subsets of a given cardinal.

update.parsimonyCost

Actualization for parsimonyCost.

enumerate_parsimony

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

enumerate_tips_under_edges

Tips descendants of nodes.

update.parsimonyNumber

Actualization for parsimonyNumber.

find_grid_alpha

Find a reasonable grid for alpha

extract.variance_covariance

Extract sub-matrices of variance.

Initialization of the shifts using Lasso.

init.allocate_regimes_from_shifts

Initialization for the allocation of shifts.

init.enumerate_parsimony

Initialization for the enumeration of parsimonious solutions.

init.incidence.matrix

Initialization for incidence matrix

Log Likelihood of a fitted object

matrix_of_possibles

Compute parent matrix from possibles daughter matrices.

penalty_BirgeMassart_shape1

Penalty function type Birg<U+00E9>-Massart 1

compute_residuals.simple

compute_shifts_from_betas

Computation of shifts from the vector of optimal values

correspondenceEdges

Correspondence between edges numbers

penalty_BirgeMassart_shape2

Penalty function type Birg<U+00E9>-Massart 2

plot.enumerate_parsimony

Plot all the equivalent solutions.

plot.equivalent_shifts

Plot all the equivalent solutions.

Make the result lighter

segmentation.OU.specialCase.lasso

Segmentation in the OU special case, using lasso regression

segmentation.OU.specialCase.same_shifts

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

shifts_to_simmap

Simmap format mapping from list of edges

Simulate a Stochastic Process on a tree

equivalent_shifts

Find all equivalent shifts allocations and values.

equivalent_shifts_edges

Find all the equivalent shift edges allocations.

Get Model Selection Criterion

get_variance_node

Get variance matrix of a node

init.incidence.matrix.full

Initialization for incidence matrix (full tree)

init.parsimonyCost

Initialization for parsimonyCost.

New World Monkeys dataset

Create an object params_process for a BM

test.root.state

Test state of root.

transform_branch_length

Transform branch length for a re-scaled BM

transform_shifts_values

Transform the shift values

update.allocate_regimes_from_shifts

Update function for regime allocation.

check.selection.strength

Check selection strength