Package index • PhylogeneticEM

PhyloEM

Functions for the inference of shifts.

PhyloEM(): Model Estimation with Detection of Shifts

find_grid_alpha(): Find a reasonable grid for alpha

estimateEM(): Perform One EM

PhyloEM Handling Functions

Functions to handle objects of class PhyloEM.

plot(<PhyloEM>): Plot for class PhyloEM

params_process(<PhyloEM>): Parameter estimates

imputed_traits(): Ancestral State Reconstruction

model_selection(): Model Selection of a fitted object

residuals(<PhyloEM>): Residuals of a fitted object

enlight(): Make the result lighter

log_likelihood(): Log Likelihood of a fitted object

find_rotation(): Test for rotation invariant datasets

merge_rotations(): Merge fits from independent runs of PhyloEM.

get_criterion(): Get Model Selection Criterion

plot_criterion(): Plot Model Selection Criterion

merge_alpha_grids(): Merge PhyloEM fits on various grids of alpha values

Parameters and Simulations

Functions to simulate various processes on the tree, and deal with their parameters.

simul_process(): Simulate a Stochastic Process on a tree

params_BM(): Create an object params_process for a BM

params_OU(): Create an object params_process for an OU

params_process(): Create an object params_process

params_process(<character>): Create an object params_process

plot(<params_process>): Plot for class simul_process

extract(<simul_process>): Extraction of simulated traits

log_likelihood(): Log Likelihood of a fitted object

Identifiability

Functions to deal with the non-identifiability of shifts allocations.

equivalent_shifts(): Find all equivalent shifts allocations and values.

extract(<equivalent_shifts>): Extract the shifts values for one trait.

plot(<equivalent_shifts>): Plot all the equivalent solutions.

Parsimony and Enumeration

Functions to compute parsimony scores, and enumerate all equivalent solutions to a given clustering of the tips.

enumerate_parsimony(): Enumerate all the possible regime allocations, given a clustering of the tips.

extract(<enumerate_parsimony>): Extract the result of enumerate_parsimony at a node.

plot(<enumerate_parsimony>): Plot all the equivalent solutions.

partitionsNumber(): Number of different models

extract(<partitionsNumber>): Extract from object partitionsNumber

parsimonyNumber(): Number of equivalent parsimonious allocations.

extract(<parsimonyNumber>): Extraction of the actual number of solutions.

parsimonyCost(): Minimal number of shifts needed to get a clustering.

extract(<parsimonyCost>): Extraction of the actual number of solutions.

Shifts vs Regimes

Functions to switch between representations using shifts positions, and representations using regimes allocations.

shifts_to_simmap(): Simmap format mapping from list of edges

allocate_regimes_from_shifts(): Allocation of regimes to nodes.

allocate_shifts_from_regimes(): Allocation of shifts to edges

check_parsimony(): Check Parsimony, assuming no homoplasy

clusters_from_shifts(): Clustering associated to a shift allocation, assuming no homoplasy.

compute_betas_from_shifts(): Computation of the optimal values at nodes and tips.

compute_shifts_from_betas(): Computation of shifts from the vector of optimal values

node_optimal_values(): Computation of the optimal values at nodes and tips.

correspondenceEdges(): Correspondence between edges numbers

enumerate_tips_under_edges(): Tips descendants of nodes.

Tree Matrices

Functions for computing several matrices associated with a tree.

compute_dist_phy(): Phylogenetic Distances

compute_times_ca(): Common Ancestors Times

incidence.matrix(): Incidence matrix of a tree.

incidence.matrix.full(): Incidence matrix of a tree.

shifts.list_to_matrix(): Compute the matrix of shifts.

shifts.matrix_to_list(): Compute the list of shifts.

OU Helper Functions

Miscellaneous functions to deal with the OU process

compute_stationary_variance(): Compute the stationary variance matrix

transform_branch_length(): Transform branch length for a re-scaled BM

extract(): Extraction function

Dataset

New World Monkeys dataset

monkeys: New World Monkeys dataset