Function reference • 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
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
`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

Reference

PhyloEM

PhyloEM Handling Functions

Parameters and Simulations

Identifiability

Parsimony and Enumeration

Shifts vs Regimes

Tree Matrices

OU Helper Functions

Dataset