PhyloEM                 Model Estimation with Detection of Shifts
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_dist_phy        Phylogenetic Distances
compute_shifts_from_betas
                        Computation of shifts from the vector of
                        optimal values
compute_stationary_variance
                        Compute the stationary variance matrix
compute_times_ca        Common Ancestors Times
correspondenceEdges     Correspondence between edges numbers
enlight                 Make the result lighter
enumerate_parsimony     Enumerate all the possible regime allocations,
                        given a clustering of the tips.
enumerate_tips_under_edges
                        Tips descendants of nodes.
equivalent_shifts       Find all equivalent shifts allocations and
                        values.
estimateEM              Perform One EM
extract                 Extraction function
extract.enumerate_parsimony
                        Extract the result of 'enumerate_parsimony' at
                        a node.
extract.equivalent_shifts
                        Extract the shifts values for one trait.
extract.parsimonyCost   Extraction of the actual number of solutions.
extract.parsimonyNumber
                        Extraction of the actual number of solutions.
extract.partitionsNumber
                        Extract from object 'partitionsNumber'
extract.simul_process   Extraction of simulated traits
find_grid_alpha         Find a reasonable grid for alpha
imputed_traits          Ancestral State Reconstruction
incidence.matrix        Incidence matrix of a tree.
incidence.matrix.full   Incidence matrix of a tree.
log_likelihood          Log Likelihood of a fitted object
model_selection         Model Selection of a fitted object
monkeys                 New World Monkeys dataset
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.PhyloEM
                        Parameter estimates
params_process.character
                        Create an object 'params_process'
parsimonyCost           Minimal number of shifts needed to get a
                        clustering.
parsimonyNumber         Number of equivalent parsimonious allocations.
partitionsNumber        Number of different models
plot.PhyloEM            Plot for class 'PhyloEM'
plot.enumerate_parsimony
                        Plot all the equivalent solutions.
plot.equivalent_shifts
                        Plot all the equivalent solutions.
plot.params_process     Plot for class 'simul_process'
residuals.PhyloEM       Residuals of a fitted object
shifts.list_to_matrix   Compute the matrix of shifts.
shifts.matrix_to_list   Compute the list of shifts.
shifts_to_simmap        Simmap format mapping from list of edges
simul_process           Simulate a Stochastic Process on a tree
transform_branch_length
                        Transform branch length for a re-scaled BM
