| 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 |
| enlight.PhyloEM | 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 |
| find_rotation | Test for rotation invariant datasets |
| get_criterion | Get Model Selection Criterion |
| imputed_traits | Ancestral State Reconstruction |
| imputed_traits.PhyloEM | 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 |
| log_likelihood.params_process | Log Likelihood of a fitted object |
| log_likelihood.PhyloEM | Log Likelihood of a fitted object |
| merge_rotations | Merge fits from independent runs of PhyloEM. |
| model_selection | Model Selection of a fitted object |
| model_selection.PhyloEM | 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.character | Create an object 'params_process' |
| params_process.PhyloEM | Parameter estimates |
| parsimonyCost | Minimal number of shifts needed to get a clustering. |
| parsimonyNumber | Number of equivalent parsimonious allocations. |
| partitionsNumber | Number of different models |
| PhyloEM | Model Estimation with Detection of Shifts |
| plot.enumerate_parsimony | Plot all the equivalent solutions. |
| plot.equivalent_shifts | Plot all the equivalent solutions. |
| plot.params_process | Plot for class 'simul_process' |
| plot.PhyloEM | Plot for class 'PhyloEM' |
| plot_criterion | Plot Model Selection Criterion |
| 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 |
| simul_process.params_process | Simulate a Stochastic Process on a tree |
| simul_process.PhyloEM | Simulate a Stochastic Process on a tree |
| transform_branch_length | Transform branch length for a re-scaled BM |