Man pages for PhylogeneticEM
Automatic Shift Detection using a Phylogenetic EM
| add_complementary | Add several entries, when only one is not NA. |
| allocate_regimes_from_shifts | Allocation of regimes to nodes. |
| allocate_shifts_from_regimes | Allocation of shifts to edges |
| allocate_subset_node.simulate | Iteration allocation |
| check_data | Test the format of data entry. |
| check_dimensions | Check dimensions of the parameters |
| check_parsimony | Check Parsimony, assuming no homoplasy |
| check_parsimony_clusters | Check whether an allocation of the shifts is parsimonious, in... |
| check_range_alpha | Check range of alpha |
| check.selection.strength | Check selection strength |
| clusters_from_shifts | Clustering associated to a shift allocation, assuming no... |
| compute_actualization_matrix_ultrametric | Compute Matrix W of actualization (Ultrametric case) |
| 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_dist_phy | Phylogenetic Distances |
| compute_E.simple | E step |
| compute_expectations.BM | Compute the expected states of a BM |
| compute_expectations.scOU | Compute the expected states of a scOU |
| compute_fixed_moments | Compute fixed moments for E step. |
| compute_gauss_lasso | Do a lm on top of a lasso regression. |
| compute_log_likelihood.simple | Log Likelihood |
| compute_mahalanobis_distance.simple | Squared Mahalanobis Distance |
| compute_mean_variance.simple | Compute moments of params_old |
| compute_residuals.simple | Residuals |
| compute_shifts_from_betas | Computation of shifts from the vector of optimal values |
| compute_state_filter | List of potential daughter states when parent is in state k. |
| compute_stationary_variance | Compute the stationary variance matrix |
| compute_sum_var_diff | Compute weighted sum of var_diff |
| compute_times_ca | Common Ancestors Times |
| 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_var_diff.BM | Compute variances of differences between nodes and parents. |
| compute_variance_block_diagonal.BM | Tips Variances for the BM |
| compute_variance_block_diagonal.OU | Tips Variances for the OU |
| compute_variance_covariance.BM | Complete variance covariance matrix for BM |
| compute_variance_covariance.OU | Complete variance covariance matrix for OU |
| compute_variance_covariance.OU.nonsym | Complete variance covariance matrix for OU |
| compute_variance_covariance.scOU | Complete variance covariance matrix for scOU |
| compute_var_M.BM | Computation of the variance. |
| correspondenceEdges | Correspondence between edges numbers |
| enlight | Make the result lighter |
| enumerate_parsimony | Enumerate all the possible regime allocations, given a... |
| enumerate_tips_under_edges | Tips descendants of nodes. |
| equivalent_shifts | Find all equivalent shifts allocations and values. |
| equivalent_shifts_edges | Find all the equivalent shift edges allocations. |
| equivalent_shifts_values | Find values given edges. OU stationary case. Ultrametric... |
| estimate.alpha | Function to estimate alpha |
| 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 |
| extract_variance_covariance | Extract sub-matrices of variance. |
| find_grid_alpha | Find a reasonable grid for alpha |
| find_independent_regression_vectors.glmnet_multivariate | Given a regularization path, find K selected independent... |
| find_rotation | Test for rotation invariant datasets |
| find_shift_values | Find values given edges. OU stationary case. Ultrametric... |
| format_output | Run the EM for several values of K |
| get_criterion | Get Model Selection Criterion |
| get_variance_node | Get variance matrix of a node |
| go_back_to_original_process | Scale the parameters back to the original process |
| imputed_traits | Ancestral State Reconstruction |
| incidence.matrix | Incidence matrix of a tree. |
| incidence_matrix_actualization_factors | Compute the actualization factors to apply to the incidence... |
| incidence.matrix.full | Incidence matrix of a tree. |
| init.allocate_regimes_from_shifts | Initialization for the allocation of shifts. |
| init.alpha.gamma.estimation | Initialization the selection strength alpha using robust... |
| init.compute_betas_from_shifts | Initialization for the computation of the optimal values |
| init.EM.lasso | Initialization of the shifts using Lasso. |
| init.enumerate_parsimony | Initialization for the enumeration of parsimonious solutions. |
| init.incidence.matrix | Initialization for incidence matrix |
| init.incidence.matrix.full | Initialization for incidence matrix (full tree) |
| init.parsimonyCost | Initialization for parsimonyCost. |
| init.parsimonyNumber | Initialization for parsimonyNumber. |
| init.simulate.BM | Initialize BM |
| init.simulate.OU | Initialize state and expectation matrices |
| init.simulate.StateAndExp | Initialize state and expectation matrices |
| is.in.ranges | Check whether parameters are in ranges. |
| lasso_regression_K_fixed.glmnet_multivariate | Do a lasso regression with the number of non-zero variables... |
| log_likelihood | Log Likelihood of a fitted object |
| matrix_of_possibles | Compute parent matrix from possibles daughter matrices. |
| merge_complementary_vectors | Merge several complementary vectors into one. |
| merge_params_independent | Merge a list of independent parameters into into one... |
| merge_rotations | Merge fits from independent runs of PhyloEM. |
| model_selection | Model Selection of a fitted object |
| monkeys | New World Monkeys dataset |
| node_optimal_values | Computation of the optimal values at nodes and tips. |
| 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 |
| penalty_BaraudGiraudHuet_likelihood | Penalty function type Baraud Giraud Huet. |
| penalty_BirgeMassart_shape1 | Penalty function type Birgé-Massart 1 |
| penalty_BirgeMassart_shape2 | Penalty function type Birgé-Massart 2 |
| penalty_pBIC | Penalty function type pBIC |
| PhyloEM | Model Estimation with Detection of Shifts |
| plot_criterion | Plot Model Selection Criterion |
| 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' |
| prod_index | Product of elements of a matrix |
| qr_solve_exact | exact qr.solve |
| recursionDown | Generic recursion down the tree. |
| residuals.PhyloEM | Residuals of a fitted object |
| sample_edges_intervals | Sample equally spaced edges. |
| sample_shifts_edges | Sample shifts edges in a parsimonious way. |
| scale_params | Scale variance and selection strength from a linear transform |
| segmentation.BM | Segmentation in the BM case |
| 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.list_to_matrix | Compute the matrix of shifts. |
| shifts.list_to_vector | Compute the vector of shifts. |
| shifts.matrix_to_list | Compute the list of shifts. |
| shifts_to_simmap | Simmap format mapping from list of edges |
| shifts.vector_to_list | Compute the list of shifts. |
| simulate_internal | Simulate a Stochastic Process on a tree |
| simul_process | Simulate a Stochastic Process on a tree |
| split_params_independent | Split independent parameters into a list of parameters |
| sum_partitions | Sum on all subsets. |
| sum_partitions.cardFixed | Sum on subsets of a given cardinal. |
| sum_prod.comb | Sum on a simplex |
| sum_simplex | Sum on a simplex |
| 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. |
| update.compute_betas_from_shifts | Update function for optimal value computation |
| update.enumerate_parsimony | Actualization of the enumeration. |
| update.incidence.matrix | Update function for incidence matrix |
| update.incidence.matrix.full | Update function for incidence matrix |
| update.parsimonyCost | Actualization for parsimonyCost. |
| update.parsimonyNumber | Actualization for parsimonyNumber. |
| update.partitionsNumber.gen | Update formula in the general case |
| wrapper_E_step | Wrapper for E step in EM |
