R Packages that start with:
A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .
Functions
- add_complementary()
- allocate_regimes_from_shifts()
- allocate_shifts_from_regimes()
- allocate_subset_node.simulate()
- check.selection.strength()
- check_data()
- check_dimensions()
- check_parsimony()
- check_parsimony_clusters()
- check_range_alpha()
- clusters_from_shifts()
- compute_actualization_matrix_ultrametric()
- compute_betas_from_shifts()
- compute_diff_exp.BM()
- compute_dist_phy()
- compute_E.simple()
- compute_expectations.BM()
- compute_expectations.scOU()
- compute_fixed_moments()
- compute_gauss_lasso()
- compute_log_likelihood.simple()
- compute_mahalanobis_distance.simple()
- compute_mean_variance.simple()
- compute_residuals.simple()
- compute_shifts_from_betas()
- compute_state_filter()
- compute_stationary_variance()
- compute_sum_var_diff()
- compute_times_ca()
- compute_tree_correlations_matrix.BM()
- compute_tree_correlations_matrix.scOU()
- compute_variance_block_diagonal.BM()
- compute_variance_block_diagonal.OU()
- compute_variance_covariance.BM()
- compute_variance_covariance.OU.nonsym()
- compute_variance_covariance.OU()
- compute_variance_covariance.scOU()
- compute_var_diff.BM()
- compute_var_M.BM()
- correspondenceEdges()
- enlight()
- enumerate_parsimony()
- enumerate_tips_under_edges()
- equivalent_shifts()
- equivalent_shifts_edges()
- equivalent_shifts_values()
- estimate.alpha()
- estimateEM()
- extract.enumerate_parsimony()
- extract.equivalent_shifts()
- extract()
- extract.parsimonyCost()
- extract.parsimonyNumber()
- extract.partitionsNumber()
- extract.simul_process()
- extract.variance_covariance()
- find_grid_alpha()
- find_independent_regression_vectors.glmnet_multivariate()
- find_rotation()
- find_shift_values()
- format_output()
- get_criterion()
- get_variance_node()
- go_back_to_original_process()
- imputed_traits()
- incidence.matrix.full()
- incidence.matrix()
- incidence_matrix_actualization_factors()
- init.allocate_regimes_from_shifts()
- init.alpha.gamma.estimation()
- init.compute_betas_from_shifts()
- init.EM.lasso()
- init.enumerate_parsimony()
- init.incidence.matrix.full()
- init.incidence.matrix()
- init.parsimonyCost()
- init.parsimonyNumber()
- init.simulate.BM()
- init.simulate.OU()
- init.simulate.StateAndExp()
- is.in.ranges()
- lasso_regression_K_fixed.glmnet_multivariate()
- log_likelihood()
- matrix_of_possibles()
- merge_complementary_vectors()
- merge_params_independent()
- merge_rotations()
- model_selection()
- monkeys()
- params_BM()
- params_OU()
- params_process.character()
- params_process()
- params_process.PhyloEM()
- parsimonyCost()
- parsimonyNumber()
- partitionsNumber()
- penalty_BaraudGiraudHuet_likelihood()
- penalty_BirgeMassart_shape1()
- penalty_BirgeMassart_shape2()
- penalty_pBIC()
- PhyloEM()
- plot.enumerate_parsimony()
- plot.equivalent_shifts()
- plot.params_process()
- plot.PhyloEM()
- plot_criterion()
- prod.index()
- qr.solve_exact()
- recursionDown()
- residuals.PhyloEM()
- sample_edges_intervals()
- sample_shifts_edges()
- scale_params()
- segmentation.BM()
- segmentation.OU.specialCase.lasso()
- segmentation.OU.specialCase.same_shifts()
- shifts.list_to_matrix()
- shifts.list_to_vector()
- shifts.matrix_to_list()
- shifts.vector_to_list()
- shifts_to_simmap()
- simulate_internal()
- simul_process()
- split_params_independent()
- sum.partitions.cardFixed()
- sum.partitions()
- sum.prod.comb()
- sum.simplex()
- test.root.state()
- transform_branch_length()
- transform_shifts_values()
- update.allocate_regimes_from_shifts()
- update.compute_betas_from_shifts()
- update.enumerate_parsimony()
- update.incidence.matrix.full()
- update.incidence.matrix()
- update.parsimonyCost()
- update.parsimonyNumber()
- update.partitionsNumber.gen()
- wrapper_E_step()
R Codes
Selected R package: PhylogeneticEM
Click on the specific functions, references or examples using the links on the left
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