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PhylogeneticEM  

Automatic Shift Detection using a Phylogenetic EM
View on CRAN: Click here


Download and install PhylogeneticEM package within the R console
Install from CRAN:
install.packages("PhylogeneticEM")

Install from Github:
library("remotes")
install_github("cran/PhylogeneticEM")

Install by package version:
library("remotes")
install_version("PhylogeneticEM", "1.8.1")



Attach the package and use:
library("PhylogeneticEM")
Maintained by
Paul Bastide
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2017-01-31
Latest Update: 2025-02-14
Description:
Implementation of the automatic shift detection method for Brownian Motion (BM) or Ornstein
How to cite:
Paul Bastide (2017). PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM. R package version 1.8.1, https://cran.r-project.org/web/packages/PhylogeneticEM. Accessed 06 Mar. 2026.
Previous versions and publish date:
1.0.0 (2017-01-31 14:16), 1.0.1 (2017-05-01 12:19), 1.1.0 (2017-09-08 23:51), 1.2.1 (2018-09-11 12:40), 1.3.0 (2019-10-03 06:20), 1.4.0 (2020-02-11 10:40), 1.5.0 (2021-09-16 15:30), 1.6.0 (2022-08-31 10:50), 1.7.0 (2024-01-31 17:50), 1.8.0 (2025-02-15 00:10)
Other packages that cited PhylogeneticEM R package
View PhylogeneticEM citation profile
Other R packages that PhylogeneticEM depends, imports, suggests or enhances
Complete documentation for PhylogeneticEM
Functions, R codes and Examples using the PhylogeneticEM R package
Some associated functions: PhyloEM . 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_E.simple . compute_actualization_matrix_ultrametric . compute_betas_from_shifts . compute_diff_exp.BM . compute_dist_phy . 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_var_M.BM . compute_var_diff.BM . 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 . 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.EM.lasso . init.allocate_regimes_from_shifts . init.alpha.gamma.estimation . init.compute_betas_from_shifts . 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.PhyloEM . params_process.character . params_process . parsimonyCost . parsimonyNumber . partitionsNumber . penalty_BaraudGiraudHuet_likelihood . penalty_BirgeMassart_shape1 . penalty_BirgeMassart_shape2 . penalty_pBIC . plot.PhyloEM . plot.enumerate_parsimony . plot.equivalent_shifts . plot.params_process . 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 . simul_process . simulate_internal . 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 . 
Some associated R codes: E_step.R . M_step.R . RcppExports.R . data.R . estimateEM.R . generic_functions.R . init_EM.R . model_selection.R . parsimonyNumber.R . partitionsNumber.R . plot_functions.R . shifts_manipulations.R . shutoff.R . simulate.R .  Full PhylogeneticEM package functions and examples
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