Files in pbastide/PhylogeneticEM
Automatic Shift Detection using a Phylogenetic EM

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
Phylogenetic-EM.Rproj
R/E_step.R R/M_step.R R/RcppExports.R R/data.R R/estimateEM.R R/generic_functions.R R/init_EM.R R/model_selection.R R/parsimonyNumber.R R/partitionsNumber.R R/plot_functions.R R/shifts_manipulations.R R/shutoff.R R/simulate.R README.md
_pkgdown.yml
cran-comments.md data-raw/monkeys.R
data/monkeys.rda
docs/LICENSE
docs/LICENSE.html
docs/articles/index.html
docs/articles/tutorial.html
docs/articles/tutorial_files/figure-html/unnamed-chunk-1-1.png
docs/articles/tutorial_files/figure-html/unnamed-chunk-1-2.png
docs/articles/tutorial_files/figure-html/unnamed-chunk-2-1.png
docs/articles/tutorial_files/figure-html/unnamed-chunk-4-1.png
docs/articles/tutorial_files/figure-html/unnamed-chunk-6-1.png
docs/articles/tutorial_files/figure-html/unnamed-chunk-9-1.png
docs/authors.html
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/reference/PhyloEM.html
docs/reference/add_complementary.html
docs/reference/allocate_regimes_from_shifts.html
docs/reference/allocate_shifts_from_regimes.html
docs/reference/allocate_subset_node.simulate.html
docs/reference/check.selection.strength.html
docs/reference/check_data.html
docs/reference/check_dimensions.html
docs/reference/check_parsimony.html
docs/reference/check_parsimony_clusters.html
docs/reference/clusters_from_shifts.html
docs/reference/compute_E.simple.html
docs/reference/compute_K_max.html
docs/reference/compute_actualization_matrix_ultrametric.html
docs/reference/compute_betas_from_shifts.html
docs/reference/compute_diff_exp.BM.html
docs/reference/compute_dist_phy.html
docs/reference/compute_expectations.BM.html
docs/reference/compute_expectations.scOU.html
docs/reference/compute_fixed_moments.html
docs/reference/compute_gauss_lasso.html
docs/reference/compute_log_likelihood.simple.html
docs/reference/compute_mahalanobis_distance.simple.html
docs/reference/compute_mean_variance.simple.html
docs/reference/compute_residuals.simple.html
docs/reference/compute_shifts_from_betas.html
docs/reference/compute_state_filter.html
docs/reference/compute_stationary_variance.html
docs/reference/compute_sum_var_diff.html
docs/reference/compute_times_ca.html
docs/reference/compute_tree_correlations_matrix.BM.html
docs/reference/compute_tree_correlations_matrix.scOU.html
docs/reference/compute_var_M.BM.html
docs/reference/compute_var_diff.BM.html
docs/reference/compute_variance_covariance.BM.html
docs/reference/compute_variance_covariance.OU.html
docs/reference/compute_variance_covariance.scOU.html
docs/reference/conditional_expectation_log_likelihood.OU.OLD.html
docs/reference/conditional_expectation_log_likelihood.OU.stationary_root_shifts_at_nodes.html
docs/reference/correspondenceEdges.html
docs/reference/enlight.html
docs/reference/enumerate_parsimony-1.png
docs/reference/enumerate_parsimony-2.png
docs/reference/enumerate_parsimony-3.png
docs/reference/enumerate_parsimony-4.png
docs/reference/enumerate_parsimony.html
docs/reference/enumerate_tips_under_edges.html
docs/reference/equivalent_shifts-1.png
docs/reference/equivalent_shifts-14.png
docs/reference/equivalent_shifts-2.png
docs/reference/equivalent_shifts-4.png
docs/reference/equivalent_shifts.html
docs/reference/equivalent_shifts_edges.html
docs/reference/equivalent_shifts_values.html
docs/reference/estimate.alpha.html
docs/reference/estimateEM.html
docs/reference/extract.enumerate_parsimony.html
docs/reference/extract.equivalent_shifts.html
docs/reference/extract.html
docs/reference/extract.parsimonyCost.html
docs/reference/extract.parsimonyNumber.html
docs/reference/extract.partitionsNumber.html
docs/reference/extract.simul_process.html
docs/reference/extract.variance_covariance.html
docs/reference/find_grid_alpha.html
docs/reference/find_independent_regression_vectors.glmnet_multivariate.html
docs/reference/find_shift_values.html
docs/reference/format_output.html
docs/reference/get_variance_node.html
docs/reference/go_back_to_original_process.html
docs/reference/impute.data.Rphylopars.html
docs/reference/imputed_traits.html
docs/reference/incidence.matrix.full.html
docs/reference/incidence.matrix.html
docs/reference/incidence_matrix_actualization_factors.html
docs/reference/index.html
docs/reference/init.EM.lasso.html
docs/reference/init.allocate_regimes_from_shifts.html
docs/reference/init.alpha.estimation.html
docs/reference/init.alpha.gamma.estimation.html
docs/reference/init.compute_betas_from_shifts.html
docs/reference/init.enumerate_parsimony.html
docs/reference/init.incidence.matrix.full.html
docs/reference/init.incidence.matrix.html
docs/reference/init.parsimonyCost.html
docs/reference/init.parsimonyNumber.html
docs/reference/init.simulate.BM.html
docs/reference/init.simulate.OU.html
docs/reference/init.simulate.StateAndExp.html
docs/reference/is.finite.params.BM.html
docs/reference/is.in.ranges.html
docs/reference/lasso_regression_K_fixed.glmnet_multivariate.html
docs/reference/log_likelihood.html
docs/reference/matrix_of_possibles.html
docs/reference/merge_complementary_vectors.html
docs/reference/merge_params_independent.html
docs/reference/model_selection.html
docs/reference/monkeys.html
docs/reference/optimize_costs_given_shift_position.OU.specialCase.html
docs/reference/params_BM.html
docs/reference/params_OU.html
docs/reference/params_process.PhyloEM.html
docs/reference/params_process.character.html
docs/reference/params_process.html
docs/reference/parsimonyCost-1.png
docs/reference/parsimonyCost-2.png
docs/reference/parsimonyCost.html
docs/reference/parsimonyNumber-1.png
docs/reference/parsimonyNumber-2.png
docs/reference/parsimonyNumber.html
docs/reference/partitionsNumber-1.png
docs/reference/partitionsNumber-2.png
docs/reference/partitionsNumber.html
docs/reference/penalty_BaraudGiraudHuet_likelihood.html
docs/reference/penalty_BirgeMassart_shape1.html
docs/reference/penalty_BirgeMassart_shape2.html
docs/reference/penalty_pBIC.html
docs/reference/plot.PhyloEM.html
docs/reference/plot.enumerate_parsimony.html
docs/reference/plot.equivalent_shifts.html
docs/reference/plot.params_process.html
docs/reference/prod.index.html
docs/reference/qr.solve_exact.html
docs/reference/recursionDown.html
docs/reference/residuals.PhyloEM.html
docs/reference/sample_edges_intervals.html
docs/reference/sample_shifts_edges.html
docs/reference/scale_params.html
docs/reference/segmentation.BM.html
docs/reference/segmentation.OU.specialCase.lasso.html
docs/reference/segmentation.OU.specialCase.max_costs_0.html
docs/reference/segmentation.OU.specialCase.same_shifts.html
docs/reference/segmentation.OU.specialCase.same_shifts_same_values.html
docs/reference/shifts.list_to_matrix.html
docs/reference/shifts.list_to_vector.html
docs/reference/shifts.matrix_to_list.html
docs/reference/shifts.vector_to_list.html
docs/reference/shifts_to_simmap.html
docs/reference/simul_process.html
docs/reference/simulate_internal.html
docs/reference/split_params_independent.html
docs/reference/sum.partitions.cardFixed.html
docs/reference/sum.partitions.html
docs/reference/sum.prod.comb.html
docs/reference/sum.simplex.html
docs/reference/test.root.state.html
docs/reference/transform_branch_length.html
docs/reference/transform_shifts_values.html
docs/reference/update.allocate_regimes_from_shifts.html
docs/reference/update.compute_betas_from_shifts.html
docs/reference/update.enumerate_parsimony.html
docs/reference/update.incidence.matrix.full.html
docs/reference/update.incidence.matrix.html
docs/reference/update.parsimonyCost.html
docs/reference/update.parsimonyNumber.html
docs/reference/update.partitionsNumber.gen.html
docs/reference/wrapper_E_step.html
inst/CITATION
man/PhyloEM.Rd man/add_complementary.Rd man/allocate_regimes_from_shifts.Rd man/allocate_shifts_from_regimes.Rd man/allocate_subset_node.simulate.Rd man/check.selection.strength.Rd man/check_data.Rd man/check_dimensions.Rd man/check_parsimony.Rd man/check_parsimony_clusters.Rd man/clusters_from_shifts.Rd man/compute_E.simple.Rd man/compute_actualization_matrix_ultrametric.Rd man/compute_betas_from_shifts.Rd man/compute_diff_exp.BM.Rd man/compute_dist_phy.Rd man/compute_expectations.BM.Rd man/compute_expectations.scOU.Rd man/compute_fixed_moments.Rd man/compute_gauss_lasso.Rd man/compute_log_likelihood.simple.Rd man/compute_mahalanobis_distance.simple.Rd man/compute_mean_variance.simple.Rd man/compute_residuals.simple.Rd man/compute_shifts_from_betas.Rd man/compute_state_filter.Rd man/compute_stationary_variance.Rd man/compute_sum_var_diff.Rd man/compute_times_ca.Rd man/compute_tree_correlations_matrix.BM.Rd man/compute_tree_correlations_matrix.scOU.Rd man/compute_var_M.BM.Rd man/compute_var_diff.BM.Rd man/compute_variance_covariance.BM.Rd man/compute_variance_covariance.OU.Rd man/compute_variance_covariance.scOU.Rd man/correspondenceEdges.Rd man/enlight.Rd man/enumerate_parsimony.Rd man/enumerate_tips_under_edges.Rd man/equivalent_shifts.Rd man/equivalent_shifts_edges.Rd man/equivalent_shifts_values.Rd man/estimate.alpha.Rd man/estimateEM.Rd man/extract.Rd man/extract.enumerate_parsimony.Rd man/extract.equivalent_shifts.Rd man/extract.parsimonyCost.Rd man/extract.parsimonyNumber.Rd man/extract.partitionsNumber.Rd man/extract.simul_process.Rd man/extract.variance_covariance.Rd man/find_grid_alpha.Rd man/find_independent_regression_vectors.glmnet_multivariate.Rd man/find_shift_values.Rd man/format_output.Rd man/get_variance_node.Rd man/go_back_to_original_process.Rd man/impute.data.Rphylopars.Rd man/imputed_traits.Rd man/incidence.matrix.Rd man/incidence.matrix.full.Rd man/incidence_matrix_actualization_factors.Rd man/init.EM.lasso.Rd man/init.allocate_regimes_from_shifts.Rd man/init.alpha.gamma.estimation.Rd man/init.compute_betas_from_shifts.Rd man/init.enumerate_parsimony.Rd man/init.incidence.matrix.Rd man/init.incidence.matrix.full.Rd man/init.parsimonyCost.Rd man/init.parsimonyNumber.Rd man/init.simulate.BM.Rd man/init.simulate.OU.Rd man/init.simulate.StateAndExp.Rd man/is.in.ranges.Rd man/lasso_regression_K_fixed.glmnet_multivariate.Rd man/log_likelihood.Rd man/matrix_of_possibles.Rd man/merge_complementary_vectors.Rd man/merge_params_independent.Rd man/model_selection.Rd man/monkeys.Rd man/params_BM.Rd man/params_OU.Rd man/params_process.PhyloEM.Rd man/params_process.Rd man/params_process.character.Rd man/parsimonyCost.Rd man/parsimonyNumber.Rd man/partitionsNumber.Rd man/penalty_BaraudGiraudHuet_likelihood.Rd man/penalty_BirgeMassart_shape1.Rd man/penalty_BirgeMassart_shape2.Rd man/penalty_pBIC.Rd man/plot.PhyloEM.Rd man/plot.enumerate_parsimony.Rd man/plot.equivalent_shifts.Rd man/plot.params_process.Rd man/prod.index.Rd man/qr.solve_exact.Rd man/recursionDown.Rd man/residuals.PhyloEM.Rd man/sample_edges_intervals.Rd man/sample_shifts_edges.Rd man/scale_params.Rd man/segmentation.BM.Rd man/segmentation.OU.specialCase.lasso.Rd man/segmentation.OU.specialCase.same_shifts.Rd man/shifts.list_to_matrix.Rd man/shifts.list_to_vector.Rd man/shifts.matrix_to_list.Rd man/shifts.vector_to_list.Rd man/shifts_to_simmap.Rd man/simul_process.Rd man/simulate_internal.Rd man/split_params_independent.Rd man/sum.partitions.Rd man/sum.partitions.cardFixed.Rd man/sum.prod.comb.Rd man/sum.simplex.Rd man/test.root.state.Rd man/transform_branch_length.Rd man/transform_shifts_values.Rd man/update.allocate_regimes_from_shifts.Rd man/update.compute_betas_from_shifts.Rd man/update.enumerate_parsimony.Rd man/update.incidence.matrix.Rd man/update.incidence.matrix.full.Rd man/update.parsimonyCost.Rd man/update.parsimonyNumber.Rd man/update.partitionsNumber.gen.Rd man/wrapper_E_step.Rd simulations_study/generate_inference_files.R simulations_study/merge_inference_data.R simulations_study/model_selection_post.R simulations_study/multivariate_data_generation.R simulations_study/multivariate_data_generation_two_bases.R simulations_study/multivariate_data_generation_two_bases_with errors.R simulations_study/multivariate_estimation_SUN_rBM.R simulations_study/multivariate_estimation_l1ou.R simulations_study/multivariate_exploitation.R simulations_study/multivariate_exploitation_l1ou.R simulations_study/penalty_calibration.R simulations_study/several_K_alpha_0.R simulations_study/several_K_data_generation.R simulations_study/several_K_data_generation_uncertainties.R simulations_study/several_K_estimation_FUN.R simulations_study/several_K_estimation_SUN_rBM.R simulations_study/several_K_estimations.R simulations_study/several_K_exploitation.R simulations_study/several_K_exploitation_FUN.R simulations_study/simulation_exploitation_bayou_design.R simulations_study/simulation_exploitation_bayou_design_alpha_known.R simulations_study/simulations_bayou_design_alpha_known_new_segmentation.R simulations_study/simulations_bayou_design_new_segmentation.R simulations_study/simulations_several_K.R
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/init.c
src/upward_downward.cpp
src/upward_downward.h
tests/testthat/test-EM-initialization.R tests/testthat/test-EM-no_missing.R tests/testthat/test-core-compute_variance_covariance.R tests/testthat/test-core-log_likelihood.R tests/testthat/test-independent_multivariate.R tests/testthat/test-shifts-model_selection.R tests/testthat/test-shifts-parsimonyNumber.R tests/testthat/test-shifts-partitionsNumber.R tests/testthat/test-upward_downward.R tests/testthat/test-utilities-handling_parameters.R tests/testthat/test-utilities-impute-traits.R tests/testthat/test-utilities-simulate.R tests/testthat_EM.R tests/testthat_core.R tests/testthat_independent.R tests/testthat_shifts.R tests/testthat_upward.R tests/testthat_utilities.R vignettes/tutorial.Rmd
pbastide/PhylogeneticEM documentation built on Sept. 9, 2017, 1:03 p.m.