Files in pbastide/PhylogeneticEM
Automatic Shift Detection using a Phylogenetic EM
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check-no-force-suggest.yaml
.github/workflows/check-standard.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
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
inst/CITATION
inst/WORDLIST
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/check_range_alpha.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_block_diagonal.BM.Rd
man/compute_variance_block_diagonal.OU.Rd
man/compute_variance_covariance.BM.Rd
man/compute_variance_covariance.OU.Rd
man/compute_variance_covariance.OU.nonsym.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_rotation.Rd
man/find_shift_values.Rd
man/format_output.Rd
man/get_criterion.Rd
man/get_variance_node.Rd
man/go_back_to_original_process.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/merge_rotations.Rd
man/model_selection.Rd
man/monkeys.Rd
man/node_optimal_values.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/plot_criterion.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-rotations.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/monkeys.Rmd
vignettes/tutorial.Rmd
