PhylogeneticEM
Automatic Shift Detection using a Phylogenetic EM

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417
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35
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PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM
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API

API for PhylogeneticEM
Automatic Shift Detection using a Phylogenetic EM

Global functions
PhyloEM Man page Source code
PhyloEM_alpha_estim Source code
PhyloEM_grid_alpha Source code
Phylo_EM_sequencial Source code
add_complementary Man page Source code
add_method_selection Source code
allocate_regimes_from_shifts Man page Source code
allocate_shifts_from_regimes Man page Source code
allocate_subset_node.default Source code
allocate_subset_node.simulate Man page Source code
assign_results_model_selection Source code
check.selection.strength Man page Source code
check_correlations Source code
check_data Man page Source code
check_dimensions Man page Source code
check_dimensions.matrix Source code
check_dimensions.root.state Source code
check_dimensions.shifts Source code
check_dimensions.vector Source code
check_parsimony Man page Source code
check_parsimony_clusters Man page Source code
check_range_alpha Man page Source code
choose_process_EM Source code
clusters_from_shifts Man page
coherence_stationary_case Source code
complexity_break_point Source code
compute_E.simple Man page Source code
compute_E.simple.nomissing.BM Source code
compute_E.upward_downward Source code
compute_M.BM Source code
compute_M.OU Source code
compute_M.OU.specialCase Source code
compute_M.OU.stationary.root_AND_shifts_at_nodes Source code
compute_actualization_factors Source code
compute_actualization_matrix_ultrametric Man page Source code
compute_ancestral_traits Source code
compute_betas_from_shifts Man page Source code
compute_costs_0.simple Source code
compute_diff_exp.BM Man page Source code
compute_diff_exp.OU Source code
compute_dist_phy Man page Source code
compute_expectations.BM Man page Source code
compute_expectations.scOU Man page Source code
compute_fixed_moments Man page Source code
compute_gauss_lasso Man page
compute_log_likelihood.simple Man page Source code
compute_log_likelihood.simple.nomissing.BM Source code
compute_mahalanobis_distance.simple Man page Source code
compute_mahalanobis_distance.simple.nomissing.BM Source code
compute_mean_variance.simple Man page Source code
compute_regression_matrices Source code
compute_residuals.simple Man page Source code
compute_root_value.BM Source code
compute_shifts_from_betas Man page Source code
compute_state_filter Man page
compute_stationary_variance Man page Source code
compute_sum_var_diff Man page Source code
compute_times_ca Man page Source code
compute_transformed_diff_exp_0.BM Source code
compute_tree_correlations_matrix.BM Man page Source code
compute_tree_correlations_matrix.scOU Man page Source code
compute_var_M.BM Man page Source code
compute_var_M.OU.specialCase Source code
compute_var_M.sBM Source code
compute_var_diff.BM Man page Source code
compute_var_diff.OU Source code
compute_variance_block_diagonal.BM Man page Source code
compute_variance_block_diagonal.OU Man page Source code
compute_variance_covariance.BM Man page Source code
compute_variance_covariance.OU Man page Source code
compute_variance_covariance.OU.nonsym Man page Source code
compute_variance_covariance.scOU Man page Source code
compute_variance_from_stationary Source code
conditional_expectation_log_likelihood_real_shifts.OU.stationary Source code Source code
correspondenceEdges Man page Source code
enlight Man page Source code
enlight.PhyloEM Man page Source code
enumerate_parsimony Man page Source code
enumerate_tips_under_edges Man page
equivalent_shifts Man page Source code
equivalent_shifts_edges Man page Source code
equivalent_shifts_values Man page Source code
estimate.alpha Man page Source code
estimateEM Man page Source code
estimateEM_wrapper Source code
estimateEM_wrapper_previous Source code
estimateEM_wrapper_scratch Source code
expand_method_selection Source code
extract Man page Source code
extract.covariance_parents Source code
extract.enumerate_parsimony Man page Source code
extract.equivalent_shifts Man page Source code
extract.parsimonyCost Man page Source code
extract.parsimonyNumber Man page Source code
extract.partitionsNumber Man page Source code
extract.simul_process Man page Source code
extract.variance_covariance Man page Source code
extract.variance_nodes Source code
extract_params Source code
extract_root_values Source code
extract_shifts_values Source code
extract_simulate_internal Source code
find_grid_alpha Man page Source code
find_independent_regression_vectors.gglasso Source code
find_independent_regression_vectors.glmnet_multivariate Man page Source code
find_rotation Man page Source code
find_shift_values Man page Source code
format_output Man page Source code
format_output_several_K_single Source code
getAncestor Source code
getAncestors Source code
get_criterion Man page Source code
get_method_selection Source code
get_variance_node Man page Source code
go_back_to_original_process Man page
has_converged_absolute Source code
has_converged_relative Source code
imputed_traits Man page Source code
imputed_traits.PhyloEM Man page Source code
incidence.matrix Man page Source code
incidence.matrix.full Man page Source code
incidence_matrix_actualization_factors Man page Source code
init.EM.default Source code
init.EM.default.BM Source code
init.EM.default.OU Source code
init.EM.lasso Man page Source code
init.allocate_regimes_from_shifts Man page Source code
init.alpha.default Source code
init.alpha.gamma.BM Source code
init.alpha.gamma.OU Source code
init.alpha.gamma.default Source code
init.alpha.gamma.estimation Man page Source code
init.compute_betas_from_shifts Man page Source code
init.enumerate_parsimony Man page Source code
init.incidence.matrix Man page Source code
init.incidence.matrix.full Man page Source code
init.parsimonyCost Man page Source code
init.parsimonyNumber Man page Source code
init.partitionsNumber Source code
init.simulate.BM Man page Source code
init.simulate.OU Man page Source code
init.simulate.StateAndExp Man page Source code
init.variance.BM.estimation Source code
is.in.ranges Man page Source code
is.in.ranges.params.BM Source code
is.in.ranges.params.BM.fixedroot Source code
is.in.ranges.params.BM.randroot Source code
is.in.ranges.params.OU Source code
is.in.ranges.params.OU.specialCase Source code
is.in.ranges.params.OU.stationary.root_AND_shifts_at_nodes Source code
kronecker_sum Source code
lasso_regression_K_fixed.gglasso Source code
lasso_regression_K_fixed.glmnet_multivariate Man page Source code
log_likelihood Man page Source code
log_likelihood.PhyloEM Man page Source code
log_likelihood.params_process Man page Source code
log_likelihood_BM Source code
log_likelihood_OU Source code
matrix_of_possibles Man page Source code
merge_complementary_vectors Man page Source code
merge_max_grid_alpha Source code
merge_min_grid_alpha Source code
merge_params_independent Man page Source code
merge_rotate Source code
merge_rotations Man page Source code
model_selection Man page Source code
model_selection.PhyloEM Man page Source code
model_selection_BGH Source code
model_selection_BGH_leastsquares Source code
model_selection_BGH_leastsquares_raw Source code
model_selection_BGH_ml Source code
model_selection_BGH_mlraw Source code
model_selection_BM1 Source code
model_selection_BM2 Source code
model_selection_capushe Source code
model_selection_pBIC Source code
model_selection_pBIC_l1ou Source code
monkeys Man page
params_BM Man page Source code
params_OU Man page Source code
params_process Man page Source code
params_process.PhyloEM Man page Source code
params_process.character Man page Source code
parsimonyCost Man page Source code
parsimonyNumber Man page Source code
partitionsNumber Man page Source code
penalty_BaraudGiraudHuet_leastsquares Source code
penalty_BaraudGiraudHuet_likelihood Man page Source code
penalty_BirgeMassart_shape1 Man page Source code
penalty_BirgeMassart_shape2 Man page Source code
penalty_pBIC Man page Source code
penalty_pBIC_independent Source code
penalty_pBIC_l1ou Source code
penalty_pBIC_l1ou_unit Source code
penalty_pBIC_scalarOU Source code
plot.PhyloEM Man page Source code
plot.data.process.actual Source code
plot.enumerate_parsimony Man page Source code
plot.equivalent_shifts Man page Source code
plot.params_process Man page Source code
plot_criterion Man page Source code
print.PhyloEM Source code
print.enumerate_parsimony Source code
print.equivalent_shifts Source code
print.params_process Source code
print.parsimonyCost Source code
print.parsimonyNumber Source code
print.partitionsNumber Source code
prod.index Man page Source code
qr.solve_exact Man page
recursionDown Man page Source code
recursionUp Source code
recursionUp_list Source code
residuals.PhyloEM Man page Source code
return_to_original_order Source code
rotate_params Source code
rtree.comb Source code
rtree.sym Source code
sample_edges_intervals Man page Source code
sample_shifts Source code
sample_shifts_GMM Source code
sample_shifts_edges Man page Source code
sample_shifts_values Source code
sample_shifts_values_GMM Source code
scale.tree Source code
scale_params Man page Source code
segmentation.BM Man page Source code
segmentation.OU.specialCase.best_single_move Source code
segmentation.OU.specialCase.lasso Man page Source code
segmentation.OU.specialCase.same_shifts Man page Source code
shifts.list_to_matrix Man page Source code
shifts.list_to_vector Man page Source code
shifts.matrix_to_list Man page Source code
shifts.vector_to_list Man page Source code
shifts_to_simmap Man page Source code
shutoff.EM.BM Source code
shutoff.EM.BM.fixedroot Source code
shutoff.EM.BM.randroot Source code
shutoff.EM.OU Source code
shutoff.EM.OU.specialCase Source code
shutoff.EM.OU.stationary.root_AND_shifts_at_nodes.alpha Source code
shutoff.EM.OU.stationary.root_AND_shifts_at_nodes.half_life Source code
simul_process Man page Source code
simul_process.PhyloEM Man page Source code
simul_process.params_process Man page Source code
simulate_internal Man page Source code
split_params_independent Man page Source code
subset_node.default Source code
subset_node.simulate Source code
sum.partitions Man page Source code
sum.partitions.cardFixed Man page Source code
sum.prod.comb Man page Source code
sum.simplex Man page
test.root.state Man page Source code
test.root.state.BM Source code
test.root.state.OU Source code
test_all_scenarii Source code
transform_branch_length Man page Source code
transform_shifts_values Man page Source code
update.allocate_regimes_from_shifts Man page Source code
update.compute_betas_from_shifts Man page Source code
update.enumerate_parsimony Man page Source code
update.incidence.matrix Man page Source code
update.incidence.matrix.full Man page Source code
update.parsimonyCost Man page Source code
update.parsimonyNumber Man page Source code
update.partitionsNumber.bin Source code
update.partitionsNumber.gen Man page Source code
update.simulate.BM Source code
update.simulate.OU Source code
update.simulate.OUBM Source code
update.simulate.StudentOU Source code
update.simulate.scOU Source code
upward_downward_BM Source code
upward_downward_OU Source code
wrapper_E_step Man page Source code
PhylogeneticEM documentation built on Aug. 31, 2022, 9:16 a.m.

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