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 |
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