add_complementary	add_complementary
allocate_regimes_from_shifts	allocate_regimes_from_shifts
allocate_shifts_from_regimes	allocate_shifts_from_regimes
allocate_subset_node.simulate	allocate_subset_node.simulate
check.selection.strength	check.selection.strength
check_data	check_data
check_dimensions	check_dimensions
check_parsimony	check_parsimony
check_parsimony_clusters	check_parsimony_clusters
check_range_alpha	check_range_alpha
clusters_from_shifts	clusters_from_shifts
compute_actualization_matrix_ultrametric	compute_actualization_matrix_ultrametric
compute_betas_from_shifts	compute_betas_from_shifts
compute_diff_exp.BM	compute_diff_exp.BM
compute_dist_phy	compute_dist_phy
compute_E.simple	compute_E.simple
compute_expectations.BM	compute_expectations.BM
compute_expectations.scOU	compute_expectations.scOU
compute_fixed_moments	compute_fixed_moments
compute_gauss_lasso	compute_gauss_lasso
compute_log_likelihood.simple	compute_log_likelihood.simple
compute_mahalanobis_distance.simple	compute_mahalanobis_distance.simple
compute_mean_variance.simple	compute_mean_variance.simple
compute_residuals.simple	compute_residuals.simple
compute_shifts_from_betas	compute_shifts_from_betas
compute_state_filter	compute_state_filter
compute_stationary_variance	compute_stationary_variance
compute_sum_var_diff	compute_sum_var_diff
compute_times_ca	compute_times_ca
compute_tree_correlations_matrix.BM	compute_tree_correlations_matrix.BM
compute_tree_correlations_matrix.scOU	compute_tree_correlations_matrix.scOU
compute_variance_block_diagonal.BM	compute_variance_block_diagonal.BM
compute_variance_block_diagonal.OU	compute_variance_block_diagonal.OU
compute_variance_covariance.BM	compute_variance_covariance.BM
compute_variance_covariance.OU	compute_variance_covariance.OU
compute_variance_covariance.OU.nonsym	compute_variance_covariance.OU.nonsym
compute_variance_covariance.scOU	compute_variance_covariance.scOU
compute_var_diff.BM	compute_var_diff.BM
compute_var_M.BM	compute_var_M.BM
correspondenceEdges	correspondenceEdges
enlight	enlight
enlight.PhyloEM	enlight
enumerate_parsimony	enumerate_parsimony
enumerate_tips_under_edges	enumerate_tips_under_edges
equivalent_shifts	equivalent_shifts
equivalent_shifts_edges	equivalent_shifts_edges
equivalent_shifts_values	equivalent_shifts_values
estimate.alpha	estimate.alpha
estimateEM	estimateEM
extract	extract
extract.enumerate_parsimony	extract.enumerate_parsimony
extract.equivalent_shifts	extract.equivalent_shifts
extract.parsimonyCost	extract.parsimonyCost
extract.parsimonyNumber	extract.parsimonyNumber
extract.partitionsNumber	extract.partitionsNumber
extract.simul_process	extract.simul_process
extract_variance_covariance	extract_variance_covariance
find_grid_alpha	find_grid_alpha
find_independent_regression_vectors.glmnet_multivariate	find_independent_regression_vectors.glmnet_multivariate
find_rotation	find_rotation
find_shift_values	find_shift_values
format_output	format_output
get_criterion	get_criterion
get_variance_node	get_variance_node
go_back_to_original_process	go_back_to_original_process
imputed_traits	imputed_traits
imputed_traits.PhyloEM	imputed_traits
incidence.matrix	incidence.matrix
incidence.matrix.full	incidence.matrix.full
incidence_matrix_actualization_factors	incidence_matrix_actualization_factors
init.allocate_regimes_from_shifts	init.allocate_regimes_from_shifts
init.alpha.gamma.estimation	init.alpha.gamma.estimation
init.compute_betas_from_shifts	init.compute_betas_from_shifts
init.EM.lasso	init.EM.lasso
init.enumerate_parsimony	init.enumerate_parsimony
init.incidence.matrix	init.incidence.matrix
init.incidence.matrix.full	init.incidence.matrix.full
init.parsimonyCost	init.parsimonyCost
init.parsimonyNumber	init.parsimonyNumber
init.simulate.BM	init.simulate.BM
init.simulate.OU	init.simulate.OU
init.simulate.StateAndExp	init.simulate.StateAndExp
is.in.ranges	is.in.ranges
lasso_regression_K_fixed.glmnet_multivariate	lasso_regression_K_fixed.glmnet_multivariate
log_likelihood	log_likelihood
log_likelihood.params_process	log_likelihood
log_likelihood.PhyloEM	log_likelihood
matrix_of_possibles	matrix_of_possibles
merge_alpha_grids	merge_alpha_grids
merge_complementary_vectors	merge_complementary_vectors
merge_params_independent	merge_params_independent
merge_rotations	merge_rotations
model_selection	model_selection
model_selection.PhyloEM	model_selection
monkeys	monkeys
node_optimal_values	node_optimal_values
params_BM	params_BM
params_OU	params_OU
params_process	params_process
params_process.character	params_process.character
params_process.PhyloEM	params_process.PhyloEM
parsimonyCost	parsimonyCost
parsimonyNumber	parsimonyNumber
partitionsNumber	partitionsNumber
penalty_BaraudGiraudHuet_likelihood	penalty_BaraudGiraudHuet_likelihood
penalty_BirgeMassart_shape1	penalty_BirgeMassart_shape1
penalty_BirgeMassart_shape2	penalty_BirgeMassart_shape2
penalty_pBIC	penalty_pBIC
PhyloEM	PhyloEM
plot.enumerate_parsimony	plot.enumerate_parsimony
plot.equivalent_shifts	plot.equivalent_shifts
plot.params_process	plot.params_process
plot.PhyloEM	plot.PhyloEM
plot_criterion	plot_criterion
prod_index	prod_index
qr_solve_exact	qr_solve_exact
recursionDown	recursionDown
residuals.PhyloEM	residuals.PhyloEM
sample_edges_intervals	sample_edges_intervals
sample_shifts_edges	sample_shifts_edges
scale_params	scale_params
segmentation.BM	segmentation.BM
segmentation.OU.specialCase.lasso	segmentation.OU.specialCase.lasso
segmentation.OU.specialCase.same_shifts	segmentation.OU.specialCase.same_shifts
shifts.list_to_matrix	shifts.list_to_matrix
shifts.list_to_vector	shifts.list_to_vector
shifts.matrix_to_list	shifts.matrix_to_list
shifts.vector_to_list	shifts.vector_to_list
shifts_to_simmap	shifts_to_simmap
simulate_internal	simulate_internal
simul_process	simul_process
simul_process.params_process	simul_process
simul_process.PhyloEM	simul_process
split_params_independent	split_params_independent
sum_partitions	sum_partitions
sum_partitions.cardFixed	sum_partitions.cardFixed
sum_prod.comb	sum_prod.comb
sum_simplex	sum_simplex
test.root.state	test.root.state
transform_branch_length	transform_branch_length
transform_shifts_values	transform_shifts_values
update.allocate_regimes_from_shifts	update.allocate_regimes_from_shifts
update.compute_betas_from_shifts	update.compute_betas_from_shifts
update.enumerate_parsimony	update.enumerate_parsimony
update.incidence.matrix	update.incidence.matrix
update.incidence.matrix.full	update.incidence.matrix.full
update.parsimonyCost	update.parsimonyCost
update.parsimonyNumber	update.parsimonyNumber
update.partitionsNumber.gen	update.partitionsNumber.gen
wrapper_E_step	wrapper_E_step
