add_complementary | Add several entries, when only one is not NA. |
allocate_regimes_from_shifts | Allocation of regimes to nodes. |
allocate_shifts_from_regimes | Allocation of shifts to edges |
allocate_subset_node.simulate | Iteration allocation |
check_data | Test the format of data entry. |
check_dimensions | Check dimensions of the parameters |
check_parsimony | Check Parsimony, assuming no homoplasy |
check_parsimony_clusters | Check whether an allocation of the shifts is parsimonious, in... |
check_range_alpha | Check range of alpha |
check.selection.strength | Check selection strength |
clusters_from_shifts | Clustering associated to a shift allocation, assuming no... |
compute_actualization_matrix_ultrametric | Compute Matrix W of actualization (Ultrametric case) |
compute_betas_from_shifts | Computation of the optimal values at nodes and tips. |
compute_diff_exp.BM | Compute differences of expectations between node and parent. |
compute_dist_phy | Phylogenetic Distances |
compute_E.simple | E step |
compute_expectations.BM | Compute the expected states of a BM |
compute_expectations.scOU | Compute the expected states of a scOU |
compute_fixed_moments | Compute fixed moments for E step. |
compute_gauss_lasso | Do a lm on top of a lasso regression. |
compute_log_likelihood.simple | Log Likelihood |
compute_mahalanobis_distance.simple | Squared Mahalanobis Distance |
compute_mean_variance.simple | Compute moments of params_old |
compute_residuals.simple | Residuals |
compute_shifts_from_betas | Computation of shifts from the vector of optimal values |
compute_state_filter | List of potential daughter states when parent is in state k. |
compute_stationary_variance | Compute the stationary variance matrix |
compute_sum_var_diff | Compute weighted sum of var_diff |
compute_times_ca | Common Ancestors Times |
compute_tree_correlations_matrix.BM | Matrix of tree-induced correlations for the BM |
compute_tree_correlations_matrix.scOU | Matrix of tree-induced correlations for the scOU |
compute_var_diff.BM | Compute variances of differences between nodes and parents. |
compute_variance_block_diagonal.BM | Tips Variances for the BM |
compute_variance_block_diagonal.OU | Tips Variances for the OU |
compute_variance_covariance.BM | Complete variance covariance matrix for BM |
compute_variance_covariance.OU | Complete variance covariance matrix for OU |
compute_variance_covariance.OU.nonsym | Complete variance covariance matrix for OU |
compute_variance_covariance.scOU | Complete variance covariance matrix for scOU |
compute_var_M.BM | Computation of the variance. |
correspondenceEdges | Correspondence between edges numbers |
enlight | Make the result lighter |
enumerate_parsimony | Enumerate all the possible regime allocations, given a... |
enumerate_tips_under_edges | Tips descendants of nodes. |
equivalent_shifts | Find all equivalent shifts allocations and values. |
equivalent_shifts_edges | Find all the equivalent shift edges allocations. |
equivalent_shifts_values | Find values given edges. OU stationary case. Ultrametric... |
estimate.alpha | Function to estimate alpha |
estimateEM | Perform One EM |
extract | Extraction function |
extract.enumerate_parsimony | Extract the result of 'enumerate_parsimony' at a node. |
extract.equivalent_shifts | Extract the shifts values for one trait. |
extract.parsimonyCost | Extraction of the actual number of solutions. |
extract.parsimonyNumber | Extraction of the actual number of solutions. |
extract.partitionsNumber | Extract from object 'partitionsNumber' |
extract.simul_process | Extraction of simulated traits |
extract_variance_covariance | Extract sub-matrices of variance. |
find_grid_alpha | Find a reasonable grid for alpha |
find_independent_regression_vectors.glmnet_multivariate | Given a regularization path, find K selected independent... |
find_rotation | Test for rotation invariant datasets |
find_shift_values | Find values given edges. OU stationary case. Ultrametric... |
format_output | Run the EM for several values of K |
get_criterion | Get Model Selection Criterion |
get_variance_node | Get variance matrix of a node |
go_back_to_original_process | Scale the parameters back to the original process |
imputed_traits | Ancestral State Reconstruction |
incidence.matrix | Incidence matrix of a tree. |
incidence_matrix_actualization_factors | Compute the actualization factors to apply to the incidence... |
incidence.matrix.full | Incidence matrix of a tree. |
init.allocate_regimes_from_shifts | Initialization for the allocation of shifts. |
init.alpha.gamma.estimation | Initialization the selection strength alpha using robust... |
init.compute_betas_from_shifts | Initialization for the computation of the optimal values |
init.EM.lasso | Initialization of the shifts using Lasso. |
init.enumerate_parsimony | Initialization for the enumeration of parsimonious solutions. |
init.incidence.matrix | Initialization for incidence matrix |
init.incidence.matrix.full | Initialization for incidence matrix (full tree) |
init.parsimonyCost | Initialization for parsimonyCost. |
init.parsimonyNumber | Initialization for parsimonyNumber. |
init.simulate.BM | Initialize BM |
init.simulate.OU | Initialize state and expectation matrices |
init.simulate.StateAndExp | Initialize state and expectation matrices |
is.in.ranges | Check whether parameters are in ranges. |
lasso_regression_K_fixed.glmnet_multivariate | Do a lasso regression with the number of non-zero variables... |
log_likelihood | Log Likelihood of a fitted object |
matrix_of_possibles | Compute parent matrix from possibles daughter matrices. |
merge_complementary_vectors | Merge several complementary vectors into one. |
merge_params_independent | Merge a list of independent parameters into into one... |
merge_rotations | Merge fits from independent runs of PhyloEM. |
model_selection | Model Selection of a fitted object |
monkeys | New World Monkeys dataset |
node_optimal_values | Computation of the optimal values at nodes and tips. |
params_BM | Create an object 'params_process' for a BM |
params_OU | Create an object 'params_process' for an OU |
params_process | Create an object params_process |
params_process.character | Create an object 'params_process' |
params_process.PhyloEM | Parameter estimates |
parsimonyCost | Minimal number of shifts needed to get a clustering. |
parsimonyNumber | Number of equivalent parsimonious allocations. |
partitionsNumber | Number of different models |
penalty_BaraudGiraudHuet_likelihood | Penalty function type Baraud Giraud Huet. |
penalty_BirgeMassart_shape1 | Penalty function type Birgé-Massart 1 |
penalty_BirgeMassart_shape2 | Penalty function type Birgé-Massart 2 |
penalty_pBIC | Penalty function type pBIC |
PhyloEM | Model Estimation with Detection of Shifts |
plot_criterion | Plot Model Selection Criterion |
plot.enumerate_parsimony | Plot all the equivalent solutions. |
plot.equivalent_shifts | Plot all the equivalent solutions. |
plot.params_process | Plot for class 'simul_process' |
plot.PhyloEM | Plot for class 'PhyloEM' |
prod_index | Product of elements of a matrix |
qr_solve_exact | exact qr.solve |
recursionDown | Generic recursion down the tree. |
residuals.PhyloEM | Residuals of a fitted object |
sample_edges_intervals | Sample equally spaced edges. |
sample_shifts_edges | Sample shifts edges in a parsimonious way. |
scale_params | Scale variance and selection strength from a linear transform |
segmentation.BM | Segmentation in the BM case |
segmentation.OU.specialCase.lasso | Segmentation in the OU special case, using lasso regression |
segmentation.OU.specialCase.same_shifts | Segmentation in the OU special case, conserving the same... |
shifts.list_to_matrix | Compute the matrix of shifts. |
shifts.list_to_vector | Compute the vector of shifts. |
shifts.matrix_to_list | Compute the list of shifts. |
shifts_to_simmap | Simmap format mapping from list of edges |
shifts.vector_to_list | Compute the list of shifts. |
simulate_internal | Simulate a Stochastic Process on a tree |
simul_process | Simulate a Stochastic Process on a tree |
split_params_independent | Split independent parameters into a list of parameters |
sum_partitions | Sum on all subsets. |
sum_partitions.cardFixed | Sum on subsets of a given cardinal. |
sum_prod.comb | Sum on a simplex |
sum_simplex | Sum on a simplex |
test.root.state | Test state of root. |
transform_branch_length | Transform branch length for a re-scaled BM |
transform_shifts_values | Transform the shift values |
update.allocate_regimes_from_shifts | Update function for regime allocation. |
update.compute_betas_from_shifts | Update function for optimal value computation |
update.enumerate_parsimony | Actualization of the enumeration. |
update.incidence.matrix | Update function for incidence matrix |
update.incidence.matrix.full | Update function for incidence matrix |
update.parsimonyCost | Actualization for parsimonyCost. |
update.parsimonyNumber | Actualization for parsimonyNumber. |
update.partitionsNumber.gen | Update formula in the general case |
wrapper_E_step | Wrapper for E step in EM |
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