HAO                     Hymenoptera Anatomy Ontology (HAO)
KDE_unnorm_trunc_Markov
                        KDE for unnormalized Markov kernel vectorized.
KDE_unnormalized_scalar_Markov_kernel
                        KDE for unnormalized Markov kernel.
MultiScale.simmap       Multidimensional scaling of character states
                        from one stochastic character map
RAC_query               Retrieve all characters under a given set of
                        terms
add_noise_MD            Adding noise to MDS from one stochastic
                        character map
add_pseudodata          Add pseudodata
anat_plot               Plot Picture
color.bar               Color bar
derivative_KDE          Calculate KDE derivative over edges
discr_Simmap            Reading unsummarized simmap for one tree
discr_Simmap_all        Reading unsummarized simmap for a list of trees
edge_profiles4plotting
                        Make edge profiles for plotting
edgeplot                Plot edge profiles and contMap
estimate_band_W         Estimate bandwidth
estimate_edge_KDE       Estimate the normalized Markov KDE
estimate_edge_KDE_Markov_kernel_unnorm
                        Estimate the unnormalized Markov KDE
get_descendants_chars   Get characters that are the descendants of a
                        selected ontology term
get_path_edges          Get edges IDs from root to a given node.
get_rough_state_cols    Multiple character state colors
get_state               Get state name for contMap plotting.
get_states_path         Get state information about a given path.
get_vector_ids_list     Wrapper for getting vector layer IDs for
                        multiple terms
get_vector_ids_per_term
                        Get vector layer IDs for single term
hym_annot               Hymenoptera character annotations
hym_graph               Hymenoptera graphics information
hym_hm                  Hamming distances object (Hymenoptera example)
hym_img                 Hymenoptera vector image
hym_kde                 pNHPP rates object (Hymenoptera example)
hym_matrix              Hymenoptera character matrix
hym_nhpp                Changing times object (Hymenoptera example)
hym_stm                 Hymenoptera stochastic character maps
hym_stm_amalg           Hymenoptera amalgamated stochastic character
                        maps
hym_stm_mds             Hymenoptera amalgamated phenome
hym_tree                Hymenoptera dated tree
integrate_edge_KDE      Calculate KDE integral over edges
join_edges              Join neighboring edges in edge profiles.
list2edges              Convert list to edge matrix
loess_smoothing_KDE     Get loess smoothing for the unnormalized Markov
                        KDE
make_colors             Make color palette for image plotting
make_colors_relative_scale
                        Make color palette for image plotting with
                        relative scale
make_contMap_KDE        Make contMap KDE object
make_data_NHPP_KDE_Markov_kernel
                        Get NHPP data for all edges (Markov KDE)
make_data_NHPP_over_edge_MarkovKDE
                        Get NHPP data for a given edge (Markov KDE)
make_pic                Assign colors to picture ID layers
make_postPois_KDE       Make posterior distribution of NHPP
mds_plot                Plot morphospace from MDS
merge_branch_cat        Merge state bins over branch
merge_tree_cat          Merge state bins over a tree
merge_tree_cat_list     Merge state bins over a tree list
normalize_KDE           Normalize loess smoothing
pNHPP                   Phylogenetic Non-Homogeneous Poisson Process
                        (pNHPP) method
paramo                  PARAMO
paramo.list             Stack multiple discrete stochastic character
                        map lists
path_hamming            Path hamming
path_hamming_over_all_edges
                        Hamming distances for a tree
path_hamming_over_trees_KDE
                        Hamming distances for a list of trees
posterior_lambda_KDE    Get analytical posterior
posterior_lambda_KDE_Distr
                        Get distributions of analytical posterior
read_Simmap_Rev         Reading stochastic character maps file from
                        ReVBayes
stack2                  Stack two discrete stochastic character map
                        lists; x and y are the list of state names
                        (i.e. maps).
stack_stm               Stack two discrete stochastic character maps.
