# Ontology-Informed Phylogenetic Comparative Analyses

## Documentation for package ‘ontophylo’ version 1.1.3

- DESCRIPTION file
- Package README

## Help Pages

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
edgeplot | Plot edge profiles and contMap
edge_profiles4plotting | Make edge profiles for plotting
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
HAO | Hymenoptera Anatomy Ontology (HAO)
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.
KDE_unnormalized_scalar_Markov_kernel | KDE for unnormalized Markov kernel.
KDE_unnorm_trunc_Markov | KDE for unnormalized Markov kernel vectorized.
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
MultiScale.simmap | Multidimensional scaling of character states from one stochastic character map
normalize_KDE | Normalize loess smoothing
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
pNHPP | Phylogenetic Non-Homogeneous Poisson Process (pNHPP) method
posterior_lambda_KDE | Get analytical posterior
posterior_lambda_KDE_Distr | Get distributions of analytical posterior
RAC_query | Retrieve all characters under a given set of terms
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.