Ontology-Informed Phylogenetic Comparative Analyses
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Documentation for package ‘ontophylo’ version 1.1.3
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. |