Man pages for ontophylo
Ontology-Informed Phylogenetic Comparative Analyses

add_noise_MDAdding noise to MDS from one stochastic character map
add_pseudodataAdd pseudodata
anat_plotPlot Picture
color.barColor bar
derivative_KDECalculate KDE derivative over edges
discr_SimmapReading unsummarized simmap for one tree
discr_Simmap_allReading unsummarized simmap for a list of trees
edgeplotPlot edge profiles and contMap
edge_profiles4plottingMake edge profiles for plotting
estimate_band_WEstimate bandwidth
estimate_edge_KDEEstimate the normalized Markov KDE
estimate_edge_KDE_Markov_kernel_unnormEstimate the unnormalized Markov KDE
get_descendants_charsGet characters that are the descendants of a selected...
get_path_edgesGet edges IDs from root to a given node.
get_rough_state_colsMultiple character state colors
get_stateGet state name for contMap plotting.
get_states_pathGet state information about a given path.
get_vector_ids_listWrapper for getting vector layer IDs for multiple terms
get_vector_ids_per_termGet vector layer IDs for single term
HAOHymenoptera Anatomy Ontology (HAO)
hym_annotHymenoptera character annotations
hym_graphHymenoptera graphics information
hym_hmHamming distances object (Hymenoptera example)
hym_imgHymenoptera vector image
hym_kdepNHPP rates object (Hymenoptera example)
hym_matrixHymenoptera character matrix
hym_nhppChanging times object (Hymenoptera example)
hym_stmHymenoptera stochastic character maps
hym_stm_amalgHymenoptera amalgamated stochastic character maps
hym_stm_mdsHymenoptera amalgamated phenome
hym_treeHymenoptera dated tree
integrate_edge_KDECalculate KDE integral over edges
join_edgesJoin neighboring edges in edge profiles.
KDE_unnormalized_scalar_Markov_kernelKDE for unnormalized Markov kernel.
KDE_unnorm_trunc_MarkovKDE for unnormalized Markov kernel vectorized.
list2edgesConvert list to edge matrix
loess_smoothing_KDEGet loess smoothing for the unnormalized Markov KDE
make_colorsMake color palette for image plotting
make_colors_relative_scaleMake color palette for image plotting with relative scale
make_contMap_KDEMake contMap KDE object
make_data_NHPP_KDE_Markov_kernelGet NHPP data for all edges (Markov KDE)
make_data_NHPP_over_edge_MarkovKDEGet NHPP data for a given edge (Markov KDE)
make_picAssign colors to picture ID layers
make_postPois_KDEMake posterior distribution of NHPP
mds_plotPlot morphospace from MDS
merge_branch_catMerge state bins over branch
merge_tree_catMerge state bins over a tree
merge_tree_cat_listMerge state bins over a tree list
MultiScale.simmapMultidimensional scaling of character states from one...
normalize_KDENormalize loess smoothing
paramoPARAMO
paramo.listStack multiple discrete stochastic character map lists
path_hammingPath hamming
path_hamming_over_all_edgesHamming distances for a tree
path_hamming_over_trees_KDEHamming distances for a list of trees
pNHPPPhylogenetic Non-Homogeneous Poisson Process (pNHPP) method
posterior_lambda_KDEGet analytical posterior
posterior_lambda_KDE_DistrGet distributions of analytical posterior
RAC_queryRetrieve all characters under a given set of terms
read_Simmap_RevReading stochastic character maps file from ReVBayes
stack2Stack two discrete stochastic character map lists; x and y...
stack_stmStack two discrete stochastic character maps.
ontophylo documentation built on May 29, 2024, 9:57 a.m.