Man pages for phenoscape/scate-shortcourse
Short Course on Phylogenetic Comparative Analysis of Integrated Anatomical Traits
| amalgamate_deps | Generates a graph and model for traits given a dependency... |
| amalgamated_fits_corHMM | A wrapper for corHMM that fits Structured Hidden State Models |
| amalgamated_simmaps_phytools | A wrapper for phytools that draws stochastic character maps... |
| comb2matrices | Combining two matrices |
| combNmatrices | Combining multiple matrices |
| discr_Simmap | Reading unsummarized Stoch Map files from ReVBayes for one... |
| discr_Simmap_all | Reading unsummarized Stoch Map files from ReVBayes |
| dropDependentTraits | Utility function for cleaning up character data table after... |
| filter_coverage | Utility function for filtering based on missing traits and... |
| get_descendants_chars | Get characters that descendants of selected ontology term |
| get_graph_matrix | Get all dependency matrices given a dependecy graph |
| get_onto_id | Get IDs for ontology names |
| init_binary_matrix | Initialize binary matrices given graph |
| init_char_matrix | Initialize binary matrices |
| list2edges | Convert list to edge matrix |
| makeTraitTree | Makes a trait tree using semantic similarity |
| make_tree_eq | make branch length and maps equal, use tree.tmp with rounded... |
| Mk_Rev | Make rate matrix for RevBayes |
| ontologyHeatMap | Plots a heatmap along with a phylogeny and trait tree |
| paramo | Final stack of maps for a set of stochastic maps stored in a... |
| paramo.list | Final stack of maps for a set of stochastic maps stored in a... |
| prepareMapsRayDISC | Function for processing revbayes stochastic maps |
| prepareMapsRev | Function for processing revbayes stochastic maps |
| print_coverage | Function to display the number of matching species and... |
| RAC_query | Function for aggregating characters under a specified set of... |
| ratemat1 | Data object for Rev scripts |
| read_Simmap_Rev | Reading unsummarized Stoch Map files from ReVBayes |
| recode_td | recodes a treedata object based on amalgamated characters |
| recode_traits | Automatically recode amalgamated traits in PARAMO Amalgamates... |
| remove_indirect | Remove indirect links in a dependency graph |
| strip_IRI | Utility function for stripping off url from IRI |
| table2list | Convert table to list |
| writeRevOntologyModels | Function to write Ontology CTMC models as a .Rev file for... |
