Function reference • SCATE.shortcourse

All functions
`Mk_Rev()`	Make rate matrix for RevBayes
`RAC_query()`	Function for aggregating characters under a specified set of terms (for example, body regions)
`amalgamate_deps()`	Generates a graph and model for traits given a dependency matrix
`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 given a corHMM fit
`comb2matrices()`	Combining two matrices
`combNmatrices()`	Combining multiple matrices
`discr_Simmap()`	Reading unsummarized Stoch Map files from ReVBayes for one tree
`discr_Simmap_all()`	Reading unsummarized Stoch Map files from ReVBayes
`dropDependentTraits()`	Utility function for cleaning up character data table after amalgamating characters
`filter_coverage()`	Utility function for filtering based on missing traits and taxa
`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 (3) edge.length
`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 directory cc chars id to stack ntrees number of trees to stack dirW directory for zip file
`paramo.list()`	Final stack of maps for a set of stochastic maps stored in a list
`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 average value across them from an Ontotrace matrix
`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 traits using the matrices returned by amalgamate_deps
`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 execution in Revbayes

Reference

All functions