R/getEdgeTable.R

In ndukler/phyloGLM: Tests for signals of variable rates of evolution between gene classes and lineages for probabalistic alleles

#' Get edge table
#'
#' Returns edge table.
#' @param model alleleData or rateModel object
#' @rdname getEdgeTable
#' @name getEdgeTable
#' @return data.table containing edge ids
#' @include alleleData-class.R
#' @include rateModel-class.R
#' @export
methods::setGeneric("getEdgeTable", function(model) {
  standardGeneric("getEdgeTable")
})

#' @name getEdgeTable
#' @rdname getEdgeTable
#' @aliases getEdgeTable,alleleData,alleleData-method
methods::setMethod("getEdgeTable", signature(model = "alleleData"), function(model) {
  data.table::data.table(parent = model@tree$edge[, 1], child = model@tree$edge[, 2])
})

#' @name getEdgeTable
#' @rdname getEdgeTable
#' @aliases getEdgeTable,rateModel,rateModel-method
methods::setMethod("getEdgeTable", signature(model = "rateModel"), function(model) {
  return(model@edgeGroups)
})