getEdgeOrder: list the tree nodes in a post-order traversal
In cecileane/WGDgc: Whole genome duplication detection using gene counts

Description Usage Arguments Details Value Author(s) See Also

View source: R/processInput.R

Preprocessing to list the edges in a post-order traversal, for future use in likelihood calculation. The output includes information on which edges the birth-death process applies to, and which edges represent a whole genome duplication or triplication event.

1	getEdgeOrder(phyloMat,nLeaf,wgdTab)

`phyloMat`	Matrix representation of the species tree and WGD events
`nLeaf`	Number of present-day species (i.e. number of leaves)
`wgdTab`	Table representation of WGD events with retention rates

This function assumes that speciation nodes in phyloMat are given lower indices than singleton nodes when the tree is read in by phyext, that speciation nodes are in pre-order in phyloMat, and that 2 singleton nodes are used to represent each WGD.

Data frame listing the edges in a post-order traversal, with the following components

`child`	index of the edge's child node
`edge`	index of the edge, i.e. its row in phyloMat
`type`	"BD" if birth-death edge, "WGD" or "WGT" if the edge is modelling a WGD/T event, or "rootPrior" if the edge is parent to the root node
`scdsib`	`TRUE` if the edge is listed after a sibling edge, `FALSE` otherwise