edgeTipIndicator: Relationships between tips and edges

In stevencarlislewalker/lme4ord: Generalized Linear Mixed Models with Flexible (Co)Variance Structures

Description

findFromNode is a recurrsive function for computing the path from a node back in time through its ancestor nodes. findEdgesFromPath returns a logical vector indicating the edges associated with a particular path. edgeTipIndicator returns a logical matrix giving the relationship between tips and the edges associated with their history. reorderPhylo is a convenience function for ordering the edges of a phylo object in a way that makes it easier to build edge-based phylogenetic models.

Usage

findPathFromNode(node, edge)

findEdgesFromPath(path, edge, scale = 1)

edgeTipIndicator(object, ...)

## Default S3 method:
edgeTipIndicator(object, ...)

## S3 method for class 'matrix'
edgeTipIndicator(object, ntip, scale = NULL, ...)

## S3 method for class 'phylo'
edgeTipIndicator(object, ...)

## S3 method for class 'hclust'
edgeTipIndicator(object, ...)

## S3 method for class 'mst'
edgeTipIndicator(object, ...)

reorderPhylo(object, ...)

Arguments

node	vector of node indices
edge	phylogenetic edge matrix
path	vector giving the path from a node back in time through its ancestor nodes (output of findFromNode)
object	either a phylo or matrix object
scale	scaling factor for edges (i.e., vector of branch lengths)
...	not used
ntip	number of tips

See Also

reorder.phylo

Examples

set.seed(1)
if (require("ape")) {
   phy <- rtree(5)
   plot(phy)
   edgelabels()
   edgeTipIndicator(phy)
   (ee <- edgeTipIndicator(phy))
   if (require("Matrix")) {
       image(Matrix(ee),sub="",xlab="tips",ylab="branches")
   }
}

stevencarlislewalker/lme4ord documentation built on May 30, 2019, 4:43 p.m.