refTreeDist: Metric function for comparing a reference 'phylo' to...

In treespace: Statistical Exploration of Landscapes of Phylogenetic Trees

Metric function for comparing a reference phylo to multiPhylo input

Description

Comparison of a single reference tree to a list of trees using the Kendall Colijn metric. Output is given as a vector of distances from the reference tree.

Usage

refTreeDist(
  refTree,
  trees,
  lambda = 0,
  return.lambda.function = FALSE,
  emphasise.tips = NULL,
  emphasise.weight = 2
)

Arguments

refTree	a tree of class phylo, the "reference tree".
trees	an object of the class multiPhylo containing the trees to be compared to the reference tree
lambda	a number in [0,1] which specifies the extent to which topology (default, with lambda=0) or branch lengths (lambda=1) are emphasised. This argument is ignored if return.lambda.function=TRUE.
return.lambda.function	If true, a function that can be invoked with different lambda values is returned. This function returns the vector of metric values for the given lambda.
emphasise.tips	an optional list of tips whose entries in the tree vectors should be emphasised. Defaults to NULL.
emphasise.weight	applicable only if a list is supplied to emphasise.tips, this value (default 2) is the number by which vector entries corresponding to those tips are emphasised.

Value

The vector of distances, where entry i corresponds to the distance between the i'th tree and the reference tree, or a function that produces the vector of distances given a value for lambda.

Author(s)

Michelle Kendall [e-mail]

Examples

## generate a single reference tree with 6 tips
refTree <- rtree(6)

## generate 10 random trees, each with 6 tips
trees <- rmtree(10,6)

## find the distances from each of the 10 random trees to the single reference tree
refTreeDist(refTree,trees)

treespace documentation built on Sept. 8, 2023, 6:04 p.m.