treeDist: Metric function

In thibautjombart/treescape: Statistical Exploration of Landscapes of Phylogenetic Trees

Description

Comparison of two trees using the Kendall Colijn metric

Usage

treeDist(tree.a, tree.b, lambda = 0, return.lambda.function = FALSE,
  emphasise.tips = NULL, emphasise.weight = 2)

Arguments

tree.a	an object of the class phylo
tree.b	an object of the class phylo (with the same tip labels as tree.a)
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 distance between the two trees according to the metric for the given value of lambda, or a function that produces the distance given a value of lambda.

Author(s)

Jacob Almagro-Garcia [e-mail]

Michelle Kendall [e-mail]

Examples

## generate random trees
tree.a <- rtree(6)
tree.b <- rtree(6)
treeDist(tree.a,tree.b) # lambda=0
treeDist(tree.a,tree.b,1)  # lambda=1
dist.func <- treeDist(tree.a,tree.b,return.lambda.function=TRUE) # distance as a function of lambda
dist.func(0) # evaluate at lambda=0. Equivalent to treeDist(tree.a,tree.b).
## We can see how the distance changes when moving from focusing on topology to length:
plot(sapply(seq(0,1,length.out=100), function(x) dist.func(x)), type="l",ylab="",xlab="")

## The distance may also change if we emphasise the position of certain tips:
plot(sapply(tree.a$tip.label, function(x) treeDist(tree.a,tree.b,emphasise.tips=x)),
     xlab="Tip number",ylab="Distance when  vector entries corresponding to tip are doubled")

thibautjombart/treescape documentation built on May 31, 2019, 10:38 a.m.