treespace (version 1.1.4.3)

refTreeDist: 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
)

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.

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.

Author

Michelle Kendall

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)