treeVec: Tree vector function

Description

Function which takes an object of class phylo and outputs the vector for the Kendall Colijn metric. The elements of the vector are numeric if return.lambda.function=FALSE (default), and otherwise they are functions of lambda.

Usage

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

Value

The vector of values according to the metric, or a function that produces the vector given a value of lambda.

Arguments

tree: an object of the class phylo
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 vector 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

Jacob Almagro-Garcia nativecoder@gmail.com

Michelle Kendall michelle.louise.kendall@gmail.com

Examples

Run this code


## generate a random tree
tree <- rtree(6)
## topological vector of mrca distances from root:
treeVec(tree)
## vector of mrca distances from root when lambda=0.5:
treeVec(tree,0.5)
## vector of mrca distances as a function of lambda:
vecAsFunction <- treeVec(tree,return.lambda.function=TRUE)
## evaluate the vector at lambda=0.5:
vecAsFunction(0.5)