Metric function for comparing a reference phylo to multiPhylo input

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.

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

Michelle Kendall michelle.louise.kendall@gmail.com

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)
#>  [1] 6.403124 4.358899 3.872983 6.082763 6.855655 6.557439 6.244998 5.744563
#>  [9] 6.324555 6.082763