ELynx.Data.Tree.Distance

Creation date: Thu Jun 13 17:15:54 2019.

Various distance functions for phylogenetic trees (and binary trees in general). All trees are assumed to be UNROOTED.

Documentation

symmetricDistance :: Ord a => Tree a -> Tree a -> Int

See symmetricDistanceWith, but with id for comparisons.

symmetricDistanceWith :: Ord b => (a -> b) -> Tree a -> Tree a -> Int

Symmetric (Robinson-Foulds) distance between two trees. Before comparing the leaf labels, apply a given function. This is useful, for example, to compare the labels of Named trees on their names only. The tree is assumed to be UNROOTED!

XXX: Comparing a list of trees with this function recomputes bipartitions.

incompatibleSplitsDistance :: (Ord a, Show a) => Tree a -> Tree a -> Int

See incompatibleSplitsDistanceWith, use id for comparisons.

incompatibleSplitsDistanceWith :: (Ord b, Show b) => (a -> b) -> Tree a -> Tree a -> Int

Number of incompatible splits. Similar to symmetricDistanceWith but merges multifurcations.

XXX: Comparing a list of trees with this function recomputes bipartitions.

computePairwiseDistances

Arguments

:: (a -> a -> b)

Distance function

-> [a]

Input trees

-> [(Int, Int, b)]

(index i, index j, distance i j)

Compute pairwise distances of a list of input trees. Use given distance measure. Returns a triple, the first two elements are the indices of the compared trees, the third is the distance.

computeAdjacentDistances

Arguments

:: (Tree a -> Tree a -> b)

Distance function

-> [Tree a]

Input trees

-> [b]

Compute distances between adjacent pairs of a list of input trees. Use given distance measure.

branchScoreDistance :: (Ord a, Measurable a, Named a) => Tree a -> Tree a -> Double

See branchScoreDistanceWith, use id for comparisons.

branchScoreDistanceWith

Arguments

:: (Ord a, Ord b, Floating c)

=> (a -> b)

Label to compare on

-> (a -> c)

Branch information (e.g., length) associated with a node

-> Tree a

-> Tree a

-> c

Compute branch score distance between two trees. Before comparing the leaf labels, apply a function. This is useful, for example, to compare the labels of Named trees on their names only. The branch information which is compared to compute the distance is extracted from the nodes with a given function. Assumes that the trees are UNROOTED.

XXX: Comparing a list of trees with this function recomputes bipartitions.