GeneralizedRF: Generalized Robinson–Foulds distance

In TreeDist: Calculate and Map Distances Between Phylogenetic Trees

Generalized Robinson–Foulds distance

Description

An internal function to calculate Generalized Robinson–Foulds distances from splits.

Usage

GeneralizedRF(
  splits1,
  splits2,
  nTip,
  PairScorer,
  maximize,
  reportMatching,
  ...
)

Arguments

splits1, splits2	Logical matrices where each row corresponds to a leaf, either listed in the same order or bearing identical names (in any sequence), and each column corresponds to a split, such that each leaf is identified as a member of the ingroup (TRUE) or outgroup (FALSE) of the respective split.
nTip	Integer specifying the number of leaves in each split.
PairScorer	function taking four arguments, splits1, splits2, nSplits1, nSplits2, which should return the score of each pair of splits in a two-dimensional matrix. Additional parameters may be specified via ....
reportMatching	Logical specifying whether to return the clade matchings as an attribute of the score.
...	Additional parameters to PairScorer

Details

Note that no checks will be made to confirm that splits1 and splits2 contain the same leaves in the same order. This is the responsibility of the calling function.

Value

A numeric value specifying the score of the tree pairs under the specified pair scorer. If reportMatching = TRUE, attribute also list:

• matching: which split in splits2 is optimally matched to each split in split1 (NA if not matched);

• matchedSplits: Textual representation of each match

• matchedScores: Scores for matched split.

• pairScores: Calculated scores for each possible matching of each split.

Author(s)

Martin R. Smith ([e-mail])

TreeDist documentation built on Sept. 11, 2024, 9:10 p.m.