TQDist: Wrapper for tqDist

In ms609/SlowQuartet: Comparison of Phylogenetic Trees Using Quartet and Split Measures

Wrapper for tqDist

Description

TQDist() and TQAE() are convenience functions that writes a list of trees to text files that can be processed by the C implementation of tqDist \insertCiteSand2014Quartet. tqDist is then called, and the temporary file is deleted when analysis is complete.

Usage

TQDist(trees)

TQAE(trees)

Arguments

trees

List of phylogenetic trees, of class list or multiPhylo.

Details

Quartets can be resolved in one of five ways, which \insertCiteBrodal2013;textualQuartet and \insertCiteHolt2014;textualQuartet distinguish using the letters A-E, and \insertCiteEstabrook1985;textualQuartet refer to as:

A

s = resolved the same in both trees;

B

d = resolved differently in both trees;

C

r1 = resolved only in tree 1;

D

r2 = resolved only in tree 2 (the comparison tree);

E

u = unresolved in both trees.

Value

TQDist() returns the quartet distance between each pair of trees.

TQAE() returns the number of resolved quartets in agreement between each pair of trees ("A" in Brodal et al. 2013) and the number of quartets that are unresolved in both trees ("E" in Brodal et al. 2013).

Author(s)

Martin R. Smith ([e-mail])

References

\insertAllCited

See Also

CompareQuartets(), QuartetStatus()

ms609/SlowQuartet documentation built on Nov. 5, 2024, 8:48 a.m.