Frequency() computes the frequency-difference consensus, which retains
each split that occurs more often than every split that conflicts with it
(Goloboff et al. 2003)
.
Value
Frequency() returns an object of class phylo denoting the
frequency consensus, rooted as in the first entry of trees.
Details
The frequency-difference consensus is at least as resolved as the
majority-rule consensus (Majority()), and is contained within the greedy
consensus (Greedy()).
This implementation builds on the FDCT algorithm of Jansson et al. (2026) ; please cite that paper when using this method.
References
Goloboff PA, Farris JS, Källersjö M, Oxelman B, Ramírez MJ, Szumik CA (2003).
“Improvements to resampling measures of group support.”
Cladistics, 19(4), 324–332.
doi:10.1111/j.1096-0031.2003.tb00376.x
.
Jansson J, Sung W, Tabatabaee SA, Yang Y (2026).
“A faster algorithm for constructing the frequency difference consensus tree.”
Journal of Computer and System Sciences, 161, 103831.
doi:10.1016/j.jcss.2026.103831
.
See also
Closely related: Majority(), MajorityPlus(),
Greedy().
Other consensus methods:
Adams(),
Average(),
Greedy(),
Local(),
Loose(),
Majority(),
MajorityPlus(),
Quartet(),
RStar(),
Strict(),
Transfer()
Examples
trees <- ape::as.phylo(0:5, 8)
Frequency(trees)
#>
#> Phylogenetic tree with 8 tips and 6 internal nodes.
#>
#> Tip labels:
#> t2, t8, t7, t6, t3, t5, ...
#>
#> Rooted; no branch length.