Loose() computes the loose consensus, also known as the semi-strict or
combinable-component consensus (Bremer 1990)
.
It contains every split that is not contradicted by any input tree.
Value
Loose() returns the consensus tree, an object of class phylo,
rooted as in the first entry of trees.
Details
The loose consensus refines the strict consensus (Strict()).
In contrast to the majority-rule consensus (Majority()), a split present
in most trees may still be contradicted by a minority, and so be excluded
from the loose consensus; yet a split that occurs in just one tree is
retained if no other tree contradicts it.
This implementation builds on the looseConsensusFast
algorithm of Jansson et al. (2016)
; please cite that
paper when using this method.
References
Bremer K (1990).
“Combinable component consensus.”
Cladistics, 6(4), 369–372.
doi:10.1111/j.1096-0031.1990.tb00551.x
.
Jansson J, Shen C, Sung W (2016).
“Improved algorithms for constructing consensus trees.”
Journal of the ACM, 63(3), 1–24.
doi:10.1145/2925985
.
See also
Closely related: Strict(), Majority(), Greedy().
Other consensus methods:
Adams(),
Average(),
Frequency(),
Greedy(),
Local(),
Majority(),
MajorityPlus(),
Quartet(),
RStar(),
Strict(),
Transfer()
Examples
trees <- ape::as.phylo(0:5, 8)
Loose(trees)
#>
#> Phylogenetic tree with 8 tips and 5 internal nodes.
#>
#> Tip labels:
#> t1, t2, t8, t7, t6, t5, ...
#>
#> Rooted; no branch length.