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Adams consensus tree

Source: R/adams.R
Adams.Rd

Adams() computes the Adams (1972) consensus tree.

Usage

Adams(trees)

Arguments

trees

A list of trees, or a multiPhylo object. All entries must share the same leaf labels.

Value

Adams() returns an object of class phylo denoting the Adams consensus tree.

Details

The Adams consensus places each species in the smallest group to which it belongs on all input trees. Consequently, it may contain groupings that do not appear in any input tree. This implementation builds on the algorithm of (Jansson et al. 2017) ; please cite this paper where you use this method.

References

Adams EN (1972). “Consensus techniques and the comparison of taxonomic trees.” Systematic Zoology, 21(4), 390–397. doi:10.2307/2412432 .

Jansson J, Li Z, Sung W (2017). “On finding the Adams consensus tree.” Information and Computation, 256, 334–347. doi:10.1016/j.ic.2017.08.002 .

See also

Other consensus methods: Average(), Frequency(), Greedy(), Local(), Loose(), Majority(), MajorityPlus(), Quartet(), RStar(), Strict(), Transfer()

Examples

# Two rooted trees that disagree only on the position of one leaf
trees <- c(ape::read.tree(text = "(((a, b), c), d);"),
           ape::read.tree(text = "(((a, b), d), c);"))
# keeps the clade (a, b); leaves c, d unresolved at the root
ape::write.tree(Adams(trees))
#> [1] "(d,c,(b,a));"