Greedy() computes the greedy consensus
(Felsenstein 1993)
, also termed the extended
majority-rule consensus (Bryant 2003)
. Distinct splits
are considered in decreasing order of their frequency across the input trees,
breaking ties arbitrarily; each is added to the growing consensus if it is
compatible with every split already accepted.
Value
Greedy() returns an object of class phylo denoting the consensus,
rooted as in the first entry of trees.
Details
The implementation builds upon the greedyConsensusFast algorithm of
(Jansson et al. 2016)
; please cite that paper when
using this method.
References
Bryant D (2003).
“A classification of consensus methods for phylogenetics.”
In Janowitz MF, Lapointe F, McMorris FR, Mirkin B, Roberts FS (eds.), Bioconsensus, volume 61 of DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 163–184.
American Mathematical Society.
doi:10.1090/dimacs/061/11
.
Felsenstein J (1993).
“PHYLIP.”
https://phylipweb.github.io/phylip/.
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(), Loose().
Other consensus methods:
Adams(),
Average(),
Frequency(),
Local(),
Loose(),
Majority(),
MajorityPlus(),
Quartet(),
RStar(),
Strict(),
Transfer()
Examples
trees <- ape::as.phylo(0:5, 8)
Greedy(trees)
#>
#> Phylogenetic tree with 8 tips and 7 internal nodes.
#>
#> Tip labels:
#> t1, t4, t6, t7, t2, t8, ...
#>
#> Rooted; no branch length.