Construct consensus trees — Consensus • TreeTools

Consensus() calculates the consensus of a set of trees, using the algorithm of (Day 1985) .

Usage

Consensus(trees, p = 1, check.labels = TRUE)

Arguments

trees: List of trees, optionally of class multiPhylo.
p: Proportion of trees that must contain a split for it to be reported in the consensus. p = 0.5 gives the majority-rule consensus; p = 1 (the default) gives the strict consensus.
check.labels: Logical specifying whether to check that all trees have identical labels. Defaults to TRUE, which is slower.

Value

Consensus() returns an object of class phylo, rooted as in the first entry of trees.

References

Day WHE (1985). “Optimal algorithms for comparing trees with labeled leaves.” Journal of Classification, 2(1), 7–28. doi:10.1007/BF01908061 .

See also

TreeDist::ConsensusInfo() calculates the information content of a consensus tree.

Other consensus tree functions: ConsensusWithout(), RoguePlot()

Other tree characterization functions: CladisticInfo(), J1Index(), Stemwardness, TotalCopheneticIndex()

Author

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

Consensus(as.phylo(0:2, 8))
#> 
#> Phylogenetic tree with 8 tips and 6 internal nodes.
#> 
#> Tip labels:
#>   t1, t2, t3, t4, t5, t6, ...
#> 
#> Rooted; no branch length.