Consensus() calculates the majority-rule or strict consensus of a set of
trees, using the cluster-table approach of Day1985TreeTools.
Consensus(trees, p = 1, check.labels = TRUE, hash = TRUE)Consensus() returns an object of class phylo, rooted as in the
first entry of trees.
List of trees, optionally of class multiPhylo.
A number from 0.5 to 1 giving the proportion of trees that must
contain a split for it to be reported in the consensus: from p = 0.5 (more
than half the trees; the majority-rule consensus) to p = 1 (every tree; the
strict consensus, the default).
Logical specifying whether to check that all trees have
identical labels. Defaults to TRUE, which is slower.
Logical; if TRUE (default), majority/threshold consensus
counts splits using 128-bit hashing, which is exact with overwhelming
probability (a collision conflating two distinct splits is vanishingly
unlikely). Set hash = FALSE for a slower but guaranteed-exact count.
Ignored when p = 1, which is always exact.
The strict consensus (p = 1) compares the clusters of the first tree
against every other tree in linear time. The majority-rule and threshold
consensus (0.5 <= p < 1) instead count the frequency of every split across
all trees in a single pass and retain those occurring in a proportion p or
more of trees (i.e. in at least ceiling(p * length(trees)) trees); this
runs in time linear in the number of trees, after
Jansson2016TreeTools. The majority threshold p = 0.5 is
strict: a split is retained only if it occurs in more than half the trees,
so that two conflicting splits can never both be reported. By default the
count uses a 128-bit hash, whose results are exact with overwhelming
probability; set hash = FALSE for a slower but guaranteed-exact count.
ConsTree implements other consensus tree algorithms.
Rogue increases the resolution of consensus trees by dropping wildcard taxa.
TreeDist::ConsensusInfo() calculates the information content of a
consensus tree.
Other consensus tree functions:
ConsensusWithout(),
RoguePlot()
Other tree characterization functions:
CladisticInfo(),
J1Index(),
Stemwardness,
TotalCopheneticIndex()