as.bitsplits {ape} | R Documentation |
bitsplits
returns the bipartitions (aka splits) for a single
tree or a list of trees.
countBipartitions
returns the frequencies of the bipartitions
from a reference tree (phy) observed in a list of trees (X).
as.bitsplits
and as.prop.part
are generic functions for
converting between the "bitsplits"
and "prop.part"
classes.
bitsplits(x) countBipartitions(phy, X) as.bitsplits(x) ## S3 method for class 'prop.part' as.bitsplits(x) ## S3 method for class 'bitsplits' print(x, ...) ## S3 method for class 'bitsplits' sort(x, decreasing = FALSE, ...) as.prop.part(x, ...) ## S3 method for class 'bitsplits' as.prop.part(x, include.trivial = FALSE, ...)
x |
an object of the appropriate class. |
phy |
an object of class |
X |
an object of class |
decreasing |
a logical value to sort the bipartitions in increasing (the default) or decreasing order of their frequency. |
include.trivial |
a logical value specifying whether to include the trivial split with all tips in the returned object. |
... |
further arguments passed to or from other methods. |
These functions count bipartitions as defined by internal branches, so
they do not work with rooted trees (see examples). The structure of
the class "bitsplits"
is described in a separate document
on ape's web site.
bitsplits
, as.bitsplits
, and sort
return an object
of class "bitsplits"
.
countBipartitions
returns a vector of integers.
as.prop.part
returns an object of class "prop.part"
.
Emmanuel Paradis
tr <- rtree(20) pp <- prop.part(tr) as.bitsplits(pp) ## doesn't work for rooted trees...: countBipartitions(rtree(10), rmtree(100, 10)) ## ... but OK with unrooted trees: countBipartitions(rtree(10, rooted = FALSE), rmtree(100, 10, rooted = FALSE))