as.bitsplits {ape} | R Documentation |
Split Frequencies and Conversion Among Split Classes
Description
bitsplits
returns the bipartitions (aka splits) for a single
tree or a list of trees. If at least one tree is rooted, an error is
returned.
countBipartitions
returns the frequencies of the bipartitions
from a reference tree (phy) observed in a list of trees (X), all unrooted.
as.bitsplits
and as.prop.part
are generic functions for
converting between the "bitsplits"
and "prop.part"
classes.
Usage
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, ...)
Arguments
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. |
Details
These functions count bipartitions as defined by internal branches, so
they work only with unrooted trees. The structure of the class
"bitsplits"
is described in a separate document on ape's web
site.
Value
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"
.
Author(s)
Emmanuel Paradis
See Also
Examples
tr <- rtree(20)
pp <- prop.part(tr)
as.bitsplits(pp)
## works only with unrooted trees (ape 5.5):
countBipartitions(rtree(10, rooted = FALSE), rmtree(100, 10, rooted = FALSE))