as.splits: Splits representation of graphs and trees.

In KlausVigo/phangorn: Phylogenetic Reconstruction and Analysis

Splits representation of graphs and trees.

Description

as.splits produces a list of splits or bipartitions.

Usage

allSplits(k, labels = NULL)

allCircularSplits(k, labels = NULL)

as.splits(x, ...)

## S3 method for class 'splits'
as.matrix(x, zero.print = 0L, one.print = 1L, ...)

## S3 method for class 'splits'
as.Matrix(x, ...)

## S3 method for class 'splits'
print(x, maxp = getOption("max.print"), zero.print = ".",
  one.print = "|", ...)

## S3 method for class 'splits'
c(..., recursive = FALSE)

## S3 method for class 'splits'
unique(x, incomparables = FALSE, unrooted = TRUE, ...)

## S3 method for class 'phylo'
as.splits(x, ...)

## S3 method for class 'multiPhylo'
as.splits(x, ...)

## S3 method for class 'networx'
as.splits(x, ...)

## S3 method for class 'splits'
as.prop.part(x, ...)

## S3 method for class 'splits'
as.bitsplits(x)

## S3 method for class 'bitsplits'
as.splits(x, ...)

compatible(obj1, obj2 = NULL)

Arguments

k	number of taxa.
labels	names of taxa.
x	An object of class phylo or multiPhylo.
...	Further arguments passed to or from other methods.
zero.print	character which should be printed for zeros.
one.print	character which should be printed for ones.
maxp	integer, default from options(max.print), influences how many entries of large matrices are printed at all.
recursive	logical. If recursive = TRUE, the function recursively descends through lists (and pairlists) combining all their elements into a vector.
incomparables	only for compatibility so far.
unrooted	todo.
obj1, obj2	an object of class splits.

Value

as.splits returns an object of class splits, which is mainly a list of splits and some attributes. Often a splits object will contain attributes confidences for bootstrap or Bayesian support values and weight storing edge weights. compatible return a lower triangular matrix where an 1 indicates that two splits are incompatible.

Note

The internal representation is likely to change.

Author(s)

Klaus Schliep [e-mail]

See Also

prop.part, lento, as.networx, distanceHadamard, read.nexus.splits

Examples

(sp <- as.splits(rtree(5)))
write.nexus.splits(sp)
spl <- allCircularSplits(5)
plot(as.networx(spl))

KlausVigo/phangorn documentation built on Nov. 20, 2024, 12:47 p.m.