phangorn (version 2.0.3)

as.splits: Splits representation of graphs and trees.

Description

as.splits produces a list of splits or bipartitions.

Usage

as.splits(x, ...)
## S3 method for class 'phylo':
as.splits(x, ...)
## S3 method for class 'multiPhylo':
as.splits(x, ...)
## S3 method for class 'splits':
print(x, maxp = getOption("max.print"), zero.print = ".", 
    one.print = "|", ...)
## S3 method for class 'splits':
as.prop.part(x, ...)    
compatible(obj)
allSplits(k, labels = NULL)
write.nexus.splits(obj, file = "", weights=NULL, taxa=TRUE, append=FALSE)
read.nexus.splits(file)
addTrivialSplits(obj)

Arguments

x

An object of class phylo or multiPhylo.

maxp

integer, default from options(max.print), influences how many entries of large matrices are printed at all.

zero.print

character which should be printed for zeroes.

one.print

character which should be printed for ones.

...

Further arguments passed to or from other methods.

obj

an object of class splits.

k

number of taxa.

labels

names of taxa.

file

a file name.

weights

Edge weights.

taxa

logical. If TRUE a taxa block is added

append

logical. If TRUE the nexus blocks will be added to a file.

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. read.nexus.splits and write.nexus.splits allow to exchange a splits object with other software like Splitstree.

  compatible return a lower triangular matrix where an 1 indicates that two splits are incompatible.

See Also

prop.part, lento, distanceHadamard, as.networx

Examples

(sp <- as.splits(rtree(5)))
write.nexus.splits(sp)