R: Splits representation of graphs and trees.

allSplits {phangorn} | R Documentation

## 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)

    compatible(obj)

### 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.
`obj` | 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 klaus.schliep@gmail.com

### 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), "2D")

[Package phangorn version 2.3.1 Index]