R: Function to import and export splits and networks

read.nexus.splits {phangorn} | R Documentation

## Function to import and export splits and networks

### Description

`read.nexus.splits`, `write.nexus.splits`, `read.nexus.networx`, `write.nexus.networx` can be used to import and export splits and networks with nexus format and allow to exchange these object with other software like Splitstree. `write.splits` returns a human readable output.

### Usage

    read.nexus.splits(file)

    write.nexus.splits(obj, file = "", weights = NULL, taxa = TRUE,
      append = FALSE)

    write.nexus.networx(obj, file = "", taxa = TRUE, splits = TRUE,
      append = FALSE)

    read.nexus.networx(file, splits = TRUE)

    write.splits(x, file = "", zero.print = ".", one.print = "|",
      print.labels = TRUE, ...)

### Arguments

`file` | a file name.
`obj` | An object of class splits.
`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.
`splits` | logical. If TRUE the nexus blocks will be added to a file.
`x` | An object of class splits.
`zero.print` | character which should be printed for zeros.
`one.print` | character which should be printed for ones.
`print.labels` | logical. If TRUE labels are printed.
`...` | Further arguments passed to or from other methods.
`labels` | names of taxa.

### Value

`write.nexus.splits` and `write.nexus.networx` write out the `splits` and `networx` object to read with other software like Splitstree. `read.nexus.splits` and `read.nexus.networx` return an `splits` and `networx` object.

### Note

`read.nexus.splits` reads in the splits block of a nexus file. It assumes that different co-variables are tab delimited and the bipartition are separated with white-space. Comments in square brackets are ignored.

### Author(s)

Klaus Schliep klaus.schliep@gmail.com

### See Also

`prop.part`, `lento`, `as.splits`, `as.networx`

### Examples

    (sp <- as.splits(rtree(5)))
    write.nexus.splits(sp)
    spl <- allCircularSplits(5)
    plot(as.networx(spl), "2D")
    write.splits(spl, print.labels = FALSE)

[Package phangorn version 2.3.1 Index]