R: Computes a consensusNetwork from a list of trees Computes a...

consensusNet {phangorn} | R Documentation

## Computes a consensusNetwork from a list of trees Computes a `networx` object from a collection of splits.

### Description

Computes a consensusNetwork, i.e. an object of class `networx` from a list of trees, i.e. an class of class `multiPhylo`. Computes a `networx` object from a collection of splits.

### Usage

    consensusNet(obj, prob = 0.3, ...)

### Arguments

`obj` | An object of class multiPhylo.
`prob` | the proportion a split has to be present in all trees to be represented in the network.
`...` | Further arguments passed to or from other methods.

### Value

`consensusNet` returns an object of class networx. This is just an intermediate to plot phylogenetic networks with igraph.

### Author(s)

Klaus Schliep klaus.schliep@gmail.com

### References

Holland B.R., Huber K.T., Moulton V., Lockhart P.J. (2004) Using consensus networks to visualize contradictory evidence for species phylogeny. Molecular Biology and Evolution, 21, 1459–61

### See Also

`splitsNetwork`, `neighborNet`, `lento`, `distanceHadamard`, `plot.networx`, `maxCladeCred`

### Examples

    data(Laurasiatherian)
    set.seed(1)
    bs <- bootstrap.phyDat(Laurasiatherian, FUN = function(x)nj(dist.hamming(x)),
        bs=50)
    cnet <- consensusNet(bs, .3)
    plot(cnet, "2D")
    ## Not run:
    library(rgl)
    open3d()
    plot(cnet, show.tip.label=FALSE, show.nodes=TRUE)
    plot(cnet, type = "2D", show.edge.label=TRUE)

    tmpfile <- normalizePath(system.file("extdata/trees/RAxML_bootstrap.woodmouse", package="phangorn"))
    trees <- read.tree(tmpfile)
    cnet_woodmouse <- consensusNet(trees, .3)
    plot(cnet_woodmouse, type = "2D", show.edge.label=TRUE)

    ## End(Not run)

[Package phangorn version 2.3.1 Index]