phangorn (version 2.12.1)

consensusNet: 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, ...)

Value

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

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.

Author

Klaus Schliep

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, angle=-60, direction="axial")
if (FALSE) {
library(rgl)
open3d()
plot(cnet, type = "3D", show.tip.label=FALSE, show.nodes=TRUE)
plot(cnet, type = "equal angle", 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 = "equal angle", show.edge.label=TRUE)
}