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

In KlausVigo/phangorn: Phylogenetic Reconstruction and Analysis

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 [e-mail]

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")
## Not run: 
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)

## End(Not run)

KlausVigo/phangorn documentation built on Nov. 20, 2024, 12:47 p.m.