Computes a consensusNetwork from a list of trees

consensusNet computes a split network, i.e. an object of class networx from a list of trees, i.e. an class of class multiPhylo (Holland, Huber, Moulton, and Lockhart 2004) .

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.

References

Holland BR, Huber KT, Moulton V, Lockhart PJ (2004). “Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny.” Molecular Biology and Evolution, 21(7), 1459-1461. doi:10.1093/molbev/msh145 .

Author

Klaus Schliep klaus.schliep@gmail.com

Examples


data(Laurasiatherian)
set.seed(1)
bs <- bootstrap.phyDat(Laurasiatherian, FUN = function(x)nj(dist.hamming(x)),
    bs=50)
cnet <- consensusNet(bs, 0.3)
plot(cnet, angle=-60)

if (FALSE) { # \dontrun{
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, 0.3)
plot(cnet_woodmouse, type = "equal angle", show.edge.label=TRUE)
} # }