Computes a consensusNetwork from a list of trees Computes a networx object from a collection of splits.
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.
consensusNet(obj, prob = 0.3, ...)
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. |
consensusNet returns an object of class networx. This is
just an intermediate to plot phylogenetic networks with igraph.
Klaus Schliep klaus.schliep@gmail.com
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
data(Laurasiatherian)
set.seed(1)
bs <- bootstrap.phyDat(Laurasiatherian, FUN = function(x)nj(dist.hamming(x)),
bs=50)
cnet <- consensusNet(bs, .3)
plot(cnet)
## 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.