consensusNet

0th

Percentile

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.

Keywords
hplot
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 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

Aliases
  • consensusNet
Examples
# NOT RUN {
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)
# }
# NOT RUN {
# }
Documentation reproduced from package phangorn, version 2.5.5, License: GPL (>= 2)

Community examples

Looks like there are no examples yet.