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)
}
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