Compare splits and add support values to an object
Add support values to a splits, phylo or networx
object.
createLabel(x, y, label_y, type = "edge", nomatch = NA) addConfidences(x, y, ...) ## S3 method for class 'phylo' addConfidences(x, y, ...) presenceAbsence(x, y)
x |
an object of class |
y |
an object of class |
label_y |
label of y matched on x. Will be usually of length(as.splits(x)). |
type |
should labels returned for edges (in |
nomatch |
default value if no match between x and y is found. |
... |
Further arguments passed to or from other methods. |
The object x with added bootstrap / MCMC support values.
Klaus Schliep klaus.schliep@gmail.com
Schliep, K., Potts, A. J., Morrison, D. A. and Grimm, G. W. (2017), Intertwining phylogenetic trees and networks. Methods Ecol Evol. 8, 1212–1220. doi:10.1111/2041-210X.12760
data(woodmouse)
woodmouse <- phyDat(woodmouse)
tmpfile <- normalizePath(system.file("extdata/trees/RAxML_bootstrap.woodmouse", package="phangorn"))
boot_trees <- read.tree(tmpfile)
dm <- dist.ml(woodmouse)
tree <- upgma(dm)
nnet <- neighborNet(dm)
tree <- addConfidences(tree, boot_trees)
nnet <- addConfidences(nnet, boot_trees)
plot(tree, show.node.label=TRUE)
plot(nnet, "2D", show.edge.label=TRUE)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.