Compare splits and add support values to an object

Add support values to a splits, phylo or networx object.

Usage

addConfidences(x, y, ...)

# S3 method for class 'phylo'
addConfidences(x, y, rooted = FALSE, ...)

presenceAbsence(x, y)

createLabel(x, y, label_y, type = "edge", nomatch = NA)

Arguments

x

an object of class splits, phylo or networx

y

an object of class splits, phylo, multiPhylo or networx

...

Further arguments passed to or from other methods.

rooted

logial, if FALSE bipartitions are considered, if TRUE clades.

label_y

label of y matched on x. Will be usually of length(as.splits(x)).

type

should labels returned for edges (in networx) or splits.

nomatch

default value if no match between x and y is found.

Value

The object x with added bootstrap / MCMC support values.

References

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

See also

as.splits, as.networx, RF.dist, plot.phylo

Author

Klaus Schliep klaus.schliep@gmail.com

Examples

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, show.edge.label=TRUE)