addConfidences: Compare splits and add support values to an object

In phangorn: Phylogenetic Reconstruction and Analysis

Compare splits and add support values to an object

Description

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.

Author(s)

Klaus Schliep [e-mail]

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

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)

phangorn documentation built on Jan. 23, 2023, 5:37 p.m.