R: Compare splits and add support values to an object

createLabel {phangorn} | R Documentation

## Compare splits and add support values to an object

### Description

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

### Usage

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

    addConfidences(x, y, ...)

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

    presenceAbsence(x, y)

### Arguments

`x` | an object of class `splits`, `phylo` or `networx`
`y` | an object of class `splits`, `phylo`, `multiPhylo` or `networx`
`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.
`...` | Further arguments passed to or from other methods.

### Value

The object `x` with added bootstrap / MCMC support values.

### Author(s)

Klaus Schliep klaus.schliep@gmail.com

### 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, "2D", show.edge.label=TRUE)

[Package phangorn version 2.6.2 Index]