R: Tree manipulation

getRoot {phangorn} | R Documentation

## Tree manipulation

### Description

`midpoint` performs midpoint rooting of a tree. `pruneTree` produces a consensus tree.

### Usage

    getRoot(tree)

    midpoint(tree, node.labels = "support", ...)

    ## S3 method for class 'phylo'
    midpoint(tree, node.labels = "support", ...)

    ## S3 method for class 'multiPhylo'
    midpoint(tree, node.labels = "support", ...)

    pruneTree(tree, ..., FUN = ">=")

### Arguments

`tree` | an object of class `phylo`
`node.labels` | are nodel labels 'support' values, 'label' or should be 'deleted'
`...` | further arguments, passed to other methods.
`FUN` | a function evaluated on the nodelabels, result must be logical.

### Details

`pruneTree` prunes back a tree and produces a consensus tree, for trees already containing nodelabels. It assumes that nodelabels are numerical or character that allows conversion to numerical, it uses as.numeric(as.character(tree$node.labels)) to convert them. `midpoint` so far does not transform node.labels properly.

### Value

`pruneTree` and `midpoint` a tree. `getRoot` returns the root node.

### Author(s)

Klaus Schliep klaus.schliep@gmail.com

### See Also

`consensus`, `root`, `multi2di`

### Examples

    tree <- rtree(10, rooted = FALSE)
    tree$node.label <- c("", round(runif(tree$Nnode-1), 3))

    tree2 <- midpoint(tree)
    tree3 <- pruneTree(tree, .5)

    old.par <- par(no.readonly = TRUE)
    par(mfrow = c(3,1))
    plot(tree, show.node.label=TRUE)
    plot(tree2, show.node.label=TRUE)
    plot(tree3, show.node.label=TRUE)
    par(old.par)

[Package phangorn version 2.6.2 Index]