slide.nodes: Stretching a tree

In TGuillerme/dispRity: Measuring Disparity

Stretching a tree

Description

Stretches a phylogenetic tree at a particular node

Usage

slide.nodes(nodes, tree, slide, allow.negative.root = FALSE)

Arguments

nodes	A list of the ID nodes to slide ("integer") or names ("character"). The first node is ape::Ntip(tree) + 1, etc.
tree	a "phylo" object.
slide	the sliding value.
allow.negative.root	logical, whether to allow negative branch lengths and moving the root node (TRUE) or not (FALSE; default).

Details

The sliding works by subtracting the slide value to the branch leading to the node and adding it to the descendant branches. Note that the slide value can be negative to slide nodes the other way (up); the only requirement is that the slide does not lead to negative branch length values.

Value

A "phylo" object.

Author(s)

Thomas Guillerme

See Also

remove.zero.brlen

Examples

set.seed(42)
## Generating a coalescent tree
tree <- rcoal(5)

## Stretching node 8 up and down
tree_slide_up <- slide.nodes(8, tree, slide = 0.075)
tree_slide_down <- slide.nodes(8, tree, slide = -0.075)

## Display the results
par(mfrow = c(3,1))
plot(tree) ; axisPhylo() ; nodelabels()
plot(tree_slide_up) ; axisPhylo() ; nodelabels()
plot(tree_slide_down) ; axisPhylo() ; nodelabels()

## Stretching many nodes
set.seed(42)
tree <- rtree(50)
move_nodes <- c(99, 93, 53, 86, 58, 63, 60, 84)
tree_slided <- slide.nodes(move_nodes, tree, slide = 0.07)

## Display the results
par(mfrow = c(2, 1))
node_colors <- c("lightblue", "orange")[((1:Nnode(tree))+Ntip(tree)) %in% move_nodes + 1]
plot(tree, show.tip.label = FALSE) ; axisPhylo()
nodelabels(bg = node_colors, cex = 0.5)
plot(tree_slided, show.tip.label = FALSE) ; axisPhylo()
nodelabels(bg = node_colors, cex = 0.5)

TGuillerme/dispRity documentation built on Dec. 21, 2024, 4:05 a.m.