remove.zero.brlen {dispRity}

Remove zero branch length

Description

Remove zero or negative branch lengths on trees by sliding nodes randomly in a postorder traversal based on slide.nodes.

Usage

remove.zero.brlen(tree, slide, verbose = FALSE)

Arguments

tree

A "phylo" or "multiPhylo" object with edge lengths

slide

An optional sliding numeric values. If left empty, 1% of the shortest branch length is used.

verbose

A logical value indicating whether to be verbose or not.

Details

The sliding value will be used to slide the nodes up and down to remove zero branch lengths by minimising the amount of branch changes. The algorithm slides the nodes up and down (when possible) on each node in a recursive way while there is still zero or negative branch lengths. If two recursions produce the same series of zero branches (e.g. by sliding node A towards node B equally so that the distance A:B becomes 0), the sliding value is divided by two until the next slide.

Value

A "phylo" object with a postorder edge table and no zero branch lengths.

Author(s)

Thomas Guillerme

See Also

slide.nodes

Examples

set.seed(42)
## Generating a tree
tree <- rtree(20)
## Adding some zero branch lengths (5)
tree$edge.length[sample(1:Nedge(tree), 5)] <- 0
any(tree$edge.length == 0) # TRUE

## And now removing these zero branch lengths!
tree_no_zero <- remove.zero.brlen(tree)
any(tree_no_zero$edge.length == 0) # FALSE

## Exaggerating the removal (to make it visible)
tree_exaggerated <- remove.zero.brlen(tree, slide = 1)

## Plot the differences
par(mfrow = c(3,1))
plot(tree, main = "zero branch length")
plot(tree_no_zero, main = "no zero branch length")
plot(tree_exaggerated, main = "exaggerated slidding")

## Removing negative branch lengths
## Generating a tree with negative branch length
set.seed(3)
tree_negative <- chronoMPL(rtree(10))
## Removing the negative branch length (and make it non-zero)
tree_positive <- remove.zero.brlen(tree_negative)
## Plot the differences
par(mfrow = c(2, 1))
plot(tree_negative, main = "Negative branch lengths")
plot(tree_positive, main = "Positive branch lengths")