paleotree (version 3.1.3)

minBranchLength: Scales Edge Lengths of a Phylogeny to a Minimum Branch Length

Description

Rescales a tree with edge lengths so that all edge lengths are at least some minimum branch length (mbl), without changing the relative distance of the tips from the root node. Edge lengths are transformed so they are greater than or equal to the input minimum branch length, by subtracting edge length from more rootward edges and added to later branches.

Usage

minBranchLength(tree, mbl)

Arguments

tree

A phylogeny with edge lengths of class 'phylo'.

mbl

The minimum branch length

Value

A phylogeny with edge lengths of class 'phylo'.

Details

This function was formally an internal segment in timePaleoPhy, and now is called by timePaleoPhy instead, allowing users to apply minBranchLength to trees that already have edge lengths.

See Also

This function was originally an internal piece of timePaleoPhy, which implements the minimum branch length time-scaling method along with others, which may be what you're looking for (instead of this miscellaneous function).

Examples

# NOT RUN {
#simulation with an example non-ultrametric tree

tree <- rtree(20)
# randomly replace edges with ZLBs, similar to multi2di output
tree <- degradeTree(tree,0.3,leave.zlb = TRUE) 	

tree2 <- minBranchLength(tree,0.1)

layout(1:2)
plot(tree);axisPhylo()
plot(tree2);axisPhylo()

layout(1)

#now let's try it with an ultrametric case

# get a random tree
tree <- rtree(30)
# randomly replace edges with ZLBs, similar to multi2di output
tree <- degradeTree(tree,0.5,leave.zlb = TRUE) 
# now randomly resolve	
tree <- di2multi(tree)
# give branch lengths so its ultrametric
tree <- compute.brlen(tree)

plot(tree) #and we have an ultrametric tree with polytomies, yay!

#now randomly resolve, get new branch lengths as would with real data
tree2 <- multi2di(tree)
tree2 <- minBranchLength(tree2,0.1)

layout(1:2)
plot(tree,show.tip.label = FALSE);axisPhylo()
plot(tree2,show.tip.label = FALSE);axisPhylo()

layout(1)
# }