Claddis (version 0.3.4)

EdgeLengthsInBins: Edge-lengths present in time-bins

Description

Given a time-scaled tree and set of time bin boundaries will sum the edge-lengths present in each bin.

Usage

EdgeLengthsInBins(tree, time.bins, pruned.tree = NULL)

Arguments

tree

A time-scaled tree in phylo format with a $root.time value.

time.bins

A vector of ages in millions of years of time bin boundaries in old-to-young order.

pruned.tree

A time-scaled tree in phylo format with a $root.time value that is a subset of tree.

Value

edge.length.in.bin

A vector giving the summed values in millions of years for each time bin. Names indicate the maximum and minimum values for each time bin.

terminal.edge.length.in.bin

As above, but counting terminal edges only.

internal.edge.length.in.bin

As above, but counting internal edges only.

Details

Calculates the total edge length present in each of a series of time bins. This is intended as an internal function for rate calculations, but may be of use to someone.

The option of using a pruned.tree allows the user to correctly classify internal and terminal branches in a subtree of the larger tree. So for example, if taxa A and B are sisters then after pruning B the subtree branch leading to A is composed of an internal and a terminal branch on the complete tree.

Examples

# NOT RUN {
# Create a random 10-taxon tree:
tree <- rtree(10)

# Add root age:
tree$root.time <- 100

# Create time bins:
time.bins <- seq(100, 0, length.out = 11)

# Get edge lengths for each bin:
EdgeLengthsInBins(tree, time.bins)

# }