Claddis (version 0.7.0)

bin_edge_lengths: 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

bin_edge_lengths(time_tree, time_bins, pruned_tree = NULL)

Value

binned_edge_lengths

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.

binned_terminal_edge_lengths

As above, but counting terminal edges only.

binned_internal_edge_lengths

As above, but counting internal edges only.

Arguments

time_tree

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

time_bins

An object of class timeBins.

pruned_tree

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

Author

Graeme T. Lloyd

Details

Calculates the total edge duration of a time-scaled tree present in 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

# Create a random 10-taxon tree:
time_tree <- ape::rtree(n = 10)

# Add root age:
time_tree$root.time <- max(diag(ape::vcv(time_tree)))

# Create time bins:
time_bins <- matrix(data = c(seq(from = time_tree$root.time, to = 0,
  length.out = 11)[1:10], seq(from = time_tree$root.time, to = 0,
  length.out = 11)[2:11]), ncol = 2, dimnames = list(LETTERS[1:10],
  c("fad", "lad")))

# Set class:
class(time_bins) <- "timeBins"

# Get edge lengths for each bin:
bin_edge_lengths(time_tree = time_tree, time_bins = time_bins)