bin_edge_lengths {Claddis} | R Documentation |
Given a time-scaled tree and set of time bin boundaries will sum the edge-lengths present in each bin.
bin_edge_lengths(time_tree, time_bins, pruned_tree = NULL)
time_tree |
A time-scaled tree in phylo format with a |
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 |
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.
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. |
Graeme T. Lloyd graemetlloyd@gmail.com
# Create a random 10-taxon tree: time_tree <- ape::rtree(n = 10) # Add root age: time_tree$root.time <- max(diag(ape::vcv(time_tree))) # Create time bins: time_bins <- seq(from = time_tree$root.time, to = 0, length.out = 11) # Get edge lengths for each bin: bin_edge_lengths(time_tree = time_tree, time_bins = time_bins)