get_tree_span {castor} | R Documentation |
Given a rooted phylogenetic tree, calculate the minimum and maximum phylogenetic distance (cumulative branch length) of any tip from the root.
get_tree_span(tree, as_edge_count=FALSE)
tree |
A rooted tree of class "phylo". The root is assumed to be the unique node with no incoming edge. |
as_edge_count |
Logical, specifying whether distances should be counted in number of edges, rather than cumulative edge length. This is the same as if all edges had length 1. |
If tree$edge.length
is missing, then every edge in the tree is assumed to be of length 1. The tree may include multi-furcations as well as mono-furcations (i.e. nodes with only one child).
The asymptotic average time complexity of this function is O(Nedges), where Nedges is the number of edges in the tree.
A named list with the following elements:
min_distance |
Minimum phylogenetic distance that any of the tips has to the root. |
max_distance |
Maximum phylogenetic distance that any of the tips has to the root. |
Stilianos Louca
# generate a random tree Ntips = 1000 params = list(birth_rate_intercept=1, death_rate_intercept=0.5) tree = generate_random_tree(params, max_tips=Ntips, coalescent=FALSE)$tree # calculate min & max tip distances from root tree_span = get_tree_span(tree) cat(sprintf("Tip min dist = %g, max dist = %g\n", tree_span$min_distance, tree_span$max_distance))