treestats (version 1.70.5)

make_unbalanced_tree: Stepwise increase the imbalance of a tree

Description

the goal of this function is to increasingly imbalance a tree, by changing the topology, one move at a time. It does so by re-attaching terminal branches to the root lineage, through the ltable. In effect, this causes the tree to become increasingly caterpillarlike. When started with a balanced tree, this allows for exploring the gradient between a fully balanced tree, and a fully unbalanced tree. Please note that the algorithm will try to increase imbalance, until a fully caterpillar like tree is reached, which may occur before unbal_steps is reached. Three methods are available: "youngest", reattaches branches in order of age, starting with the branch originating from the most recent branching event and working itself through the tree. "Random" picks a random branch to reattach. "Terminal" also picks a random branch, but only from terminal branches (e.g. branches that don't have any daughter lineages, which is maximized in a fully imbalanced tree).

Usage

make_unbalanced_tree(
  init_tree,
  unbal_steps,
  group_method = "any",
  selection_method = "random"
)

Value

phylo object

Arguments

init_tree

starting tree to work with

unbal_steps

number of imbalance generating steps

group_method

choice of "any" and "terminal"

selection_method

choice of "random", "youngest" and "oldest"

Examples

simulated_tree <- ape::rphylo(n = 16, birth = 1, death = 0)
balanced_tree <- treestats::create_fully_balanced_tree(simulated_tree)
unbalanced_tree <- treestats::create_fully_unbalanced_tree(simulated_tree)
intermediate_tree <- make_unbalanced_tree(balanced_tree, 8)
colless(balanced_tree)
colless(intermediate_tree) # should be intermediate value
colless(unbalanced_tree) # should be highest colless value