attach_subtree {ddtlcm}

Attach a subtree to a given DDT at a randomly selected location

Description

Attach a subtree to a given DDT at a randomly selected location

Usage

attach_subtree(
  subtree,
  tree_kept,
  detach_div_time,
  pa_detach_node_label,
  c,
  c_order = 1,
  theta = 0,
  alpha = 0
)

Arguments

subtree

subtree to attach to tree_kept

tree_kept

the tree to be attached to

detach_div_time

divergence time of subtree when it was extracted from the original tree

pa_detach_node_label

label of the parent node of the detached node

c

hyparameter of divergence function a(t)

c_order

equals 1 (default) or 2 to choose divergence function

alpha, theta

hyparameter of branching probability a(t) Gamma(m-alpha) / Gamma(m+1+theta) For DDT, alpha = theta = 0. For general multifurcating tree from a Pitman-Yor process, specify positive values to alpha and theta. It is, however, recommended using alpha = theta = 0 in inference because multifurcating trees have not been tested rigorously.

See Also

Other sample trees: random_detach_subtree(), reattach_point()