ddtlcm (version 0.2.1)

proposal_log_prob: Calculate proposal likelihood

Description

Given an old tree, propose a new tree and calculate the original and proposal tree likelihood in the DDT process

Usage

proposal_log_prob(
  old_tree_phylo4,
  tree_kept,
  old_detach_pa_div_time,
  old_pa_detach_node_label,
  old_detach_node_label,
  new_div_time,
  new_attach_root,
  new_attach_to,
  c,
  c_order = 1
)

Value

a list containing the following elements:

q_new

a "phylo" tree detached from the input tree

q_old

the remaining "phylo" tree after detachment

Arguments

old_tree_phylo4

the old "phylo4" object

tree_kept

the remaining "phylo" tree after detachment

old_detach_pa_div_time

a number in (0, 1) indicating the divergence time of the detached node on the old tree

old_pa_detach_node_label

a character label of the parent of the detached node on the old tree

old_detach_node_label

a character label of the detached node on the old tree

new_div_time

a number in (0, 1) indicating the divergence time at which the detached subtree will be re-attached on the proposal tree

new_attach_root, new_attach_to

a character label of the starting and ending nodes of the branch on the proposal tree, which the detached subtree will be re-attached to

c

hyparameter of divergence function a(t)

c_order

equals 1 (default) or 2 to choose divergence function