build_coal_tree.structured: Generate a Newick string representation of a tree...

In dhelekal/CaveDive: Phylodynamics for Clonal Expansion

Generate a Newick string representation of a tree corresponding to a realisation of a structured,linage-based coalescent process. Note: the topology is RANDOM, If you wish for the topology to be consistent, use set.seed before calling this function.

Description

Generate a Newick string representation of a tree corresponding to a realisation of a structured,linage-based coalescent process. Note: the topology is RANDOM, If you wish for the topology to be consistent, use set.seed before calling this function.

Usage

build_coal_tree.structured(
  sampling_times,
  coalescent_times,
  leaf_colours,
  coalescent_colours,
  div_times,
  div_events,
  div_from
)

Arguments

sampling_times	times of leaves.
coalescent_times	times of coalescent events / internal nodes.
leaf_colours	leaf colouring
coalescent_colours	a numeric vector where number at j-th position indicates that the j-th coalescent event corresponds to j-th lineage.
div_times	times of lineage divergence events.
div_events	a numeric vector where number at j-th position indicates that the j-th divergence time corresponds to j-th lineage
div_from	numeric vector identifying the parent of the j-th diverging lineage

Value

a list with the Newick string corresponding to the tree, and a list of leaf colouring assignments

dhelekal/CaveDive documentation built on June 11, 2024, 4:32 p.m.