extract_lineage_times: Extracts Lineage times (but faster) from a parent phylogeny...

In dhelekal/CaveDive: Phylodynamics for Clonal Expansion

Extracts Lineage times (but faster) from a parent phylogeny based on provided divergence MRCA nodes and times.

Description

Extracts Lineage times (but faster) from a parent phylogeny based on provided divergence MRCA nodes and times.

Usage

extract_lineage_times(
  phylo.preprocessed,
  div.MRCA.nodes,
  div_times,
  return_partitions = FALSE
)

Arguments

phylo.preprocessed	preprocessed phylogeny
div.MRCA.nodes	labels of MRCA nodes of diverging lineages
div_times	absolute divergence times
return_partitions	if true, return a list named 'partitions' containing tip labels for each partition

Value

A list containing lists of sampling time vectors sam.times and coalescent time vectors coal.times for each lineage.

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