simulate_clonal_tree: Simulate an instance of coalescent process with local...

In dhelekal/CaveDive: Phylodynamics for Clonal Expansion

Simulate an instance of coalescent process with local population structure

Description

Simulate an instance of coalescent process with local population structure

Usage

simulate_clonal_tree(
  n_exp,
  N,
  K,
  A,
  sampling_times,
  tip_colours,
  div_times,
  div_cols,
  div_from = NA
)

Arguments

n_exp	number of expansions
N	background population size
K	carrying capacities
A	growth rates
sampling_times	sampling times
tip_colours	tip clade assignment
div_times	clade divergence times
div_cols	vector of colours ordered in sequence
div_from	(optional) parent populations for individual clades. If NA will be randomised equiprobably.

Value

list of: 'co' - list containing event times, event colour assignment and parents of clonal expansions; log_lh: the log likelihood

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