simulate_expansion_phylo: A phylogeny containing clonal expansions. Note: The resulting...

In dhelekal/CaveDive: Phylodynamics for Clonal Expansion

A phylogeny containing clonal expansions. Note: The resulting phylogeny contains single child nodes denoting divergence events. use 'collapse.singles' to remove these.

Description

A phylogeny containing clonal expansions. Note: The resulting phylogeny contains single child nodes denoting divergence events. use 'collapse.singles' to remove these.

Usage

simulate_expansion_phylo(
  priors,
  sampling_times,
  concentration = 2,
  given = list(),
  collapse_singles = FALSE
)

Arguments

priors	List of priors to simulate parameters from. See 'standard priors' for details
sampling_times	Vector sampling times, entries must be negative or 0
concentration	Scalar concentration hyperparameter for dirichlet expansion model
given	A list of variables with values given. Supported names: 'n_exp' - number of expansions, 'tip_colours' - tip expansion assignment, N' - Background population size, 'K' - Expansion carrying capacities, 't_mid' - Expansion times to midpoints, 'div_times' - Expansion divergence times, 'div_from' - parent lineages
collapse_singles	Whether to remove (collapse) divergence event nodes. Default: FALSE

Value

list of: 'tree' - The simulated genealogy, 'params' - the simulated parameters for the process

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