run_expansion_inference: Run rjmcmc inference on the provided phylogeny and supplied...

In dhelekal/CaveDive: Phylodynamics for Clonal Expansion

Run rjmcmc inference on the provided phylogeny and supplied priors This is the standard method for mcmc expansion inference.

Description

Run rjmcmc inference on the provided phylogeny and supplied priors This is the standard method for mcmc expansion inference.

Usage

run_expansion_inference(
  phy,
  priors,
  concentration = 1,
  n_it = 1e+06,
  thinning = 1,
  init = NULL
)

Arguments

phy	phylogeny to run inference on
priors	a list of prior likelihoods and sampling functions with names 'prior_i', 'prior_i.sample', 'prior_N', 'prior_N.sample', 'prior_t_mid_given_N', 'prior_t_mid_given_N.sample', 'prior_K_given_N', 'prior_K_given_N.sample', 'prior_t_given_N', 'prior_t_given_N.sample'. See 'standard_priors' for details.
concentration	concentration parameter for the dirichlet prior on expansion membership probabilities
n_it	number of MCMC iterations
thinning	mcmc output thinning
init	initial state for the mcmc chain

Value

list with names 'phylo_preprocessed', the preprocessed phylogeny, and 'mcmc_out' a list of MCMC states

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