expansions_infer: Run rjmcmc inference on the provided preprocessed phylogeny,...

In dhelekal/CaveDive: Phylodynamics for Clonal Expansion

Run rjmcmc inference on the provided preprocessed phylogeny, and using provided prior distributions This is a barebones method for advanced usage. For standard usage refer to 'run_expansion_inference'

Description

Run rjmcmc inference on the provided preprocessed phylogeny, and using provided prior distributions This is a barebones method for advanced usage. For standard usage refer to 'run_expansion_inference'

Usage

expansions_infer(
  pre,
  prior_i,
  prior_N,
  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,
  concentration,
  n_it = 1e+06,
  thinning = 1,
  init = NULL,
  debug = FALSE
)

Arguments

pre	Preprocessed phylogeny
prior_i	Prior likelihood on number of expansions
prior_N	Prior likelihood on background population size
prior_t_mid_given_N	Prior likelihood on expansion time to midpoint given background population size
prior_t_mid_given_N.sample	Sampling function for prior on time to midpoint given background population size
prior_t_given_N	Prior likelihood on expansion time given background population size
prior_t_given_N.sample	Sampling function for prior on expansion timegiven background population size
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
debug	debug flag
prior_K_mid_given_N	Prior likelihood on expansion carrying capacity given background population size
prior_K_mid_given_N.sample	Sampling function for prior on expansion carrying capacity given background population size

Value

a list of MCMC states

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