standard_priors: Generates a list of priors of the form described in the paper...

In dhelekal/CaveDive: Phylodynamics for Clonal Expansion

Generates a list of priors of the form described in the paper to use with MCMC inference.

Description

Generates a list of priors of the form described in the paper to use with MCMC inference.

Usage

standard_priors(
  expansion_rate = 1,
  N_mean_log = 3,
  N_sd_log = 3,
  t_mid_rate = 5,
  K_sd_log = 1/2,
  exp_time_nu = 1/2,
  exp_time_kappa = 1/2
)

Arguments

expansion_rate	corresponds to 'phi' in paper
N_mean_log	corresponds to 'mu_anc' in paper
N_sd_log	corresponds to 'sigma_anc' in paper
t_mid_rate	corresponds to 'lambda_r' in paper
K_sd_log	corresponds to 'sigma_exp' in paper
exp_time_nu	corresponds to 'nu' in paper
exp_time_kappa	corresponds to 'kappa' in paper

Value

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.

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