run_metrop_priors {cophescan}

Run the hierarchical Metropolis Hastings model to infer priors

Description

Run the hierarchical Metropolis Hastings model to infer priors

Usage

run_metrop_priors(
  multi.dat,
  covar = FALSE,
  covar_vec = NULL,
  is_covar_categorical = FALSE,
  nits = 10000,
  thin = 1,
  posterior = FALSE,
  avg_pik = TRUE,
  avg_posterior = TRUE,
  pik = FALSE,
  alpha_mean = -10,
  alpha_sd = 0.5,
  beta_shape = 2,
  beta_scale = 2,
  gamma_shape = 2,
  gamma_scale = 2
)

Arguments

multi.dat

matrix of bf values, rows=traits, named columns=("lBF.Ha","lBF.Hc","nsnps")

covar

whether to include covariates

covar_vec

vector of covariates

is_covar_categorical

only two categories supported (default=FALSE) - Experimental

nits

number of iterations

thin

burnin

posterior

default: FALSE, estimate posterior probabilities of the hypotheses

avg_pik

default: FALSE, estimate the average of the pik

avg_posterior

default: FALSE, estimate the average of the posterior probabilities of the hypotheses

pik

default: FALSE, inferred prior probabilities

alpha_mean

prior for the mean of alpha

alpha_sd

prior for the standard deviation of alpha

beta_shape

prior for the shape (gamma distibution) of beta

beta_scale

prior for the scale of beta

gamma_shape

prior for the shape (gamma distibution) of gamma

gamma_scale

prior for the scale of gamma

Value

List containing the posterior distribution of the parameters alpha, beta, gamma (if covariate included) and the loglikelihood

if avg_posterior=TRUE matrix with average of all the posterior probabilities of Hn, Ha and Hc

if avg_pik=TRUE matrix with average of all the priors: pn, pa and pc

data, nits and thin contain the input data, number of iterations and burnin respectively specified for the hierarchical model