Convert a Coda object to a tibble with specified parameter transformations

This function converts a Coda object (mcmc.list or mcmc) into a tibble format, facilitating further analysis and visualisation. It supports transformation for specific parameter types: rho, alpha, omega, and beta.

Usage

coda_to_tibble(
  coda_object = NULL,
  posterior_type = NULL,
  env_file = ".env",
  n_omega = 100
)

Arguments

coda_object

An object of class mcmc.list or mcmc, representing the MCMC output.

posterior_type

Character. The parameter type to transform and extract. Must be one of rho, alpha, omega, or beta.

env_file

Character. Path to the environment file containing paths to data sources. Defaults to .env.

n_omega

Integer. The number of species to be sampled for the Omega parameter transformation. Defaults to 100.

Value

A tibble containing the transformed parameters based on the specified posterior_type. The structure of the returned tibble varies depending on the posterior_type parameter.

Author

Ahmed El-Gabbas

Examples

ecokit::load_packages(Hmsc, coda, dplyr)

coda_object <- Hmsc::convertToCodaObject(Hmsc::TD$m)
ecokit::ht(
  IASDT.R::coda_to_tibble(
    coda_object = coda_object$Alpha[[1]], posterior_type = "Alpha"))
#>                Alpha AlphaNum  Factor  Chain  Iter Value
#>               <fctr>   <fctr>  <fctr> <fctr> <int> <num>
#>   1: Alpha1[factor1]   Alpha1 factor1      1    51     0
#>   2: Alpha1[factor1]   Alpha1 factor1      1    52     0
#>   3: Alpha1[factor1]   Alpha1 factor1      1    53     0
#>   4: Alpha1[factor1]   Alpha1 factor1      1    54     0
#>   5: Alpha1[factor1]   Alpha1 factor1      1    55     0
#>  ---                                                    
#> 396: Alpha1[factor2]   Alpha1 factor2      2   146     0
#> 397: Alpha1[factor2]   Alpha1 factor2      2   147     0
#> 398: Alpha1[factor2]   Alpha1 factor2      2   148     0
#> 399: Alpha1[factor2]   Alpha1 factor2      2   149     0
#> 400: Alpha1[factor2]   Alpha1 factor2      2   150     0