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 visualization. It supports transformation for specific parameter types: rho, alpha, omega, and beta.

Usage

Coda_to_tibble(CodaObj = NULL, Type = NULL, EnvFile = ".env", NOmega = 100)

Arguments

CodaObj: An object of class mcmc.list or mcmc, representing the MCMC output.
Type: Character. The parameter type to transform and extract. Must be one of rho, alpha, omega, or beta.
EnvFile: Character. Path to the environment file containing paths to data sources. Defaults to .env.
NOmega: 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 Type. The structure of the returned tibble varies depending on the Type parameter.

Author

Ahmed El-Gabbas

Examples

library(Hmsc)
#> Loading required package: coda
library(coda)
library(dplyr)
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:raster’:
#> 
#>     intersect, select, union
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union
Coda <- Hmsc::convertToCodaObject(Hmsc::TD$m)
IASDT.R::Coda_to_tibble(CodaObj = Coda$Alpha[[1]], Type = "Alpha")
#> # A tibble: 400 × 6
#>    Alpha           AlphaNum Factor  Chain  Iter Value
#>    <fct>           <fct>    <fct>   <fct> <int> <dbl>
#>  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
#>  6 Alpha1[factor1] Alpha1   factor1 1        56     0
#>  7 Alpha1[factor1] Alpha1   factor1 1        57     0
#>  8 Alpha1[factor1] Alpha1   factor1 1        58     0
#>  9 Alpha1[factor1] Alpha1   factor1 1        59     0
#> 10 Alpha1[factor1] Alpha1   factor1 1        60     0
#> # ℹ 390 more rows