R/two_source_priors_ar.R

In trps: Bayesian Trophic Position Models using 'stan'

#' Bayesian priors - Two Source Trophic Position with \eqn{\alpha_r}
#'
#' Create priors for trophic position using a two source model
#' with \eqn{\alpha_r} derived from [Post 2002](https://esajournals.onlinelibrary.wiley.com/doi/full/10.1890/0012-9658%282002%29083%5B0703%3AUSITET%5D2.0.CO%3B2)
#' and Heuvel et al. (2024) \doi{doi:10.1139/cjfas-2024-0028}.
#'
#' @param bp logical value that controls whether informed priors are
#' supplied to the model for  \eqn{\delta^{15}}N baselines.
#' Default is `FALSE` meaning the model will
#' use uninformed priors, however, the supplied `data.frame` needs values
#' for both \eqn{\delta^{15}}N baseline
#' (`n1`, and `n2`).
#'
#' @return returns priors for two source model to be used in a `brms()` call.
#'
#' @seealso [brms::brms()]
#' @examples
#' two_source_priors_ar()
#'
#' @import brms
#' @export

two_source_priors_ar <- function(bp = FALSE) {

  if (!(is.logical(bp))) {

    cli::cli_abort(c(
      "`bp` argument must be a logical value",
      "i" = "Please provide TRUE or FALSE"
    ))
  }


  if (isFALSE(bp)) {

    #  set priors
    priors <- c(

      # alpha priors

      brms::prior(beta(a, b), lb = 0, ub = 1, resp = "alpha", nlpar = "ar"),
      brms::prior(beta(a, b), lb = 0, ub = 1, resp = "d15n", nlpar = "ar"),
      # Trophic enrichment factor (ΔN)
      brms::prior(normal(dn, dn_sigma), resp = "d15n", nlpar = "dn"),
      # Trophic Position (tp)
      brms::prior(uniform(tp_lb, tp_ub), lb = tp_lb, ub = tp_ub, resp = "d15n",
                  nlpar = "tp"),
      # Standard deviation prior
      brms::prior(uniform(sigma_lb, sigma_ub), resp = "alpha",
                  class = "sigma", ub = sigma_ub),
      brms::prior(uniform(sigma_lb, sigma_ub), resp = "d15n",
                  class = "sigma", ub = sigma_ub)
    )
  }

  if (isTRUE(bp)) {
    #  set priors
    priors <- c(
         # alpha priors

      brms::prior(beta(a, b), lb = 0, ub = 1, resp = "alpha", nlpar = "ar"),
      brms::prior(beta(a, b), lb = 0, ub = 1, resp = "d15n", nlpar = "ar"),

      # Baseline 1 δ15N (n1)
      brms::prior(normal(n1, n1_sigma), resp = "d15n",
                  nlpar = "n1"),
      # Baseline 2 δ15N (n2)
      brms::prior(normal(n2, n2_sigma),  resp = "d15n",
                  nlpar = "n2"),
      # Trophic enrichment factor (ΔN)
      brms::prior(normal(dn, dn_sigma), resp = "d15n", nlpar = "dn"),
      # Trophic Position (tp)
      brms::prior(uniform(tp_lb, tp_ub), lb = tp_lb, ub = tp_ub, resp = "d15n",
                  nlpar = "tp"),
      # Standard deviation prior
      brms::prior(uniform(sigma_lb, sigma_ub), resp = "alpha",
                  class = "sigma", ub = sigma_ub),
      brms::prior(uniform(sigma_lb, sigma_ub), resp = "d15n",
                  class = "sigma", ub = sigma_ub)
    )
  }



  return(priors)
}