R/prior_beta.R

In psborrow2: Bayesian Dynamic Borrowing Analysis and Simulation

#' `PriorBeta` Class
#'
#' A class for defining beta priors to be translated to Stan code.
#' Objects of class `PriorBeta` should not be created directly but by
#' the constructor [prior_beta()].
#'
#' @slot stan_code character. Stan implementation of the prior, with
#' placeholders for beta stan function parameters surrounded with
#' `{{` and `}}` to be replaced with [glue::glue()].
#' @slot n_param integer. Number of prior parameters (2).
#' @slot constraint character. Support of prior distribution,
#' `"<lower=0, upper=1>"`.
#' @slot alpha numeric. Shape (>=0).
#' @slot beta numeric. Shape (>=0).
#' @include prior_class.R
#' @family prior classes
.prior_beta <- setClass(
  "PriorBeta",
  contains = "Prior",
  slots = c(
    alpha = "numeric",
    beta = "numeric"
  ),
  prototype = list(
    n_param = 2L,
    stan_code = "beta({{object@alpha}}, {{object@beta}})",
    constraint = "<lower=0, upper=1>"
  ),
  validity = function(object) {
    if (object@alpha < 0 || object@beta < 0) {
      return("Both alpha and beta must be >= 0")
    }
    return(TRUE)
  }
)

#' Prior beta distribution
#'
#' @param alpha numeric. Shape (>=0).
#' @param beta numeric. Shape (>=0).
#'
#' @details
#' Stan reference <https://mc-stan.org/docs/functions-reference/beta-distribution.html>
#'
#' @return Object of class [`PriorBeta`][PriorBeta-class]
#' @export
#' @family priors
#' @examples
#' bp <- prior_beta(9, 235)
prior_beta <- function(alpha, beta) {
  .prior_beta(alpha = alpha, beta = beta)
}

# show ----
setMethod(
  f = "show",
  signature = "PriorBeta",
  definition = function(object) {
    cat("Beta Distribution\n")
    cat("Parameters:\n")
    print.data.frame(
      data.frame(
        Stan = c("alpha", "beta"),
        R = c("shape1", "shape2"),
        Value = c(object@alpha, object@beta)
      ),
      row.names = FALSE, right = FALSE
    )
    if (object@constraint != "") print(h_glue("Constraints: {{object@constraint}}"))
  }
)

# plot ----
#' @rdname plot
#' @examples
#' plot(prior_beta(2, 2))
setMethod(
  f = "plot",
  signature = c("PriorBeta", "missing"),
  definition = function(x, y, add = FALSE, ...) {
    limits <- c(0, 1)
    density_fun <- function(values) stats::dbeta(values, shape1 = x@alpha, shape2 = x@beta)
    dist_type <- "continuous"
    callNextMethod(default_limits = limits, density_fun = density_fun, dist_type = dist_type, add = add, ...)
  }
)


#' Legacy function for the beta prior
#'
#' Please use `prior_beta()` instead.
#' @param ... Deprecated arguments to `beta_prior()`.
#' 
#' @return
#' This function does not return a value. When called, it triggers an error 
#' message indicating that `beta_prior()` is deprecated and that 
#' `prior_beta()` should be used instead.
#' 
#' @export
beta_prior <- function(...) {
  .Defunct(
    "prior_beta",
    "psborrow2",
    "`beta_prior()` is deprecated. Use `prior_beta()` instead."
  )
}