R/starts.R

In wlandau/fbseq: fbseq

#' @title Class \code{Starts}
#' @description Set MCMC starting values and model constants listed
#' by \code{help("Starts-class")}.
#' @exportClass Starts
#' 
#' @slot a initialization constant  
#' @slot b initialization constant 
#' @slot c initialization constants 
#' @slot d initialization constant 
#' @slot h initialization constants 
#' @slot k initialization constants 
#' @slot q initialization constants 
#' @slot r initialization constants 
#' @slot s initialization constants 
#' 
#' @slot beta MCMC starting values
#' @slot epsilon MCMC starting values
#' @slot gamma MCMC starting values
#' @slot nu MCMC starting values
#' @slot sigmaSquared MCMC starting values
#' @slot tau MCMC starting values
#' @slot theta MCMC starting values
#' @slot xi MCMC starting values
setClass("Starts", 
  slots = list(
    a = "numeric",
    b = "numeric",
    c = "numeric",
    d = "numeric",
    h = "numeric",
    k = "numeric",
    q = "numeric",
    r = "numeric",
    s = "numeric",

    beta = "numeric",
    epsilon = "numeric",
    gamma = "numeric",
    nu = "numeric",
    sigmaSquared = "numeric",
    tau = "numeric",
    theta = "numeric",
    xi = "numeric"
  ),

  prototype = list(
    a = 1,
    b = 1,
    c = 10,
    d = 1000,
    k = 1,
    q = 3,
    r = 2,
    s = 100
  )
)

#' @title Constructor for class \code{Starts}
#' @description Create a \code{Starts} from a \code{Chain} object or by
#' setting individual slots.
#' @seealso \code{help("Starts-class")}
#' @export
#' @param obj a \code{Chain} or \code{list} object to get slots from.
#' @param ... additional slots.
Starts = function(obj = NULL, ...){
  starts = new("Starts", ...)

  if(class(obj) == "list") {
    for(n in slotNames(starts)){
      x = paste(n, "Start", sep = "")
      if(x %in% names(obj) && n %in% slotNames(starts))
        slot(starts, n) = as(obj[[x]], class(slot(starts, n)))
      else if(n %in% intersect(names(obj), slotNames(starts)))
        slot(starts, n) = as(obj[[n]], class(slot(starts, n)))
    }
  } else if(class(obj) == "Chain") {
    for(n in slotNames(starts)){
      x = paste(n, "Start", sep = "")
      if(x %in% slotNames(obj) && n %in% slotNames(starts))
        slot(starts, n) = as(slot(obj, x), class(slot(starts, n)))
      else if(n %in% intersect(slotNames(obj), slotNames(starts)))
        slot(starts, n) = as(slot(obj, n), class(slot(starts, n)))
    }
  }

  starts
}