old_files/class-skrmdb.r

In ABS-dev/skrmdb: Package to estimate ED50

#' @title Class definition for skrmdb object
#' @description The skrmdb object holds output from functions in the skrmdb
#'   package.
#' @details
#'
#' \describe{
#'
#' \item{\code{eval}}{Evaluation method. One of 'ReedMuench', 'SpearKarb', or
#' 'DragBehr'. Character string.}
#'
#' \item{\code{ed}}{Median effective dose by eval method. Numeric.}
#'
#' }
#' @name skrmdb-class
#' @rdname skrmdb-class
#' @exportClass skrmdb
#' @seealso \code{\link{sk-class}}
#' @author \link{skrmdb-package}
#' @examples
#' new("skrmdb", ed = 2.906593, eval = "DragBehr")
#' @importFrom methods setRefClass
skrmdb <- setRefClass("skrmdb",
                      fields = list(ed = "numeric",
                                    eval = "character"),
                      methods = list(initialize = function(ed = numeric(),
                                                           eval = character()) {
                        initFields(ed = ed, eval = eval)
                      },
                      print = function() {
                        if (length(.self$ed) == 0) {
                          cat("empty construct\n")
                        } else {
                          cat(paste0("ED50 by method ", .self$eval, "\n"))
                          cat(.self$ed, "\n")
                        }
                      }
                      ))

#' @importFrom methods setMethod
setMethod("show", "skrmdb",
          function(object) {
            object$print()
          })

#' @importFrom methods setMethod
setMethod("print", "skrmdb",
          function(x, ...) {
            x$print()
          })

#' @name getED
#' @title Accessor to retrieve the numeric median effective dose from a skrmdb
#'   or sk object
#' @description This is an accessor function for retrieving the numeric value of
#'   effective from a skrmdb or sk data object object generated by ReedMuench,
#'   SpearKarb or DragBehr
#' @param object class skrmdb or sk
#' @docType methods
#' @rdname getED-methods
#' @export
#' @seealso \code{\link{skrmdb-class}}, \code{\link{sk-class}}
#' @author \link{skrmdb-package}
#' @examples
#' ## with an object of class skrmdb
#' temp1 <- DragBehr(y = c(0, 3, 5, 8, 10, 10),
#'                   n = rep(10, 6),
#'                   x = 1:6)
#' getED(temp1)
#' ##  with an object of class sk
#' X <- data.frame(dead = c(0, 3, 5, 8, 10),
#'                 total = rep(10, 5),
#'                 dil = 1:5)
#'
#' temp2 <- SpearKarb(cbind(dead, total) ~ dil, X)
#' getED(temp2)
#' @importFrom methods setGeneric
setGeneric(name = "getED",
           def = function(object) {
             standardGeneric("getED")
           })

#' @rdname getED-methods
#' @aliases getED, skrmdb-method
#' @importFrom methods setMethod
setMethod("getED", "skrmdb",
          function(object) {
            return(as.numeric(object$ed))
          })

#' @title Class definition for sk object
#' @description The sk object holds values for the Spear Karb estimator for
#'   median estimated dose. It extends the skrmdb data object with value for
#'   variance.
#' @details
#'
#' \describe{
#'
#' \item{\code{eval}}{Evaluation method. "SpearKarb". Character string.}
#'
#' \item{\code{ed}}{Median effective dose by eval method. Numeric.}
#'
#' \item{\code{sk.var}}{variance. Numeric.}
#'
#' }
#' @name sk-class
#' @rdname sk-class
#' @exportClass sk
#' @seealso \code{\link{skrmdb-class}}
#' @author \link{skrmdb-package}
#' @examples
#' new('sk', sk.var = 0.06888889, ed = 2.9, eval = "SpearKarb")
#' @importFrom methods setRefClass
sk <- setRefClass("sk",
                  contains = "skrmdb",
                  fields = list(sk.var = "numeric"),
                  methods = list(
                    initialize = function(ed = numeric(),
                                          eval = "SpearKarb",
                                          sk.var = numeric()) {
                      if (eval != "SpearKarb") {
                        stop("[sk: validation] the estimator",
                             "must be \"SpearKarb\"")
                      } else {
                        initFields(ed = ed, eval = eval, sk.var = sk.var)
                      }
                    },
                    print = function() {
                      if (length(.self$ed) == 0) {
                        cat("Empty Construct\n")
                      } else {
                        cat(paste0("ED50 by method ", .self$eval, "\n"))
                        cat(paste("ed: ", ed = getED(.self), "\n"))
                        cat(paste("sk.var: ", sk.var = .self$sk.var, "\n"))
                      }
                    }
                  ))

#' @importFrom methods setMethod
setMethod("show", "sk",
          function(object) {
            object$print()
          })

#' @importFrom methods setMethod
setMethod("print", "sk",
          function(x, ...) {
            x$print()
          })