R/compare.R

In agrobioinfoservices/gosset: Tools for Data Analysis in Experimental Agriculture

#' Compare agreement between two methods
#' 
#' Measures the agreement between two methods
#'  
#' @param x a numeric vector, or an object  
#'  of class \code{PlackettLuce}
#' @param y a numeric vector, or an object  
#'  of class \code{PlackettLuce}
#' @param labels optional, a vector with the same length \var{x}
#'  to plot values
#' @param ... additional arguments passed to methods
#' @return a ggplot with the agreement
#' @examples
#' set.seed(1)
#' x = runif(10, -1, 2)
#' 
#' set.seed(2)
#' y = runif(10, -1, 2)
#' 
#' compare(x, y)
#' 
#' @references 
#' Bland, M. J., and Altman, D. G. (1986).
#'  Lancet (8476):307-10.
#' @importFrom methods addNextMethod asMethodDefinition assignClassDef
#' @importFrom ggplot2 geom_hline geom_point
#' @importFrom stats coefficients sd
#' @importFrom ggrepel geom_text_repel
#' @export
compare = function(x, y, ...){
  
  UseMethod("compare")
  
}

#' @rdname compare
#' @export
compare.default = function(x, y, labels = NULL, ...){
  
  if (is.null(labels)) {
    labels = LETTERS[1:length(x)]
  }
  
  comp = data.frame(diff = x - y,
                    aver = rowMeans(cbind(x, y)),
                    item = labels)
  
  # the mean of the difference
  d = mean(comp$diff)
  
  # the standard deviation of the difference
  s = stats::sd(comp$diff)
  
  # limits of agreement
  llim = d - (2 * s)
  ulim = d + (2 * s)
  
  aver = comp$aver
  item = comp$item
  
  diff_plot = 
    ggplot2::ggplot(comp,
                    ggplot2::aes(x = aver, y = diff, label = item)) +
    ggplot2::geom_hline(yintercept = llim, linetype = "dashed", col = "grey30") +
    ggplot2::geom_hline(yintercept = ulim, linetype = "dashed", col = "grey30") +
    ggplot2::geom_hline(yintercept = mean(comp$diff), col = "red") +
    ggplot2::geom_point() +
    ggplot2::theme_bw() +
    ggrepel::geom_text_repel() +
    ggplot2::theme(panel.grid = ggplot2::element_blank(),
                   text = ggplot2::element_text(size = 15),
                   axis.text = ggplot2::element_text(size = 13, color = "grey20", face = 2),
                   axis.title = ggplot2::element_text(size = 12, color = "grey20", face = 2)) +
    ggplot2::labs(x = "Average", 
                  y = "Difference (x - y)")
  
  return(diff_plot)
  
}

#' @rdname compare
#' @method compare PlackettLuce
#' @export
compare.PlackettLuce = function(x, y, ...){
  
  # get the probability of winning and than set back as log
  X = log(stats::coefficients(x, log = FALSE))
  
  Y = log(stats::coefficients(y, log = FALSE))
  
  lab = names(X)
  
  compare(x = X, y = Y, labels = lab)
  
}