R/plot.sa_est_gs.R

In mjg211/singlearm: Design and analysis of single-arm clinical trials

#' Plot the point estimates, and the point estimation procedures performance, in a group sequential
#' single-arm trial design for a single binary endpoint
#'
#' Plots the point estimates, and the performance of the point estimation procedure,
#' in a group sequential single-arm trial design for a single binary endpoint
#' determined using \code{est_gs()}. A range of plots are available, of which
#' the point estimates and the bias curve will be printed by
#' default.
#'
#' @param x An object of class \code{"sa_est_gs"}, as returned by \code{est_gs()}.
#' @param ... Included for compatibility with the generic. Not currently used.
#' @param output A logical variable indicating whether the outputs described below
#' should be returned.
#' @return If \code{output = TRUE}, a list containing the following elements is returned
#' \itemize{
#' \item A list in the slot \code{$plot_des} containing the available plots.
#' \item Each of the input variables as specified, subject to internal modification.
#' }
#' @examples
#' # Find the optimal group sequential design for the default parameters
#' des <- des_gs()
#' # Determine the performance of the point estimation procedure for a range of
#' # possible response probabilities
#' est <- est_gs(des, pi = seq(0, 1, 0.01))
#' # Plot the point estimates and the estimation procedure performance
#' plot(est)
#' @seealso \code{\link{des_gs}}, \code{\link{opchar_gs}}, \code{\link{est_gs}},
#' \code{\link{pval_gs}}, \code{\link{ci_gs}}, and their associated \code{plot}
#' family of functions.
#' @export
plot.sa_est_gs <- function(x, ..., output = F) {

  est <- x

  ##### Input Checking #########################################################

  check_sa_est_gs(est)
  check_logical(output, "output")

  ##### Main Computations ######################################################

  plot_est <- list()

  new_levels <- levels(est$est$method)
  for (i in 1:length(new_levels)) {
    if (new_levels[i] == "bias_adj") {
      new_levels[i] <- "Bias adjusted"
    } else if (new_levels[i] == "bias_sub") {
      new_levels[i] <- "Bias subtracted"
    } else if (new_levels[i] == "conditional") {
      new_levels[i] <- "Conditional"
    } else if (new_levels[i] == "naive") {
      new_levels[i] <- "Naive"
    } else if (new_levels[i] == "mue") {
      new_levels[i] <- "MUE"
    } else if (new_levels[i] == "umvue") {
      new_levels[i] <- "UMVUE"
    } else {
      new_levels[i] <- "UMVCUE"
    }
  }
  est$est$method <- plyr::mapvalues(est$est$method,
                                    from = levels(est$est$method),
                                    to = new_levels)

  est$est$k <- plyr::mapvalues(est$est$k, from = levels(est$est$k),
                               to = paste("k =", levels(est$est$k)))

  plot_est$est <- ggplot2::ggplot(data = est$est,
                                  ggplot2::aes(x = s, y = `hat(pi)(s,m)`,
                                               color = method)) +
    ggplot2::geom_hline(yintercept = est$des$pi0, linetype = 2) +
    ggplot2::geom_hline(yintercept = est$des$pi1, linetype = 2) +
    ggplot2::geom_point() +
    ggplot2::geom_line() +
    ggplot2::facet_grid(.~k) +
    ggplot2::xlab(expression(italic(s))) +
    ggplot2::ylab(expression(paste(hat(pi), "(", italic(s), ",",
                                   italic(m), ")", sep = ""))) +
    theme_singlearm()
  print(plot_est$est)
  if (!is.null(est$perf)) {

    new_levels <- levels(est$perf$method)
    for (i in 1:length(new_levels)) {
      if (new_levels[i] == "bias_adj") {
        new_levels[i] <- "Bias adjusted"
      } else if (new_levels[i] == "bias_sub") {
        new_levels[i] <- "Bias subtracted"
      } else if (new_levels[i] == "conditional") {
        new_levels[i] <- "Conditional"
      } else if (new_levels[i] == "naive") {
        new_levels[i] <- "Naive"
      } else if (new_levels[i] == "mue") {
        new_levels[i] <- "MUE"
      } else if (new_levels[i] == "umvue") {
        new_levels[i] <- "UMVUE"
      } else {
        new_levels[i] <- "UMVCUE"
      }
    }
    est$perf$method <- plyr::mapvalues(est$perf$method,
                                      from = levels(est$perf$method),
                                      to = new_levels)

    if (min(est$pi) < est$des$des$pi0) {
      red   <- tibble::tibble(start = min(est$pi),
                              end = min(est$des$des$pi0, max(est$pi)))
    }
    if (all(min(est$pi) <= est$des$des$pi1,
            max(est$pi) >= est$des$des$pi0)) {
      amber <- tibble::tibble(start = max(est$des$des$pi0, min(est$pi)),
                              end = min(est$des$des$pi1, max(est$pi)))
    }
    if (max(est$pi) > est$des$des$pi1) {
      green <- tibble::tibble(start = max(est$des$des$pi1,
                                          min(est$pi)), end = max(est$pi))
    }

    plot_est$`E(hat(pi)|pi)` <- ggplot2::ggplot()
      if (min(est$pi) < est$des$des$pi0) {
        plot_est$`E(hat(pi)|pi)` <- plot_est$`E(hat(pi)|pi)` +
          ggplot2::geom_rect(data = red,
                             ggplot2::aes(xmin = start,
                                          xmax = end,
                                          ymin = -Inf,
                                          ymax = Inf),
                             alpha = 0.1,
                             fill = "firebrick2")
      }
    if (all(min(est$pi) <= est$des$des$pi1,
            max(est$pi) >= est$des$des$pi0)) {
      plot_est$`E(hat(pi)|pi)` <- plot_est$`E(hat(pi)|pi)` +
        ggplot2::geom_rect(data = amber,
                           ggplot2::aes(xmin = start,
                                        xmax = end,
                                        ymin = -Inf,
                                        ymax = Inf),
                           alpha = 0.1,
                           fill = "orange")
    }
    if (max(est$pi) > est$des$des$pi1) {
      plot_est$`E(hat(pi)|pi)` <- plot_est$`E(hat(pi)|pi)` +
        ggplot2::geom_rect(data = green,
                           ggplot2::aes(xmin = start,
                                        xmax = end,
                                        ymin = -Inf,
                                        ymax = Inf),
                           alpha = 0.1,
                           fill = "green4")
    }
    plot_est$`E(hat(pi)|pi)` <- plot_est$`E(hat(pi)|pi)` +
      ggplot2::geom_abline(slope = 1,
                           intercept = 0,
                           linetype = 2) +
      ggplot2::geom_hline(yintercept = est$des$pi0,
                          linetype = 2) +
      ggplot2::geom_hline(yintercept = est$des$pi1,
                          linetype = 2) +
      ggplot2::geom_line(data = est$perf,
                         ggplot2::aes(x = pi,
                                      y = `E(hat(pi)|pi)`, colour = method)) +
      ggplot2::xlab(expression(pi)) +
      ggplot2::ylab(expression(paste("E(", hat(pi),
                                     "|", pi, ")",
                                     sep = ""))) +
      theme_singlearm() +
      ggplot2::scale_x_continuous(expand = c(0, 0),
                                  limits = c(min(est$perf$pi),
                                             max(est$perf$pi)))

    plot_est$`Var(hat(pi)|pi)` <- ggplot2::ggplot()
      if (min(est$pi) < est$des$des$pi0) {
        plot_est$`Var(hat(pi)|pi)` <- plot_est$`Var(hat(pi)|pi)` +
          ggplot2::geom_rect(data = red,
                             ggplot2::aes(xmin = start,
                                          xmax = end,
                                          ymin = -Inf,
                                          ymax = Inf),
                             alpha = 0.1,
                             fill = "firebrick2")
      }
    if (all(min(est$pi) <= est$des$des$pi1,
            max(est$pi) >= est$des$des$pi0)) {
      plot_est$`Var(hat(pi)|pi)` <- plot_est$`Var(hat(pi)|pi)` +
        ggplot2::geom_rect(data = amber,
                           ggplot2::aes(xmin = start,
                                        xmax = end,
                                        ymin = -Inf,
                                        ymax = Inf),
                           alpha = 0.1,
                           fill = "orange")
    }
    if (max(est$pi) > est$des$des$pi1) {
      plot_est$`Var(hat(pi)|pi)` <- plot_est$`Var(hat(pi)|pi)` +
        ggplot2::geom_rect(data = green,
                           ggplot2::aes(xmin = start,
                                        xmax = end,
                                        ymin = -Inf,
                                        ymax = Inf),
                           alpha = 0.1,
                           fill = "green4")
    }
    plot_est$`Var(hat(pi)|pi)` <- plot_est$`Var(hat(pi)|pi)` +
      ggplot2::geom_line(data = est$perf,
                         ggplot2::aes(x = pi,
                                      y = `Var(hat(pi)|pi)`, colour = method)) +
      ggplot2::xlab(expression(pi)) +
      ggplot2::ylab(expression(paste(italic(Var), "(",
                                     hat(pi), "|",
                                     pi, ")",
                                     sep = ""))) +
      theme_singlearm() +
      ggplot2::scale_x_continuous(expand = c(0, 0),
                                  limits = c(min(est$perf$pi),
                                             max(est$perf$pi)))

    plot_est$`Bias(hat(pi)|pi)` <- ggplot2::ggplot()
      if (min(est$pi) < est$des$des$pi0) {
        plot_est$`Bias(hat(pi)|pi)` <- plot_est$`Bias(hat(pi)|pi)` +
          ggplot2::geom_rect(data = red,
                             ggplot2::aes(xmin = start,
                                          xmax = end,
                                          ymin = -Inf,
                                          ymax = Inf),
                             alpha = 0.1,
                             fill = "firebrick2")
      }
    if (all(min(est$pi) <= est$des$des$pi1,
            max(est$pi) >= est$des$des$pi0)) {
      plot_est$`Bias(hat(pi)|pi)` <- plot_est$`Bias(hat(pi)|pi)` +
        ggplot2::geom_rect(data = amber,
                           ggplot2::aes(xmin = start,
                                        xmax = end,
                                        ymin = -Inf,
                                        ymax = Inf),
                           alpha = 0.1,
                           fill = "orange")
    }
    if (max(est$pi) > est$des$des$pi1) {
      plot_est$`Bias(hat(pi)|pi)` <- plot_est$`Bias(hat(pi)|pi)` +
        ggplot2::geom_rect(data = green,
                           ggplot2::aes(xmin = start,
                                        xmax = end,
                                        ymin = -Inf,
                                        ymax = Inf),
                           alpha = 0.1,
                           fill = "green4")
    }
    plot_est$`Bias(hat(pi)|pi)` <- plot_est$`Bias(hat(pi)|pi)` +
      ggplot2::geom_hline(yintercept = 0,
                          linetype = 2) +
      ggplot2::geom_line(data = est$perf,
                         ggplot2::aes(x = pi,
                                      y = `Bias(hat(pi)|pi)`, colour = method)) +
      ggplot2::xlab(expression(pi)) +
      ggplot2::ylab(expression(paste(italic(Bias), "(",
                                     hat(pi),
                                     "|", pi,
                                     ")",
                                     sep = ""))) +
      theme_singlearm() +
      ggplot2::scale_x_continuous(expand = c(0, 0),
                                  limits = c(min(est$perf$pi),
                                             max(est$perf$pi)))
    print(plot_est$`Bias(hat(pi)|pi)`)

    plot_est$`RMSE(hat(pi)|pi)` <- ggplot2::ggplot()
      if (min(est$pi) < est$des$des$pi0) {
        plot_est$`RMSE(hat(pi)|pi)` <- plot_est$`RMSE(hat(pi)|pi)` +
          ggplot2::geom_rect(data = red,
                             ggplot2::aes(xmin = start,
                                          xmax = end,
                                          ymin = -Inf,
                                          ymax = Inf),
                             alpha = 0.1,
                             fill = "firebrick2")
      }
    if (all(min(est$pi) <= est$des$des$pi1,
            max(est$pi) >= est$des$des$pi0)) {
      plot_est$`RMSE(hat(pi)|pi)` <- plot_est$`RMSE(hat(pi)|pi)` +
        ggplot2::geom_rect(data = amber,
                           ggplot2::aes(xmin = start,
                                        xmax = end,
                                        ymin = -Inf,
                                        ymax = Inf),
                           alpha = 0.1,
                           fill = "orange")
    }
    if (max(est$pi) > est$des$des$pi1) {
      plot_est$`RMSE(hat(pi)|pi)` <- plot_est$`RMSE(hat(pi)|pi)` +
        ggplot2::geom_rect(data = green,
                           ggplot2::aes(xmin = start,
                                        xmax = end,
                                        ymin = -Inf,
                                        ymax = Inf),
                           alpha = 0.1,
                           fill = "green4")
    }
    plot_est$`RMSE(hat(pi)|pi)` <- plot_est$`RMSE(hat(pi)|pi)` +
      ggplot2::geom_line(data = est$perf,
                         ggplot2::aes(x = pi,
                                      y = `RMSE(hat(pi)|pi)`, colour = method)) +
      ggplot2::xlab(expression(pi)) +
      ggplot2::ylab(expression(paste(italic(RMSE), "(",
                                     hat(pi),
                                     "|", pi,
                                     ")",
                                     sep = ""))) +
      theme_singlearm() +
      ggplot2::scale_x_continuous(expand = c(0, 0),
                                  limits = c(min(est$perf$pi),
                                             max(est$perf$pi)))

  }

  ##### Outputting #############################################################

  if (output) {
    output <- list(plot_est = plot_est, est = est)
    return(output)
  }
}