#' Plot the operating characteristics of curtailed group sequential single-arm trial designs for a
#' single binary endpoint
#'
#' Plots the operating characteristics of curtailed group sequential single-arm trial designs
#' determined using \code{opchar_curtailed()}. A range of plots are available, of which
#' the expected sample size and power curves will be printed by default.
#'
#' @param x An object of class \code{"sa_opchar_curtailed"}, as returned by \code{opchar_curtailed()}.
#' @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{$plot_des} containing the available plots.
#' \item Each of the input variables as specified, subject to internal modification.
#' }
#' @examples
#' # Find the optimal group sequential design for the default parameters with NSC
#' des <- des_curtailed()
#' # Determine operating characteristics for a range of response probabilities
#' opchar <- opchar_curtailed(des, pi = seq(0, 1, 0.01))
#' # Plot the expected sample size and power curve
#' plot(opchar)
#' @seealso \code{\link{des_curtailed}}, \code{\link{opchar_curtailed}},
#' and their associated \code{plot} family of functions.
#' @export
plot.sa_opchar_curtailed <- function(x, ..., output = F) {
opchar <- x
##### Input Checking #########################################################
check_sa_opchar_curtailed(opchar)
check_logical(output, "output")
##### Main Computations ######################################################
plot_opchar <- list()
if (min(opchar$pi) < opchar$des$des$pi0) {
red <- tibble::tibble(start = min(opchar$pi),
end = min(opchar$des$des$pi0, max(opchar$pi)))
}
if (all(min(opchar$pi) <= opchar$des$des$pi1,
max(opchar$pi) >= opchar$des$des$pi0)) {
amber <- tibble::tibble(start = max(opchar$des$des$pi0, min(opchar$pi)),
end = min(opchar$des$des$pi1, max(opchar$pi)))
}
if (max(opchar$pi) > opchar$des$des$pi1) {
green <- tibble::tibble(start = max(opchar$des$des$pi1,
min(opchar$pi)), end = max(opchar$pi))
}
if (is.null(opchar$add_des)) {
if (length(unique(opchar$pmf$pi)) > 1) {
plot_opchar$`ESS(pi)` <- ggplot2::ggplot()
if (min(opchar$pi) < opchar$des$des$pi0) {
plot_opchar$`ESS(pi)` <- plot_opchar$`ESS(pi)` +
ggplot2::geom_rect(data = red,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "firebrick2")
}
if (all(min(opchar$pi) <= opchar$des$des$pi1,
max(opchar$pi) >= opchar$des$des$pi0)) {
plot_opchar$`ESS(pi)` <- plot_opchar$`ESS(pi)` +
ggplot2::geom_rect(data = amber,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "orange")
}
if (max(opchar$pi) > opchar$des$des$pi1) {
plot_opchar$`ESS(pi)` <- plot_opchar$`ESS(pi)` +
ggplot2::geom_rect(data = green,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "green4")
}
plot_opchar$`ESS(pi)` <- plot_opchar$`ESS(pi)` +
ggplot2::geom_line(data = opchar$opchar,
ggplot2::aes(x = pi,
y = `ESS(pi)`)) +
ggplot2::xlab(expression(pi)) +
ggplot2::ylab(expression(paste(italic(ESS), "(",
pi, ")",
sep = ""))) +
theme_singlearm() +
ggplot2::scale_x_continuous(expand = c(0, 0),
limits = c(min(opchar$opchar$pi),
max(opchar$opchar$pi)))
print(plot_opchar$`ESS(pi)`)
plot_opchar$`VSS(pi)` <- ggplot2::ggplot()
if (min(opchar$pi) < opchar$des$des$pi0) {
plot_opchar$`VSS(pi)` <- plot_opchar$`VSS(pi)` +
ggplot2::geom_rect(data = red,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "firebrick2")
}
if (all(min(opchar$pi) <= opchar$des$des$pi1,
max(opchar$pi) >= opchar$des$des$pi0)) {
plot_opchar$`VSS(pi)` <- plot_opchar$`VSS(pi)` +
ggplot2::geom_rect(data = amber,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "orange")
}
if (max(opchar$pi) > opchar$des$des$pi1) {
plot_opchar$`VSS(pi)` <- plot_opchar$`VSS(pi)` +
ggplot2::geom_rect(data = green,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "green4")
}
plot_opchar$`VSS(pi)` <- plot_opchar$`VSS(pi)` +
ggplot2::geom_line(data = opchar$opchar,
ggplot2::aes(x = pi,
y = `VSS(pi)`)) +
ggplot2::xlab(expression(pi)) +
ggplot2::ylab(expression(paste(italic(VSS), "(",
pi, ")",
sep = ""))) +
theme_singlearm() +
ggplot2::scale_x_continuous(expand = c(0, 0),
limits = c(min(opchar$opchar$pi),
max(opchar$opchar$pi)))
plot_opchar$`Med(pi)` <- ggplot2::ggplot()
if (min(opchar$pi) < opchar$des$des$pi0) {
plot_opchar$`Med(pi)` <- plot_opchar$`Med(pi)` +
ggplot2::geom_rect(data = red,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "firebrick2")
}
if (all(min(opchar$pi) <= opchar$des$des$pi1,
max(opchar$pi) >= opchar$des$des$pi0)) {
plot_opchar$`Med(pi)` <- plot_opchar$`Med(pi)` +
ggplot2::geom_rect(data = amber,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "orange")
}
if (max(opchar$pi) > opchar$des$des$pi1) {
plot_opchar$`Med(pi)` <- plot_opchar$`Med(pi)` +
ggplot2::geom_rect(data = green,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "green4")
}
plot_opchar$`Med(pi)` <- plot_opchar$`Med(pi)` +
ggplot2::geom_line(data = opchar$opchar,
ggplot2::aes(x = pi,
y = `Med(pi)`)) +
ggplot2::xlab(expression(pi)) +
ggplot2::ylab(expression(paste(italic(Med), "(",
pi, ")",
sep = ""))) +
theme_singlearm() +
ggplot2::scale_x_continuous(expand = c(0, 0),
limits = c(min(opchar$opchar$pi),
max(opchar$opchar$pi)))
plot_opchar$`P(pi)` <- ggplot2::ggplot()
if (min(opchar$pi) < opchar$des$des$pi0) {
plot_opchar$`P(pi)` <- plot_opchar$`P(pi)` +
ggplot2::geom_rect(data = red,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "firebrick2")
}
if (all(min(opchar$pi) <= opchar$des$des$pi1,
max(opchar$pi) >= opchar$des$des$pi0)) {
plot_opchar$`P(pi)` <- plot_opchar$`P(pi)` +
ggplot2::geom_rect(data = amber,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "orange")
}
if (max(opchar$pi) > opchar$des$des$pi1) {
plot_opchar$`P(pi)` <- plot_opchar$`P(pi)` +
ggplot2::geom_rect(data = green,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "green4")
}
plot_opchar$`P(pi)` <- plot_opchar$`P(pi)` +
ggplot2::geom_hline(yintercept =
c(opchar$des$des$alpha,
1 - opchar$des$des$beta),
linetype = 2) +
ggplot2::geom_line(data = opchar$opchar,
ggplot2::aes(x = pi,
y = `P(pi)`)) +
ggplot2::xlab(expression(pi)) +
ggplot2::ylab(expression(paste(italic(P), "(", pi,
")", sep = ""))) +
theme_singlearm() +
ggplot2::scale_x_continuous(expand = c(0, 0),
limits = c(min(opchar$opchar$pi),
max(opchar$opchar$pi)))
print(plot_opchar$`P(pi)`)
} else {
plot_opchar$`ESS(pi)` <- NULL
plot_opchar$`VSS(pi)` <- NULL
plot_opchar$`Med(pi)` <- NULL
plot_opchar$`P(pi)` <- NULL
}
} else {
if (length(unique(opchar$pmf$pi)) > 1) {
plot_opchar$`ESS(pi)` <- ggplot2::ggplot()
if (min(opchar$pi) < opchar$des$des$pi0) {
plot_opchar$`ESS(pi)` <- plot_opchar$`ESS(pi)` +
ggplot2::geom_rect(data = red,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "firebrick2")
}
if (all(min(opchar$pi) <= opchar$des$des$pi1,
max(opchar$pi) >= opchar$des$des$pi0)) {
plot_opchar$`ESS(pi)` <- plot_opchar$`ESS(pi)` +
ggplot2::geom_rect(data = amber,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "orange")
}
if (max(opchar$pi) > opchar$des$des$pi1) {
plot_opchar$`ESS(pi)` <- plot_opchar$`ESS(pi)` +
ggplot2::geom_rect(data = green,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "green4")
}
plot_opchar$`ESS(pi)` <- plot_opchar$`ESS(pi)` +
ggplot2::geom_line(data = opchar$opchar,
ggplot2::aes(x = pi,
y = `ESS(pi)`,
colour = Design)) +
ggplot2::xlab(expression(pi)) +
ggplot2::ylab(expression(paste(italic(ESS), "(",
pi, ")",
sep = ""))) +
theme_singlearm() +
ggplot2::scale_x_continuous(expand = c(0, 0),
limits = c(min(opchar$opchar$pi),
max(opchar$opchar$pi)))
print(plot_opchar$`ESS(pi)`)
plot_opchar$`VSS(pi)` <- ggplot2::ggplot()
if (min(opchar$pi) < opchar$des$des$pi0) {
plot_opchar$`VSS(pi)` <- plot_opchar$`VSS(pi)` +
ggplot2::geom_rect(data = red,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "firebrick2")
}
if (all(min(opchar$pi) <= opchar$des$des$pi1,
max(opchar$pi) >= opchar$des$des$pi0)) {
plot_opchar$`VSS(pi)` <- plot_opchar$`VSS(pi)` +
ggplot2::geom_rect(data = amber,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "orange")
}
if (max(opchar$pi) > opchar$des$des$pi1) {
plot_opchar$`VSS(pi)` <- plot_opchar$`VSS(pi)` +
ggplot2::geom_rect(data = green,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "green4")
}
plot_opchar$`VSS(pi)` <- plot_opchar$`VSS(pi)` +
ggplot2::geom_line(data = opchar$opchar,
ggplot2::aes(x = pi,
y = `VSS(pi)`,
colour = Design)) +
ggplot2::xlab(expression(pi)) +
ggplot2::ylab(expression(paste(italic(VSS), "(",
pi, ")",
sep = ""))) +
theme_singlearm() +
ggplot2::scale_x_continuous(expand = c(0, 0),
limits = c(min(opchar$opchar$pi),
max(opchar$opchar$pi)))
plot_opchar$`Med(pi)` <- ggplot2::ggplot()
if (min(opchar$pi) < opchar$des$des$pi0) {
plot_opchar$`Med(pi)` <- plot_opchar$`Med(pi)` +
ggplot2::geom_rect(data = red,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "firebrick2")
}
if (all(min(opchar$pi) <= opchar$des$des$pi1,
max(opchar$pi) >= opchar$des$des$pi0)) {
plot_opchar$`Med(pi)` <- plot_opchar$`Med(pi)` +
ggplot2::geom_rect(data = amber,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "orange")
}
if (max(opchar$pi) > opchar$des$des$pi1) {
plot_opchar$`Med(pi)` <- plot_opchar$`Med(pi)` +
ggplot2::geom_rect(data = green,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "green4")
}
plot_opchar$`Med(pi)` <- plot_opchar$`Med(pi)` +
ggplot2::geom_line(data = opchar$opchar,
ggplot2::aes(x = pi,
y = `Med(pi)`,
colour = Design)) +
ggplot2::xlab(expression(pi)) +
ggplot2::ylab(expression(paste(italic(Med), "(",
pi, ")",
sep = ""))) +
theme_singlearm() +
ggplot2::scale_x_continuous(expand = c(0, 0),
limits = c(min(opchar$opchar$pi),
max(opchar$opchar$pi)))
plot_opchar$`P(pi)` <- ggplot2::ggplot()
if (min(opchar$pi) < opchar$des$des$pi0) {
plot_opchar$`P(pi)` <- plot_opchar$`P(pi)` +
ggplot2::geom_rect(data = red,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "firebrick2")
}
if (all(min(opchar$pi) <= opchar$des$des$pi1,
max(opchar$pi) >= opchar$des$des$pi0)) {
plot_opchar$`P(pi)` <- plot_opchar$`P(pi)` +
ggplot2::geom_rect(data = amber,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "orange")
}
if (max(opchar$pi) > opchar$des$des$pi1) {
plot_opchar$`P(pi)` <- plot_opchar$`P(pi)` +
ggplot2::geom_rect(data = green,
ggplot2::aes(xmin = start,
xmax = end,
ymin = -Inf,
ymax = Inf),
alpha = 0.1,
fill = "green4")
}
plot_opchar$`P(pi)` <- plot_opchar$`P(pi)` +
ggplot2::geom_hline(yintercept =
c(opchar$des$des$alpha,
1 - opchar$des$des$beta),
linetype = 2) +
ggplot2::geom_line(data = opchar$opchar,
ggplot2::aes(x = pi,
y = `P(pi)`,
colour = Design)) +
ggplot2::xlab(expression(pi)) +
ggplot2::ylab(expression(paste(italic(P), "(", pi,
")", sep = ""))) +
theme_singlearm() +
ggplot2::scale_x_continuous(expand = c(0, 0),
limits = c(min(opchar$opchar$pi),
max(opchar$opchar$pi)))
print(plot_opchar$`P(pi)`)
} else {
plot_opchar$`ESS(pi)` <- NULL
plot_opchar$`VSS(pi)` <- NULL
plot_opchar$`Med(pi)` <- NULL
plot_opchar$`P(pi)` <- NULL
}
}
##### Outputting #############################################################
if (output) {
return(list(plot_opchar = plot_opchar, opchar = opchar))
}
}
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