R/plot.sa_opchar_gs.R
In mjg211/singlearm: Design and analysis of single-arm clinical trials
Defines functions
plot.sa_opchar_gs
Documented in
plot.sa_opchar_gs
#' Plot the operating characteristics of group sequential single-arm trial designs for a
#' single binary endpoint
#'
#' Plots the operating characteristics of group sequential single-arm trial designs
#' determined using \code{opchar_gs()}. 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_gs"}, as returned by \code{opchar_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{$plot_des} containing the available plots.
#' \item Each of the input variables as specified, subject to internal modification.
#' }
#' @examples
#' # Find the optimal group sequential design for the default parameters
#' des <- des_gs()
#' # Determine operating characteristics for a range of response probabilities
#' opchar <- opchar_gs(des, pi = seq(from = 0, to = 1, by = 0.01))
#' # Plot the expected sample size and power curve
#' plot(opchar)
#' @seealso \code{\link{des_gs}}, \code{\link{opchar_gs}}, \code{\link{est_gs}}, \code{\link{pval_gs}},
#' and \code{\link{ci_gs}}, and their associated \code{plot} family of functions.
#' @export
plot.sa_opchar_gs <- function(x, ..., output = F) {
opchar <- x
##### Input Checking #########################################################
check_sa_opchar_gs(opchar)
check_logical(output, "output")
##### Main Computations ######################################################
plot_opchar <- list()
if (is.null(opchar$add_des)) {
if (all(opchar$des$des$pi0 %in% opchar$pmf$pi,
!opchar$des$des$pi1 %in% opchar$pmf$pi)) {
pmf_pi0 <- dplyr::filter(opchar$pmf, pi == opchar$des$des$pi0)
outcome <- numeric(nrow(pmf_pi0))
for (i in 1:nrow(pmf_pi0)) {
if (pmf_pi0$s[i] >= opchar$des$des$r[as.numeric(pmf_pi0$k[i])]) {
outcome[i] <- "Reject"
} else {
outcome[i] <- "Accept"
}
}
pmf_pi0$k <- plyr::mapvalues(pmf_pi0$k, from = levels(pmf_pi0$k),
to = paste("k =",
levels(pmf_pi0$k)))
pmf_pi0 <- dplyr::mutate(pmf_pi0,
outcome = factor(outcome,
levels = c("Accept",
"Reject")))
plot_opchar$`f(s,m|pi)` <- ggplot2::ggplot(data = pmf_pi0,
ggplot2::aes(x = s,
y = `f(s,m|pi)`,
fill = outcome)) +
ggplot2::geom_bar(stat = "identity") +
ggplot2::xlab(expression(italic(s))) +
ggplot2::ylab(expression(paste(italic(f), "(",
italic(s), ",",
italic(m), "|",
pi[0], ")",
sep = ""))) +
ggplot2::scale_fill_manual(values = c("firebrick2",
"green4")) +
theme_singlearm() + ggplot2::facet_grid(.~k)
print(plot_opchar$`f(s,m|pi)`)
} else if (all(!opchar$des$des$pi0 %in% opchar$pmf$pi,
opchar$des$des$pi1 %in% opchar$pmf$pi)) {
pmf_pi1 <- dplyr::filter(opchar$pmf, pi == opchar$des$des$pi1)
outcome <- numeric(nrow(pmf_pi1))
for (i in 1:nrow(pmf_pi1)) {
if (pmf_pi1$s[i] >= opchar$des$des$r[as.numeric(pmf_pi1$k[i])]) {
outcome[i] <- "Reject"
} else {
outcome[i] <- "Accept"
}
}
pmf_pi1 <- dplyr::mutate(pmf_pi1,
outcome = factor(outcome,
levels = c("Accept",
"Reject")))
pmf_pi1$k <- plyr::mapvalues(pmf_pi1$k, from = levels(pmf_pi1$k),
to = paste("k =",
levels(pmf_pi1$k)))
plot_opchar$`f(s,m|pi)` <- ggplot2::ggplot(data = pmf_pi1,
ggplot2::aes(x = s,
y = `f(s,m|pi)`,
fill = outcome)) +
ggplot2::geom_bar(stat = "identity") +
ggplot2::xlab(expression(italic(s))) +
ggplot2::ylab(expression(paste(italic(f), "(",
italic(s), ",",
italic(m), "|",
pi[1], ")",
sep = ""))) +
ggplot2::scale_fill_manual(values = c("firebrick2",
"green4")) +
theme_singlearm() + ggplot2::facet_grid(.~k)
print(plot_opchar$`f(s,m|pi)`)
} else if (all(opchar$des$des$pi0 %in% opchar$pmf$pi,
opchar$des$des$pi1 %in% opchar$pmf$pi)) {
pmf_pi0pi1 <- dplyr::filter(opchar$pmf, pi %in% c(opchar$des$des$pi0,
opchar$des$des$pi1))
outcome <- numeric(nrow(pmf_pi0pi1))
for (i in 1:nrow(pmf_pi0pi1)) {
if (pmf_pi0pi1$s[i] >=
opchar$des$des$r[as.numeric(pmf_pi0pi1$k[i])]) {
outcome[i] <- "Reject"
} else {
outcome[i] <- "Accept"
}
}
pmf_pi0pi1 <- dplyr::mutate(pmf_pi0pi1,
outcome = factor(outcome,
levels = c("Accept",
"Reject")))
pmf_pi0pi1$k <- plyr::mapvalues(pmf_pi0pi1$k,
from = levels(pmf_pi0pi1$k),
to = paste("k =",
levels(pmf_pi0pi1$k)))
facet_pi <- numeric(nrow(pmf_pi0pi1))
facet_k <- numeric(nrow(pmf_pi0pi1))
for (i in 1:nrow(pmf_pi0pi1)) {
if (pmf_pi0pi1$pi[i] == opchar$des$des$pi0) {
facet_pi[i] <- "pi == pi[0]"
} else {
facet_pi[i] <- "pi == pi[1]"
}
local <- strsplit(as.character(pmf_pi0pi1$k[i]), " ")[[1]]
local[1] <- "italic(k)"
local[2] <- "=="
facet_k[i] <- paste(local, collapse = " ")
}
pmf_pi0pi1$pi <- factor(facet_pi, levels = unique(facet_pi))
pmf_pi0pi1$k <- factor(facet_k, levels = unique(facet_k))
plot_opchar$`f(s,m|pi)` <- ggplot2::ggplot(data = pmf_pi0pi1,
ggplot2::aes(x = s,
y = `f(s,m|pi)`,
fill = outcome)) +
ggplot2::geom_bar(stat = "identity") +
ggplot2::xlab(expression(italic(s))) +
ggplot2::ylab(expression(paste(italic(f), "(",
italic(s), ",",
italic(m), "|",
pi, ")",
sep = ""))) +
ggplot2::scale_fill_manual(values =
c("firebrick2",
"green4")) +
theme_singlearm() +
ggplot2::facet_grid(pi~k,
labeller = ggplot2::label_parsed)
print(plot_opchar$`f(s,m|pi)`)
}
}
if (min(opchar$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
}
int_tibble <- tidyr::gather(opchar$opchar, "key", "value",
6:(5 + 2*opchar$des$des$J))
plot_opchar$rejection <- ggplot2::ggplot(int_tibble,
ggplot2::aes(pi, value,
fill = key)) +
ggplot2::geom_area() +
ggplot2::xlab(expression(pi)) +
ggplot2::ylab("Stopping probability") +
theme_singlearm() +
ggplot2::scale_x_continuous(expand = c(0, 0),
limits = c(min(opchar$opchar$pi),
max(opchar$opchar$pi))) +
ggplot2::scale_y_continuous(expand = c(0, 0))
int_tibble <- tidyr::gather(opchar$opchar, "key", "value",
(6 + 2*opchar$des$des$J):
(5 + 3*opchar$des$des$J))
plot_opchar$stopping <- ggplot2::ggplot(int_tibble,
ggplot2::aes(pi, value,
fill = key)) +
ggplot2::geom_area() +
ggplot2::xlab(expression(pi)) +
ggplot2::ylab("Stopping probability") +
theme_singlearm() +
ggplot2::scale_x_continuous(expand = c(0, 0),
limits = c(min(opchar$opchar$pi),
max(opchar$opchar$pi))) +
ggplot2::scale_y_continuous(expand = c(0, 0))
} else {
if (length(unique(opchar$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$pi))) +
ggplot2::guides(colour = ggplot2::guide_legend(nrow = 2))
print(plot_opchar$`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$`P(pi)` <- NULL
}
}
##### Outputting #############################################################
if (output) {
output <- list(plot_opchar = plot_opchar, opchar = opchar)
return(output)
}
}
mjg211/singlearm documentation built on May 8, 2021, 3:17 a.m.
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Defines functions plot.sa_opchar_gs
Documented in plot.sa_opchar_gs
#' Plot the operating characteristics of group sequential single-arm trial designs for a
#' single binary endpoint
#'
#' Plots the operating characteristics of group sequential single-arm trial designs
#' determined using \code{opchar_gs()}. A range of plots are available, of which
#' the expected sample size and power curves will be printed by default.
#'
#' @param x An object of class \code{"sa_opchar_gs"}, as returned by \code{opchar_gs()}.
#' @param ... Included for compatibility with the generic. Not currently used.
#' @param output A logical variable indicating whether the outputs described below
#' should be returned.
#' @return If \code{output = TRUE}, a list containing the following elements is returned
#' \itemize{
#' \item A list in the slot \code{$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 operating characteristics for a range of response probabilities
#' opchar <- opchar_gs(des, pi = seq(from = 0, to = 1, by = 0.01))
#' # Plot the expected sample size and power curve
#' plot(opchar)
#' @seealso \code{\link{des_gs}}, \code{\link{opchar_gs}}, \code{\link{est_gs}}, \code{\link{pval_gs}},
#' and \code{\link{ci_gs}}, and their associated \code{plot} family of functions.
#' @export
plot.sa_opchar_gs <- function(x, ..., output = F) {
opchar <- x
##### Input Checking #########################################################
check_sa_opchar_gs(opchar)
check_logical(output, "output")
##### Main Computations ######################################################
plot_opchar <- list()
if (is.null(opchar$add_des)) {
if (all(opchar$des$des$pi0 %in% opchar$pmf$pi,
!opchar$des$des$pi1 %in% opchar$pmf$pi)) {
pmf_pi0 <- dplyr::filter(opchar$pmf, pi == opchar$des$des$pi0)
outcome <- numeric(nrow(pmf_pi0))
for (i in 1:nrow(pmf_pi0)) {
if (pmf_pi0$s[i] >= opchar$des$des$r[as.numeric(pmf_pi0$k[i])]) {
outcome[i] <- "Reject"
} else {
outcome[i] <- "Accept"
}
}
pmf_pi0$k <- plyr::mapvalues(pmf_pi0$k, from = levels(pmf_pi0$k),
to = paste("k =",
levels(pmf_pi0$k)))
pmf_pi0 <- dplyr::mutate(pmf_pi0,
outcome = factor(outcome,
levels = c("Accept",
"Reject")))
plot_opchar$`f(s,m|pi)` <- ggplot2::ggplot(data = pmf_pi0,
ggplot2::aes(x = s,
y = `f(s,m|pi)`,
fill = outcome)) +
ggplot2::geom_bar(stat = "identity") +
ggplot2::xlab(expression(italic(s))) +
ggplot2::ylab(expression(paste(italic(f), "(",
italic(s), ",",
italic(m), "|",
pi[0], ")",
sep = ""))) +
ggplot2::scale_fill_manual(values = c("firebrick2",
"green4")) +
theme_singlearm() + ggplot2::facet_grid(.~k)
print(plot_opchar$`f(s,m|pi)`)
} else if (all(!opchar$des$des$pi0 %in% opchar$pmf$pi,
opchar$des$des$pi1 %in% opchar$pmf$pi)) {
pmf_pi1 <- dplyr::filter(opchar$pmf, pi == opchar$des$des$pi1)
outcome <- numeric(nrow(pmf_pi1))
for (i in 1:nrow(pmf_pi1)) {
if (pmf_pi1$s[i] >= opchar$des$des$r[as.numeric(pmf_pi1$k[i])]) {
outcome[i] <- "Reject"
} else {
outcome[i] <- "Accept"
}
}
pmf_pi1 <- dplyr::mutate(pmf_pi1,
outcome = factor(outcome,
levels = c("Accept",
"Reject")))
pmf_pi1$k <- plyr::mapvalues(pmf_pi1$k, from = levels(pmf_pi1$k),
to = paste("k =",
levels(pmf_pi1$k)))
plot_opchar$`f(s,m|pi)` <- ggplot2::ggplot(data = pmf_pi1,
ggplot2::aes(x = s,
y = `f(s,m|pi)`,
fill = outcome)) +
ggplot2::geom_bar(stat = "identity") +
ggplot2::xlab(expression(italic(s))) +
ggplot2::ylab(expression(paste(italic(f), "(",
italic(s), ",",
italic(m), "|",
pi[1], ")",
sep = ""))) +
ggplot2::scale_fill_manual(values = c("firebrick2",
"green4")) +
theme_singlearm() + ggplot2::facet_grid(.~k)
print(plot_opchar$`f(s,m|pi)`)
} else if (all(opchar$des$des$pi0 %in% opchar$pmf$pi,
opchar$des$des$pi1 %in% opchar$pmf$pi)) {
pmf_pi0pi1 <- dplyr::filter(opchar$pmf, pi %in% c(opchar$des$des$pi0,
opchar$des$des$pi1))
outcome <- numeric(nrow(pmf_pi0pi1))
for (i in 1:nrow(pmf_pi0pi1)) {
if (pmf_pi0pi1$s[i] >=
opchar$des$des$r[as.numeric(pmf_pi0pi1$k[i])]) {
outcome[i] <- "Reject"
} else {
outcome[i] <- "Accept"
}
}
pmf_pi0pi1 <- dplyr::mutate(pmf_pi0pi1,
outcome = factor(outcome,
levels = c("Accept",
"Reject")))
pmf_pi0pi1$k <- plyr::mapvalues(pmf_pi0pi1$k,
from = levels(pmf_pi0pi1$k),
to = paste("k =",
levels(pmf_pi0pi1$k)))
facet_pi <- numeric(nrow(pmf_pi0pi1))
facet_k <- numeric(nrow(pmf_pi0pi1))
for (i in 1:nrow(pmf_pi0pi1)) {
if (pmf_pi0pi1$pi[i] == opchar$des$des$pi0) {
facet_pi[i] <- "pi == pi[0]"
} else {
facet_pi[i] <- "pi == pi[1]"
}
local <- strsplit(as.character(pmf_pi0pi1$k[i]), " ")[[1]]
local[1] <- "italic(k)"
local[2] <- "=="
facet_k[i] <- paste(local, collapse = " ")
}
pmf_pi0pi1$pi <- factor(facet_pi, levels = unique(facet_pi))
pmf_pi0pi1$k <- factor(facet_k, levels = unique(facet_k))
plot_opchar$`f(s,m|pi)` <- ggplot2::ggplot(data = pmf_pi0pi1,
ggplot2::aes(x = s,
y = `f(s,m|pi)`,
fill = outcome)) +
ggplot2::geom_bar(stat = "identity") +
ggplot2::xlab(expression(italic(s))) +
ggplot2::ylab(expression(paste(italic(f), "(",
italic(s), ",",
italic(m), "|",
pi, ")",
sep = ""))) +
ggplot2::scale_fill_manual(values =
c("firebrick2",
"green4")) +
theme_singlearm() +
ggplot2::facet_grid(pi~k,
labeller = ggplot2::label_parsed)
print(plot_opchar$`f(s,m|pi)`)
}
}
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$`P(pi)` <- NULL
}
int_tibble <- tidyr::gather(opchar$opchar, "key", "value",
6:(5 + 2*opchar$des$des$J))
plot_opchar$rejection <- ggplot2::ggplot(int_tibble,
ggplot2::aes(pi, value,
fill = key)) +
ggplot2::geom_area() +
ggplot2::xlab(expression(pi)) +
ggplot2::ylab("Stopping probability") +
theme_singlearm() +
ggplot2::scale_x_continuous(expand = c(0, 0),
limits = c(min(opchar$opchar$pi),
max(opchar$opchar$pi))) +
ggplot2::scale_y_continuous(expand = c(0, 0))
int_tibble <- tidyr::gather(opchar$opchar, "key", "value",
(6 + 2*opchar$des$des$J):
(5 + 3*opchar$des$des$J))
plot_opchar$stopping <- ggplot2::ggplot(int_tibble,
ggplot2::aes(pi, value,
fill = key)) +
ggplot2::geom_area() +
ggplot2::xlab(expression(pi)) +
ggplot2::ylab("Stopping probability") +
theme_singlearm() +
ggplot2::scale_x_continuous(expand = c(0, 0),
limits = c(min(opchar$opchar$pi),
max(opchar$opchar$pi))) +
ggplot2::scale_y_continuous(expand = c(0, 0))
} 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))) +
ggplot2::guides(colour = ggplot2::guide_legend(nrow = 2))
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) {
output <- list(plot_opchar = plot_opchar, opchar = opchar)
return(output)
}
}
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