R/opchar_curtailed.R
In mjg211/singlearm: Design and analysis of single-arm clinical trials
Defines functions
opchar_curtailed
Documented in
opchar_curtailed
#' Determine the operating characteristics of group sequential single-arm trial
#' designs for a single binary endpoint
#'
#' \code{opchar_gs()} supports the simultaneous evaluation of the operating
#' characteristics of multiple group sequential single-arm clinical trial
#' designs for a single binary primary endpoint, determined using
#' \code{des_gs()}.
#'
#' Note that each of the supplied designs must have been designed for the same
#' value of \ifelse{html}{\out{<i>π</i><sub>0</sub>}}{\deqn{\pi_0}}.
#'
#' For each value of \ifelse{html}{\out{<i>π</i>}}{\eqn{\pi}} in
#' the supplied vector \ifelse{html}{\out{<b><i>π</i></b>}}{\eqn{\bold{\pi}}},
#' \code{opchar_gs()} evaluates the power, ESS, and other key characteristics,
#' of each of the supplied designs.
#'
#' Calculations are performed conditional on the trial stopping in one of the
#' stages specified using the input (vector) \code{k}.
#'
#' @param des An object of class \code{"sa_des_gs"}, as returned by
#' \code{des_gs()}.
#' @param ... Additional objects of class \code{"sa_gs_gs"}. These will be
#' grouped in to a list named \code{"add_des"}.
#' @param k Calculations are performed conditional on the trial stopping in one
#' of the stages listed in vector \code{k}. Thus, \code{k} should be a vector of
#' integers, with elements between one and the maximum number of possible stages
#' across the supplied designs. If left unspecified, it will internally default
#' to all possible stages.
#' @param pi A vector of response probabilities to evaluate operating
#' characteristics at. This will internally default to be the
#' \ifelse{html}{\out{<i>π</i><sub>0</sub>}}{\deqn{\pi_0}} and
#' \ifelse{html}{\out{<i>π</i><sub>1</sub>}}{\deqn{\pi_1}} from the
#' supplied designs if it is left unspecified.
#' @param summary A logical variable indicating whether a summary of the
#' function's progress should be printed to the console.
#' @return A list of class \code{"sa_opchar_gs"} containing the following
#' elements
#' \itemize{
#' \item A tibble in the slot \code{$opchar} summarising the operating
#' characteristics of the supplied designs.
#' \item Each of the input variables as specified, subject to internal
#' modification.
#' }
#' @examples
#' # Find the optimal two-stage design for the default parameters
#' des <- des_gs()
#' # Determine operating characteristics for a range of response probabilities
#' opchar <- opchar_gs(des, pi = seq(0, 1, 0.01))
#' # Find the optimal two-stage design for a 10% type-I error rate
#' des_10 <- des_gs(alpha = 0.1)
#' # Determine operating characteristics for both designs at the same time
#' opchar_both <- opchar_gs(des, des_10, pi = seq(0, 1, 0.01))
#' @references Simon R (1989) Optimal two-stage designs for phase II clinical
#' trials. \emph{Controlled Clinical Trials} \strong{10:}1-10.
#' @seealso \code{\link{des_gs}}, \code{\link{est_gs}}, \code{\link{pval_gs}},
#' \code{\link{ci_gs}}, and their associated \code{plot} family of functions.
#' @export
#' @export
opchar_curtailed <- function(des, ..., k, pi, summary = F) {
##### Input Checking #########################################################
check_sa_des_curtailed(des, "des")
add_des <- pryr::named_dots(...)
num_add_des <- length(add_des)
if (num_add_des > 0) {
for (i in 1:num_add_des) {
check_sa_des_curtailed(eval(add_des[[i]]), paste("add_des", i, sep = ""))
}
for (i in 1:num_add_des) {
if (eval(add_des[[i]])$des$pi0 != des$des$pi0) {
stop("Each supplied design must have been designed for the same value of pi0")
}
}
}
if (!missing(pi)) {
check_pi(pi, "any")
} else {
pi <- c(des$des$pi0, des$des$pi1)
}
if (all(missing(k), num_add_des == 0)) {
k <- 1:des$des$J
} else if (all(missing(k), num_add_des > 0)) {
Js <- numeric(num_add_des + 1)
Js[1] <- des$des$J
for (i in 1:num_add_des) {
Js[i + 1] <- eval(add_des[[i]])$des$J
}
k <- 1:max(Js)
} else if (!missing(k)){
check_k(k, des, add_des)
}
check_logical(summary, "summary")
##### Print Summary ##########################################################
if (summary){
message(rep("-", 10))
message("Operating characteristic determination for curtailed group-sequential single-arm trials with a single binary endpoint")
message(rep("-", 10))
Sys.sleep(2)
message("You have chosen to make your calculations conditional on k \u2208 {", k[1], ",...,", k[length(k)], "}.\n")
Sys.sleep(2)
message("Beginning the required calculations...")
}
##### Main Computations ######################################################
if (num_add_des == 0) {
pmf <- pmf_curtailed(pi, des$des$J, des$des$J_curt, des$des$a_curt,
des$des$r_curt, des$des$n, des$des$n_curt, k)
opchar <- int_opchar_curtailed(pi, des$des$J, des$des$J_curt,
des$des$a_curt, des$des$r_curt,
des$des$n, des$des$n_curt,
cumsum(des$des$n), cumsum(des$des$n_curt),
k, pmf)
add_des <- NULL
} else {
opchar <- pmf <- list()
if (Js[1] == 1) {
des_val <- paste("Design 1: (", des$des$a, ",", des$des$r, ")/",
des$des$n, ", thetaF = ", des$des$thetaF,
", thetaE = ", des$des$thetaE, sep = "")
} else {
des_val <- paste("Design 1: ",
paste("(", des$des$a, ",", des$des$r, ")/",
cumsum(des$des$n), sep = "",
collapse = ", "), ", thetaF = (",
paste(des$des$thetaF, sep = "",
collapse = ","), "), thetaE = (",
paste(des$des$thetaE, sep = "", collapse = ","),
")", sep = "", collapse = "")
}
pmf[[1]] <-
cbind("Design" = des_val,
pmf_curtailed(pi, des$des$J, des$des$J_curt, des$des$a_curt,
des$des$r_curt, des$des$n, des$des$n_curt,
k[which(k <= Js[1])]))
opchar[[1]] <-
cbind("Design" = des_val,
int_opchar_curtailed(pi, des$des$J, des$des$J_curt,
des$des$a_curt, des$des$r_curt, des$des$n,
des$des$n_curt, cumsum(des$des$n),
cumsum(des$des$n_curt), k, pmf[[1]]))
if (summary) {
message("...performance for Design 1 evaluated...")
}
for (i in 1:num_add_des) {
des_i <- eval(add_des[[i]])
if (Js[i + 1] == 1) {
des_val <- paste("Design ", i + 1, ": (", des_i$des$a, ",", des_i$des$r,
")/", des_i$des$n, ", thetaF = ", des_i$des$thetaF,
", thetaE = ", des_i$des$thetaE, sep = "")
} else {
des_val <- paste("Design ", i + 1, ": ",
paste("(", des_i$des$a, ",", des_i$des$r, ")/",
cumsum(des_i$des$n), sep = "",
collapse = ", "), ", thetaF = (",
paste(des_i$des$thetaF, sep = "",
collapse = ","), "), thetaE = (",
paste(des_i$des$thetaE, sep = "", collapse = ","),
")", sep = "", collapse = "")
}
pmf[[i + 1]] <-
cbind("Design" = des_val,
pmf_curtailed(pi, des_i$des$J, des_i$des$J_curt, des_i$des$a_curt,
des_i$des$r_curt, des_i$des$n, des_i$des$n_curt,
k[which(k <= Js[i + 1])]))
opchar[[i + 1]] <-
cbind("Design" = des_val,
int_opchar_curtailed(pi, des_i$des$J, des_i$des$J_curt,
des_i$des$a_curt, des_i$des$r_curt, des_i$des$n,
des_i$des$n_curt, cumsum(des_i$des$n),
cumsum(des_i$des$n_curt),
k[which(k <= Js[i + 1])], pmf[[i + 1]]))
if (summary) {
message("...performance for Design ", i + 1, " evaluated...")
}
}
pmf <- tibble::as_tibble(plyr::rbind.fill(pmf))
pmf$m <- as.integer(pmf$m)
opchar <- tibble::as_tibble(plyr::rbind.fill(opchar))
opchar$Design <- as.factor(opchar$Design)
}
##### Outputting #############################################################
if (summary) {
message("...outputting.")
}
output <- list(opchar = opchar, pmf = pmf, des = des,
add_des = add_des, pi = pi, summary = summary)
class(output) <- "sa_opchar_curtailed"
return(output)
}
mjg211/singlearm documentation built on May 8, 2021, 3:17 a.m.
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Defines functions opchar_curtailed
Documented in opchar_curtailed
#' Determine the operating characteristics of group sequential single-arm trial
#' designs for a single binary endpoint
#'
#' \code{opchar_gs()} supports the simultaneous evaluation of the operating
#' characteristics of multiple group sequential single-arm clinical trial
#' designs for a single binary primary endpoint, determined using
#' \code{des_gs()}.
#'
#' Note that each of the supplied designs must have been designed for the same
#' value of \ifelse{html}{\out{<i>π</i><sub>0</sub>}}{\deqn{\pi_0}}.
#'
#' For each value of \ifelse{html}{\out{<i>π</i>}}{\eqn{\pi}} in
#' the supplied vector \ifelse{html}{\out{<b><i>π</i></b>}}{\eqn{\bold{\pi}}},
#' \code{opchar_gs()} evaluates the power, ESS, and other key characteristics,
#' of each of the supplied designs.
#'
#' Calculations are performed conditional on the trial stopping in one of the
#' stages specified using the input (vector) \code{k}.
#'
#' @param des An object of class \code{"sa_des_gs"}, as returned by
#' \code{des_gs()}.
#' @param ... Additional objects of class \code{"sa_gs_gs"}. These will be
#' grouped in to a list named \code{"add_des"}.
#' @param k Calculations are performed conditional on the trial stopping in one
#' of the stages listed in vector \code{k}. Thus, \code{k} should be a vector of
#' integers, with elements between one and the maximum number of possible stages
#' across the supplied designs. If left unspecified, it will internally default
#' to all possible stages.
#' @param pi A vector of response probabilities to evaluate operating
#' characteristics at. This will internally default to be the
#' \ifelse{html}{\out{<i>π</i><sub>0</sub>}}{\deqn{\pi_0}} and
#' \ifelse{html}{\out{<i>π</i><sub>1</sub>}}{\deqn{\pi_1}} from the
#' supplied designs if it is left unspecified.
#' @param summary A logical variable indicating whether a summary of the
#' function's progress should be printed to the console.
#' @return A list of class \code{"sa_opchar_gs"} containing the following
#' elements
#' \itemize{
#' \item A tibble in the slot \code{$opchar} summarising the operating
#' characteristics of the supplied designs.
#' \item Each of the input variables as specified, subject to internal
#' modification.
#' }
#' @examples
#' # Find the optimal two-stage design for the default parameters
#' des <- des_gs()
#' # Determine operating characteristics for a range of response probabilities
#' opchar <- opchar_gs(des, pi = seq(0, 1, 0.01))
#' # Find the optimal two-stage design for a 10% type-I error rate
#' des_10 <- des_gs(alpha = 0.1)
#' # Determine operating characteristics for both designs at the same time
#' opchar_both <- opchar_gs(des, des_10, pi = seq(0, 1, 0.01))
#' @references Simon R (1989) Optimal two-stage designs for phase II clinical
#' trials. \emph{Controlled Clinical Trials} \strong{10:}1-10.
#' @seealso \code{\link{des_gs}}, \code{\link{est_gs}}, \code{\link{pval_gs}},
#' \code{\link{ci_gs}}, and their associated \code{plot} family of functions.
#' @export
#' @export
opchar_curtailed <- function(des, ..., k, pi, summary = F) {
##### Input Checking #########################################################
check_sa_des_curtailed(des, "des")
add_des <- pryr::named_dots(...)
num_add_des <- length(add_des)
if (num_add_des > 0) {
for (i in 1:num_add_des) {
check_sa_des_curtailed(eval(add_des[[i]]), paste("add_des", i, sep = ""))
}
for (i in 1:num_add_des) {
if (eval(add_des[[i]])$des$pi0 != des$des$pi0) {
stop("Each supplied design must have been designed for the same value of pi0")
}
}
}
if (!missing(pi)) {
check_pi(pi, "any")
} else {
pi <- c(des$des$pi0, des$des$pi1)
}
if (all(missing(k), num_add_des == 0)) {
k <- 1:des$des$J
} else if (all(missing(k), num_add_des > 0)) {
Js <- numeric(num_add_des + 1)
Js[1] <- des$des$J
for (i in 1:num_add_des) {
Js[i + 1] <- eval(add_des[[i]])$des$J
}
k <- 1:max(Js)
} else if (!missing(k)){
check_k(k, des, add_des)
}
check_logical(summary, "summary")
##### Print Summary ##########################################################
if (summary){
message(rep("-", 10))
message("Operating characteristic determination for curtailed group-sequential single-arm trials with a single binary endpoint")
message(rep("-", 10))
Sys.sleep(2)
message("You have chosen to make your calculations conditional on k \u2208 {", k[1], ",...,", k[length(k)], "}.\n")
Sys.sleep(2)
message("Beginning the required calculations...")
}
##### Main Computations ######################################################
if (num_add_des == 0) {
pmf <- pmf_curtailed(pi, des$des$J, des$des$J_curt, des$des$a_curt,
des$des$r_curt, des$des$n, des$des$n_curt, k)
opchar <- int_opchar_curtailed(pi, des$des$J, des$des$J_curt,
des$des$a_curt, des$des$r_curt,
des$des$n, des$des$n_curt,
cumsum(des$des$n), cumsum(des$des$n_curt),
k, pmf)
add_des <- NULL
} else {
opchar <- pmf <- list()
if (Js[1] == 1) {
des_val <- paste("Design 1: (", des$des$a, ",", des$des$r, ")/",
des$des$n, ", thetaF = ", des$des$thetaF,
", thetaE = ", des$des$thetaE, sep = "")
} else {
des_val <- paste("Design 1: ",
paste("(", des$des$a, ",", des$des$r, ")/",
cumsum(des$des$n), sep = "",
collapse = ", "), ", thetaF = (",
paste(des$des$thetaF, sep = "",
collapse = ","), "), thetaE = (",
paste(des$des$thetaE, sep = "", collapse = ","),
")", sep = "", collapse = "")
}
pmf[[1]] <-
cbind("Design" = des_val,
pmf_curtailed(pi, des$des$J, des$des$J_curt, des$des$a_curt,
des$des$r_curt, des$des$n, des$des$n_curt,
k[which(k <= Js[1])]))
opchar[[1]] <-
cbind("Design" = des_val,
int_opchar_curtailed(pi, des$des$J, des$des$J_curt,
des$des$a_curt, des$des$r_curt, des$des$n,
des$des$n_curt, cumsum(des$des$n),
cumsum(des$des$n_curt), k, pmf[[1]]))
if (summary) {
message("...performance for Design 1 evaluated...")
}
for (i in 1:num_add_des) {
des_i <- eval(add_des[[i]])
if (Js[i + 1] == 1) {
des_val <- paste("Design ", i + 1, ": (", des_i$des$a, ",", des_i$des$r,
")/", des_i$des$n, ", thetaF = ", des_i$des$thetaF,
", thetaE = ", des_i$des$thetaE, sep = "")
} else {
des_val <- paste("Design ", i + 1, ": ",
paste("(", des_i$des$a, ",", des_i$des$r, ")/",
cumsum(des_i$des$n), sep = "",
collapse = ", "), ", thetaF = (",
paste(des_i$des$thetaF, sep = "",
collapse = ","), "), thetaE = (",
paste(des_i$des$thetaE, sep = "", collapse = ","),
")", sep = "", collapse = "")
}
pmf[[i + 1]] <-
cbind("Design" = des_val,
pmf_curtailed(pi, des_i$des$J, des_i$des$J_curt, des_i$des$a_curt,
des_i$des$r_curt, des_i$des$n, des_i$des$n_curt,
k[which(k <= Js[i + 1])]))
opchar[[i + 1]] <-
cbind("Design" = des_val,
int_opchar_curtailed(pi, des_i$des$J, des_i$des$J_curt,
des_i$des$a_curt, des_i$des$r_curt, des_i$des$n,
des_i$des$n_curt, cumsum(des_i$des$n),
cumsum(des_i$des$n_curt),
k[which(k <= Js[i + 1])], pmf[[i + 1]]))
if (summary) {
message("...performance for Design ", i + 1, " evaluated...")
}
}
pmf <- tibble::as_tibble(plyr::rbind.fill(pmf))
pmf$m <- as.integer(pmf$m)
opchar <- tibble::as_tibble(plyr::rbind.fill(opchar))
opchar$Design <- as.factor(opchar$Design)
}
##### Outputting #############################################################
if (summary) {
message("...outputting.")
}
output <- list(opchar = opchar, pmf = pmf, des = des,
add_des = add_des, pi = pi, summary = summary)
class(output) <- "sa_opchar_curtailed"
return(output)
}
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