#' Optimal phase II/III drug development planning for multi-arm programs with
#' normally distributed endpoint
#'
#' The \code{\link{optimal_multiarm_normal}} function enables planning of
#' multi-arm phase II/III drug development programs with optimal sample size
#' allocation and go/no-go decision rules. For normally distributed endpoints,
#' the treatment effect is measured by the standardized difference in means
#' (Delta). So far, only three-arm trials with two treatments and one control
#' are supported. The assumed true treatment effects can be assumed fixed or
#' modelled by a prior distribution. The R Shiny application
#' \href{https://web.imbi.uni-heidelberg.de/prior/}{prior} visualizes the
#' prior distributions used in this package. Fast computing is enabled by
#' parallel programming.
#'
#' @name optimal_multiarm_normal
#' @inheritParams optimal_multiarm_generic
#' @inheritParams optimal_normal_generic
#' @param Delta1 assumed true treatment effect as the standardized difference in
#' means for treatment arm 1
#' @param Delta2 assumed true treatment effect as the standardized difference in
#' means for treatment arm 2
#'
#' @return
#' `r optimal_return_doc(type = "normal", setting = "multiarm")`
#'
#' @importFrom progressr progressor
#'
#' @examples
#' # Activate progress bar (optional)
#' \dontrun{progressr::handlers(global = TRUE)}
#' # Optimize
#' \donttest{
#' optimal_multiarm_normal(Delta1 = 0.375, Delta2 = 0.625,
#' n2min = 20, n2max = 100, stepn2 = 4, # define optimization set for n2
#' kappamin = 0.02, kappamax = 0.2, stepkappa = 0.02, # define optimization set for kappa
#' alpha = 0.025, beta = 0.1, # drug development planning parameters
#' c2 = 0.675, c3 = 0.72, c02 = 15, c03 = 20, # fixed/variable costs for phase II/III
#' K = Inf, N = Inf, S = -Inf, # set constraints
#' steps1 = 0, # define lower boundary for "small"
#' stepm1 = 0.5, # "medium"
#' stepl1 = 0.8, # and "large" effect size categories
#' b1 = 3000, b2 = 8000, b3 = 10000, # define expected benefits
#' strategy = 1,
#' num_cl = 1) # number of cores for parallelized computing
#' }
#' @references
#' Cohen, J. (1988). Statistical power analysis for the behavioral sciences.
#'
#' @export
optimal_multiarm_normal <- function(Delta1, Delta2,
n2min, n2max, stepn2,
kappamin, kappamax, stepkappa,
alpha, beta,
c2, c3, c02, c03,
K = Inf, N = Inf, S = -Inf,
steps1 = 0, stepm1 = 0.5, stepl1 = 0.8,
b1, b2, b3,
strategy, num_cl = 1){
steps2 <- stepm1
stepm2 <- stepl1
stepl2 <- Inf
date <- Sys.time()
KAPPA <- seq(kappamin, kappamax, stepkappa)
N2 <- seq(n2min, n2max, stepn2)
if(strategy==1){STRATEGY = 1}
if(strategy==2){STRATEGY = 2}
if(strategy==3){STRATEGY = c(1, 2)}
result <- NULL
kappa <- NA_real_
strategy <- NA_real_
cl <- parallel::makeCluster(getOption("cl.cores", num_cl)) #define cluster
parallel::clusterExport(cl, c("pmvnorm", "dmvnorm","qmvnorm","adaptIntegrate", "pgo_normal", "ss_normal", "Ess_normal",
"PsProg_normal", "alpha", "beta",
"steps1", "steps2", "stepm1", "stepm2", "stepl1", "stepl2",
"K", "N", "S", "strategy",
"c2", "c3", "c02", "c03",
"b1", "b2", "b3", "KAPPA",
"Delta1", "Delta2"), envir = environment())
for(strategy in STRATEGY){
ufkt <- spfkt <- pgofkt <- K2fkt <- K3fkt <-
sp2fkt <- sp3fkt <- n3fkt <- matrix(0, length(N2), length(KAPPA))
pb <- progressr::progressor(steps = length(KAPPA),
label = "Optimization progress",
message = "Optimization progress")
pb(paste("Performing optimization for strategy", strategy),
class = "sticky", amount = 0)
for(j in 1:length(KAPPA)){
kappa <- KAPPA[j]
res <- parallel::parSapply(cl, N2, utility_multiarm_normal, kappa,
alpha,beta, Delta1,Delta2,strategy,
c2,c02,c3,c03,K,N,S,
steps1, stepm1, stepl1,b1, b2, b3)
pb()
ufkt[, j] <- res[1, ]
n3fkt[, j] <- res[2, ]
spfkt[, j] <- res[3, ]
pgofkt[, j] <- res[4, ]
sp2fkt[, j] <- res[5, ]
sp3fkt[, j] <- res[6, ]
K2fkt[, j] <- res[7, ]
K3fkt[, j] <- res[8, ]
}
ind <- which(ufkt == max(ufkt), arr.ind <- TRUE)
I <- as.vector(ind[1, 1])
J <- as.vector(ind[1, 2])
Eud <- ufkt[I, J]
n3 <- n3fkt[I, J]
prob <- spfkt[I, J]
pg <- pgofkt[I, J]
k2 <- K2fkt[I, J]
k3 <- K3fkt[I, J]
prob2 <- sp2fkt[I, J]
prob3 <- sp3fkt[I, J]
result <- rbind(result, data.frame(Strategy = strategy,u = round(Eud,2), Kappa = KAPPA[J], n2 = N2[I],
n3 = n3, n = N2[I] + n3,
pgo = round(pg,2), sProg = round(prob,2),
Delta1 = Delta1, Delta2 = Delta2,
K = K, N = N, S = S, K2 = round(k2), K3 = round(k3),
sProg2 = round(prob2,2), sProg3 = round(prob3,2),
steps1 = round(steps1,2), stepm1 = round(stepm1,2), stepl1 = round(stepl1,2),
alpha = alpha, beta = beta,
c02 = c02, c03 = c03, c2 = c2, c3 = c3,
b1 = b1, b2 = b2, b3 = b3))
}
comment(result) <- c("\noptimization sequence Kappa:", KAPPA,
"\noptimization sequence n2:", N2,
"\nonset date:", as.character(date),
"\nfinish date:", as.character(Sys.time()))
class(result) <- c("drugdevelopResult", class(result))
parallel::stopCluster(cl)
return(result)
}
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