R/updateBoundaries.R
In paulowhite/DelayedGSD: Planning and analysis of group sequential trial with pipeline data
Defines functions
updateBoundaries
Documented in
updateBoundaries
## * updateBoundaries (documentation)
#' @title Update Boundaries of a GSD
#' @description Recompute the boundaries based according to the current information.
#'
#' @param object Object of type \code{delayedGSD}, typically output from \code{\link{CalcBoundaries}}.
#' @param Info.i [numeric vector of size k] Optional argument used to update the information at interim (only past or current information).
#' @param Info.d [numeric vector of size k] Optional argument used to update the information at decision or final (observed or predicted information).
#' @param k [integer] Index of the analysis.
#' @param type.k [character] Type of analysis: \code{"interim"} (after continuing recruitment),
#' \code{"decision"} (after stopping recruitment for efficacy or futility),
#' or \code{"final"} (after reaching the last stage of the trial).
#' @param trace [logical] should the execution of the function be traced?
#' @param update.stage [logical] should the arguments \code{k} and \code{type.k} be used to update to stage of the trial?
#'
## * updateBoundaries (example)
#' @examples
#'
#' #### Planning #####
#' theAlpha <- 0.025
#' theBeta <- 0.2
#' theDelta <- 1.5
#' theK <- 2
#' theN <- 82
#'
#' myBound0 <- CalcBoundaries(kMax=theK,
#' alpha=theAlpha,
#' beta=theBeta,
#' InfoR.i=c(0.5,1),
#' rho_alpha=2,
#' rho_beta=2,
#' method=1,
#' delta=theDelta,
#' InfoR.d=0.55)
#'
#' #### Simulate data ####
#' ## generate data with all data for in case trial completes
#' set.seed(10)
#' theData <- GenData(n=theN*2,delta=theDelta*0.8,ar=5)
#'
#' theAR <- 10 #accrual rate (pt per month)
#' theDelay <- 0.7500001 #time in months to process data
#' tau.i <- theData$d$t3[theN + ceiling(theAR*theDelay)] #time point at which to do IA
#'
#'
#' #### Analyse data at the first interim ####
#' theInterimData <- SelectData(theData$d, t = tau.i)
#'
#' myLMM <- analyzeData(theInterimData)
#' myBound1 <- update(myBound0, delta = myLMM)
#' print(myBound1)
#' print(myBound1, planned = FALSE)
#' print(myBound1, planned = "only")
#'
#' par(mfrow = c(1,2))
#' plot(myBound1, planned = "only")
#' plot(myBound1)
#'
#' #### Analyse data at the final ####
#' theFinalData <- SelectData(theData$d, t = 1e7, Delta.t = theDelay)
#'
#' myLMM <- analyzeData(theFinalData)
#' myBound2 <- update(myBound1, delta = myLMM)
#' plot(myBound2)
## * updateBoundaries (code)
#' @export
updateBoundaries <- function(object, delta, Info.i, Info.d, k, type.k, update.stage, trace = FALSE){
kMax <- object$kMax
Info.max <- object$planned$Info.max
uk <- object$uk
lk <- object$lk
ck <- object$ck
bindingFutility <- object$bindingFutility
method <- object$method
## ** update information
if(missing(Info.i)){
Info.i <- object$Info.i
}else{
if(type.k=="decision"){
object$Info.i[k+1] <- Info.i
}else{
object$Info.i[k] <- Info.i
}
}
if(missing(Info.d)){
Info.d <- object$Info.d
}else{
if(type.k=="decision"){
object$Info.d[k+1] <- Info.d
}else{
object$Info.d[k] <- Info.d
}
}
if(!missing(delta)){
if(type.k=="decision"){
object$delta$estimate[k+1] <- delta
}else{
object$delta$estimate[k] <- delta
}
}
## ** update boundaries
#browser()
## *** at interim
if(type.k == "interim"){
if(k>1 && (Info.i[k] < Info.i[k-1])){
## continue to the next interim when information decreased
object$lk[k] <- -Inf
object$uk[k] <- +Inf
object$ck[k] <- NA
object$conclusion["interim",k] <- "continue"
object$conclusion["reason.interim",k] <- "decreasing information"
object$alphaSpent[k] <- object$alphaSpent[k-1]
object$betaSpent[k] <- object$betaSpent[k-1]
}else if((Info.i[k] >= Info.max) || (!is.na(Info.d[k]) && Info.d[k] >= Info.max)){
## stop and do decision when Imax is already reached or anticipated to be reached
object$lk[k] <- -Inf
object$uk[k] <- +Inf
object$ck[k] <- NA
object$conclusion["interim",k] <- "stop"
object$conclusion["reason.interim",k] <- "Imax reached"
object$alphaSpent[k] <- object$alpha
object$betaSpent[k] <- object$beta
}else{
## usual evaluation
if(method==1){
newBounds <- updateMethod1(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = FALSE,
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = object$Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding = bindingFutility,
Trace = trace,
cMin = object$cMin,
PowerCorrection=object$PowerCorrection)
} else if(method==2){
newBounds <- updateMethod2(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = FALSE,
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = object$Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace,
cMin = object$cMin)
} else if(method==3){
newBounds <- updateMethod3(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = FALSE,
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = object$Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace)
}
object$lk[k] <- newBounds$lk[k]
object$uk[k] <- newBounds$uk[k]
object$ck[k] <- newBounds$ck
object$ck.unrestricted[k] <- newBounds$ck.unrestricted
object$alphaSpent[k] <- newBounds$alphaSpent[k]
object$betaSpent[k] <- newBounds$betaSpent[k]
object$lk[(k+1):kMax] <- NA
object$uk[(k+1):kMax] <- NA
#if(k<kMax){
# object$lk[(k+1):kMax] <- NA
#
# if(k<kMax-1){
# object$ck[(k+1):kMax] <- NA
# object$ck.unrestricted[(k+1):kMax] <- NA
# }
#}
}
}
## *** at decision
if(type.k == "decision"){
if(Info.d[k] < Info.i[k]){ ## if information has decreased since interim analysis
object$conclusion["comment.decision",k] <- "decreasing information"
warning("Information has decreased between interim and decision, replacing information at decision with information at interim + epsilon. \n")
Info.d[k] <- Info.i[k]+Info.i[k]/10000
## Possible solution: when estimating ck by balancing the probability of reversal, add a term corresponding to the type 1 error we should have spent vs. the type 1 error we spent.
## usual evaluation
if(method==1){
newBounds <- updateMethod1(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = (object$conclusion["reason.interim",k]=="Imax reached"),
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace,
cMin = object$cMin,
PowerCorrection=object$PowerCorrection)
} else if(method==2){
newBounds <- updateMethod2(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = (object$conclusion["reason.interim",k]=="Imax reached"),
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace,
cMin = object$cMin)
} else if(method==3){
newBounds <- updateMethod3(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = (object$conclusion["reason.interim",k]=="Imax reached"),
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace)
}
object$ck[k] <- newBounds$ck
if(k<kMax){
object$ck.unrestricted[k] <- newBounds$ck.unrestricted
}
if(k<kMax-1){
object$ck[(k+1):kMax] <- NA
}
}else{
## NOTE: include special case Info.d[k] >= Info.max which is treated as usual - conservative procedure
## usual evaluation
if(method==1){
newBounds <- updateMethod1(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = (object$conclusion["reason.interim",k]=="Imax reached"),
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = object$Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace,
cMin = object$cMin,
PowerCorrection=object$PowerCorrection)
} else if(method==2){
newBounds <- updateMethod2(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = (object$conclusion["reason.interim",k]=="Imax reached"),
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = object$Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace,
cMin = object$cMin)
} else if(method==3){
newBounds <- updateMethod3(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = (object$conclusion["reason.interim",k]=="Imax reached"),
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = object$Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding = bindingFutility,
Trace = trace)
}
object$ck[k] <- newBounds$ck
object$ck.unrestricted[k] <- newBounds$ck.unrestricted
if(k<kMax-1){
object$ck[(k+1):kMax] <- NA
object$ck.unrestricted[(k+1):kMax] <- NA
}
}
}
## *** at final
if(type.k == "final"){ ## that could be replace by a call to CalcBoundaries
if(Info.d[k] < Info.i[k-1]){
object$conclusion["comment.decision",k] <- "decreasing information"
warning("boundaries will not be computed correctly")
}
if(method==1){
newBounds <- updateMethod1(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = FALSE,
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = object$Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace,
cMin = object$cMin,
PowerCorrection=object$PowerCorrection)
} else if(method==2){
newBounds <- updateMethod2(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = FALSE,
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = object$Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace,
cMin = object$cMin)
} else if(method==3){
newBounds <- updateMethod3(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = FALSE,
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = object$Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace)
}
#object$uk[k] <- newBounds$uk[k]
#object$lk[k] <- newBounds$lk[k]
object$ck[k] <- newBounds$ck
object$ck.unrestricted[k] <- newBounds$ck.unrestricted
object$alphaSpent[k] <- newBounds$alphaSpent[k]
object$betaSpent[k] <- newBounds$betaSpent[k]
}
## ** export stage
if(update.stage){
object$stage$k <- k
object$stage$type <- type.k
}
## ** export object
return(object)
}
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Defines functions updateBoundaries
Documented in updateBoundaries
## * updateBoundaries (documentation)
#' @title Update Boundaries of a GSD
#' @description Recompute the boundaries based according to the current information.
#'
#' @param object Object of type \code{delayedGSD}, typically output from \code{\link{CalcBoundaries}}.
#' @param Info.i [numeric vector of size k] Optional argument used to update the information at interim (only past or current information).
#' @param Info.d [numeric vector of size k] Optional argument used to update the information at decision or final (observed or predicted information).
#' @param k [integer] Index of the analysis.
#' @param type.k [character] Type of analysis: \code{"interim"} (after continuing recruitment),
#' \code{"decision"} (after stopping recruitment for efficacy or futility),
#' or \code{"final"} (after reaching the last stage of the trial).
#' @param trace [logical] should the execution of the function be traced?
#' @param update.stage [logical] should the arguments \code{k} and \code{type.k} be used to update to stage of the trial?
#'
## * updateBoundaries (example)
#' @examples
#'
#' #### Planning #####
#' theAlpha <- 0.025
#' theBeta <- 0.2
#' theDelta <- 1.5
#' theK <- 2
#' theN <- 82
#'
#' myBound0 <- CalcBoundaries(kMax=theK,
#' alpha=theAlpha,
#' beta=theBeta,
#' InfoR.i=c(0.5,1),
#' rho_alpha=2,
#' rho_beta=2,
#' method=1,
#' delta=theDelta,
#' InfoR.d=0.55)
#'
#' #### Simulate data ####
#' ## generate data with all data for in case trial completes
#' set.seed(10)
#' theData <- GenData(n=theN*2,delta=theDelta*0.8,ar=5)
#'
#' theAR <- 10 #accrual rate (pt per month)
#' theDelay <- 0.7500001 #time in months to process data
#' tau.i <- theData$d$t3[theN + ceiling(theAR*theDelay)] #time point at which to do IA
#'
#'
#' #### Analyse data at the first interim ####
#' theInterimData <- SelectData(theData$d, t = tau.i)
#'
#' myLMM <- analyzeData(theInterimData)
#' myBound1 <- update(myBound0, delta = myLMM)
#' print(myBound1)
#' print(myBound1, planned = FALSE)
#' print(myBound1, planned = "only")
#'
#' par(mfrow = c(1,2))
#' plot(myBound1, planned = "only")
#' plot(myBound1)
#'
#' #### Analyse data at the final ####
#' theFinalData <- SelectData(theData$d, t = 1e7, Delta.t = theDelay)
#'
#' myLMM <- analyzeData(theFinalData)
#' myBound2 <- update(myBound1, delta = myLMM)
#' plot(myBound2)
## * updateBoundaries (code)
#' @export
updateBoundaries <- function(object, delta, Info.i, Info.d, k, type.k, update.stage, trace = FALSE){
kMax <- object$kMax
Info.max <- object$planned$Info.max
uk <- object$uk
lk <- object$lk
ck <- object$ck
bindingFutility <- object$bindingFutility
method <- object$method
## ** update information
if(missing(Info.i)){
Info.i <- object$Info.i
}else{
if(type.k=="decision"){
object$Info.i[k+1] <- Info.i
}else{
object$Info.i[k] <- Info.i
}
}
if(missing(Info.d)){
Info.d <- object$Info.d
}else{
if(type.k=="decision"){
object$Info.d[k+1] <- Info.d
}else{
object$Info.d[k] <- Info.d
}
}
if(!missing(delta)){
if(type.k=="decision"){
object$delta$estimate[k+1] <- delta
}else{
object$delta$estimate[k] <- delta
}
}
## ** update boundaries
#browser()
## *** at interim
if(type.k == "interim"){
if(k>1 && (Info.i[k] < Info.i[k-1])){
## continue to the next interim when information decreased
object$lk[k] <- -Inf
object$uk[k] <- +Inf
object$ck[k] <- NA
object$conclusion["interim",k] <- "continue"
object$conclusion["reason.interim",k] <- "decreasing information"
object$alphaSpent[k] <- object$alphaSpent[k-1]
object$betaSpent[k] <- object$betaSpent[k-1]
}else if((Info.i[k] >= Info.max) || (!is.na(Info.d[k]) && Info.d[k] >= Info.max)){
## stop and do decision when Imax is already reached or anticipated to be reached
object$lk[k] <- -Inf
object$uk[k] <- +Inf
object$ck[k] <- NA
object$conclusion["interim",k] <- "stop"
object$conclusion["reason.interim",k] <- "Imax reached"
object$alphaSpent[k] <- object$alpha
object$betaSpent[k] <- object$beta
}else{
## usual evaluation
if(method==1){
newBounds <- updateMethod1(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = FALSE,
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = object$Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding = bindingFutility,
Trace = trace,
cMin = object$cMin,
PowerCorrection=object$PowerCorrection)
} else if(method==2){
newBounds <- updateMethod2(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = FALSE,
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = object$Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace,
cMin = object$cMin)
} else if(method==3){
newBounds <- updateMethod3(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = FALSE,
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = object$Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace)
}
object$lk[k] <- newBounds$lk[k]
object$uk[k] <- newBounds$uk[k]
object$ck[k] <- newBounds$ck
object$ck.unrestricted[k] <- newBounds$ck.unrestricted
object$alphaSpent[k] <- newBounds$alphaSpent[k]
object$betaSpent[k] <- newBounds$betaSpent[k]
object$lk[(k+1):kMax] <- NA
object$uk[(k+1):kMax] <- NA
#if(k<kMax){
# object$lk[(k+1):kMax] <- NA
#
# if(k<kMax-1){
# object$ck[(k+1):kMax] <- NA
# object$ck.unrestricted[(k+1):kMax] <- NA
# }
#}
}
}
## *** at decision
if(type.k == "decision"){
if(Info.d[k] < Info.i[k]){ ## if information has decreased since interim analysis
object$conclusion["comment.decision",k] <- "decreasing information"
warning("Information has decreased between interim and decision, replacing information at decision with information at interim + epsilon. \n")
Info.d[k] <- Info.i[k]+Info.i[k]/10000
## Possible solution: when estimating ck by balancing the probability of reversal, add a term corresponding to the type 1 error we should have spent vs. the type 1 error we spent.
## usual evaluation
if(method==1){
newBounds <- updateMethod1(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = (object$conclusion["reason.interim",k]=="Imax reached"),
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace,
cMin = object$cMin,
PowerCorrection=object$PowerCorrection)
} else if(method==2){
newBounds <- updateMethod2(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = (object$conclusion["reason.interim",k]=="Imax reached"),
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace,
cMin = object$cMin)
} else if(method==3){
newBounds <- updateMethod3(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = (object$conclusion["reason.interim",k]=="Imax reached"),
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace)
}
object$ck[k] <- newBounds$ck
if(k<kMax){
object$ck.unrestricted[k] <- newBounds$ck.unrestricted
}
if(k<kMax-1){
object$ck[(k+1):kMax] <- NA
}
}else{
## NOTE: include special case Info.d[k] >= Info.max which is treated as usual - conservative procedure
## usual evaluation
if(method==1){
newBounds <- updateMethod1(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = (object$conclusion["reason.interim",k]=="Imax reached"),
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = object$Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace,
cMin = object$cMin,
PowerCorrection=object$PowerCorrection)
} else if(method==2){
newBounds <- updateMethod2(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = (object$conclusion["reason.interim",k]=="Imax reached"),
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = object$Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace,
cMin = object$cMin)
} else if(method==3){
newBounds <- updateMethod3(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = (object$conclusion["reason.interim",k]=="Imax reached"),
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = object$Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding = bindingFutility,
Trace = trace)
}
object$ck[k] <- newBounds$ck
object$ck.unrestricted[k] <- newBounds$ck.unrestricted
if(k<kMax-1){
object$ck[(k+1):kMax] <- NA
object$ck.unrestricted[(k+1):kMax] <- NA
}
}
}
## *** at final
if(type.k == "final"){ ## that could be replace by a call to CalcBoundaries
if(Info.d[k] < Info.i[k-1]){
object$conclusion["comment.decision",k] <- "decreasing information"
warning("boundaries will not be computed correctly")
}
if(method==1){
newBounds <- updateMethod1(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = FALSE,
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = object$Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace,
cMin = object$cMin,
PowerCorrection=object$PowerCorrection)
} else if(method==2){
newBounds <- updateMethod2(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = FALSE,
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = object$Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace,
cMin = object$cMin)
} else if(method==3){
newBounds <- updateMethod3(rho_alpha = object$planned$rho_alpha,
rho_beta = object$planned$rho_beta,
alpha = object$alpha, alphaSpent = object$alphaSpent,
beta = object$beta, betaSpent = object$betaSpent,
Kmax = object$kMax,
Info.max = object$planned$Info.max,
uk = object$uk,
lk = object$lk,
k = k, type.k = type.k, ImaxAnticipated = FALSE,
InfoR.i = object$Info.i/object$planned$Info.max,
InfoR.d = object$Info.d/object$planned$Info.max,
delta = object$planned$delta, ## object$delta$estimate,
alternative = object$alternative,
binding=bindingFutility,
Trace = trace)
}
#object$uk[k] <- newBounds$uk[k]
#object$lk[k] <- newBounds$lk[k]
object$ck[k] <- newBounds$ck
object$ck.unrestricted[k] <- newBounds$ck.unrestricted
object$alphaSpent[k] <- newBounds$alphaSpent[k]
object$betaSpent[k] <- newBounds$betaSpent[k]
}
## ** export stage
if(update.stage){
object$stage$k <- k
object$stage$type <- type.k
}
## ** export object
return(object)
}
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