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#' @include randPar.R
NULL
###############################################
# --------------------------------------------#
# Class bbcdPar #
# --------------------------------------------#
###############################################
# --------------------------------------------
# Function for validity check
# --------------------------------------------
# Validity check function for objects of the bbcdPar class
#
# @inheritParams overview
#
# @return Returns a \code{TRUE}, if the settings of the object are valid.
validatebbcdPar <- function(object) {
errors <- character()
a <- object@a
lengtha <- length(a)
if(lengtha != 1) {
msg <- paste("a has length ", lengtha, ". Should be length one.",
sep = "", collapse = "")
errors <- c(errors, msg)
}
if (a < 0) {
msg <- paste("First element of a is ", a, ". Should be positive.",
sep = "", collapse = "")
errors <- c(errors, msg)
}
if(length(errors) == 0) TRUE else errors
}
# --------------------------------------------
# Class definition for bbcdPar
# --------------------------------------------
# Randomization parameters generic
setClass("bbcdPar",
slots = c(a = "numeric"),
contains = "randPar",
validity = validatebbcdPar)
# --------------------------------------------
# Constructor function for bbcdPar
# --------------------------------------------
#' Representing Bayesian Biased Coin Design
#'
#' Represents the randomization procedure Bayesian Biased Coin Design.
#'
#' @details
#' Extension of Efron's biased coin design.
#'
#' @family randomization procedures
#'
#' @inheritParams overview
#'
#' @references
#' A. B. Antognini and Maroussa Zagoraiou (2014) Balance and randomness in sequential
#' clinical trials: the dominant biased coin design.
#' \emph{Pharmaceutical Statistics}
#' \strong{13(2)}, 119-127
#'
#' @return
#' \code{S4} object of the class \code{bbcdPar}.
#'
#' @export
bbcdPar <- function(N, a, groups = LETTERS[1:2]) {
new("bbcdPar", N = N, a = a, K = 2, ratio = c(1, 1), groups = groups)
}
# --------------------------------------------
# Sampling algorithm for bbcd
# --------------------------------------------
#' Sampling algorithm for bbcd
#'
#' @inheritParams overview
#'
#' @return A vector with the allocation sequence for a clinical trial.
#' It will contain a zero (resp. 1) at position \code{i}, when patient \code{i}
#' is allocated to treatment A (resp. B).
#'
#' @keywords internal
#'
#' @references
#' A. B. Antognini and Maroussa Zagoraiou (2014) Balance and randomness in sequential
#' clinical trials: the dominant biased coin design.
#' \emph{Pharmaceutical Statistics}
#' \strong{13(2)}, 119-127
#'
bbcdRand <- function(N, a, K = 2) {
stopifnot(round(N) == N)
if (!(K == 2)) stop("bbcd: K > 2 not available yet.")
R <- numeric(N); nA <- 0; nB <- 0
# special case for n = 1 and n = 2 (PBR for n = 2)
R[1] <- rbinom(1, 1, 0.5)
nB <- sum(R[1])
nA <- 1 - nB
R[2] <- ifelse(nB == 1, 0, 1)
reps <- 2
# n > 2
while(reps < N) {
nB <- sum(R[1:reps])
nA <- reps - nB
# case analysis
if (nA == nB) {
R[reps+1] <- rbinom(1, 1, 0.5)
} else {
f <- (1+nB/(reps*nA))^(1/a)/((1+nB/(reps*nA))^(1/a) + (1+nA/(reps*nB))^(1/a))
R[reps + 1] <- rbinom(1, 1, 1 - f)
}
reps <- reps + 1
}
R
}
# --------------------------------------------
# Methods for bbcdPar
# --------------------------------------------
#' @rdname generateAllSequences
setMethod("getAllSeq", signature(obj = "bbcdPar"),
function(obj) {
allSeqs <- compltSet(obj)
# Two successive treatment assignments at the beginning of the trial
# cannot be the same
inside <- which(apply(allSeqs, 1, function(x) sum(x[1:2]) == 1) == TRUE)
new("bbcdSeq",
M = allSeqs[inside,],
a = a(obj),
N = N(obj),
K = K(obj),
ratio = obj@ratio,
groups = obj@groups
)
}
)
#' @rdname generateRandomSequences
setMethod("genSeq", signature(obj = "bbcdPar", r = "numeric", seed = "numeric"),
function(obj, r, seed) {
set.seed(seed)
new("rbbcdSeq",
M = t(sapply(1:r, function(x) {
bbcdRand(N = N(obj), a = a(obj))
})),
N = N(obj),
a = a(obj),
K = K(obj),
ratio = obj@ratio,
groups = obj@groups,
seed = seed)
}
)
#' @rdname generateRandomSequences
setMethod("genSeq", signature(obj = "bbcdPar", r = "numeric", seed = "missing"),
function(obj, r, seed) {
seed <- sample(.Machine$integer.max, 1)
set.seed(seed)
new("rbbcdSeq",
M = t(sapply(1:r, function(x) {
bbcdRand(N = N(obj), a = a(obj))
})),
N = N(obj),
a = a(obj),
K = K(obj),
groups = obj@groups,
ratio = obj@ratio,
seed = seed)
}
)
#' @rdname generateRandomSequences
setMethod("genSeq", signature(obj = "bbcdPar", r = "missing", seed = "numeric"),
function(obj, r, seed) {
set.seed(seed)
new("rbbcdSeq",
M = t(bbcdRand(N = N(obj), a = a(obj))),
a = a(obj),
N = N(obj),
K = K(obj),
groups = obj@groups,
ratio = obj@ratio,
seed = seed)
}
)
#' @rdname generateRandomSequences
setMethod("genSeq", signature(obj = "bbcdPar", r = "missing", seed = "missing"),
function(obj, r, seed) {
seed <- sample(.Machine$integer.max, 1)
set.seed(seed)
new("rbbcdSeq",
M = t(bbcdRand(N = N(obj), a = a(obj))),
a = a(obj),
N = N(obj),
K = K(obj),
groups = obj@groups,
ratio = obj@ratio,
seed = seed)
}
)
#' @rdname getDesign
setMethod("getDesign",
signature(obj = "bbcdPar"),
function(obj) {
paste("BBCD(", obj@a, ")", sep = "")
}
)
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