Nothing
#' @include randPar.R
NULL
###############################################
# --------------------------------------------#
# Class abcdPar #
# --------------------------------------------#
###############################################
# --------------------------------------------
# Function for validity check
# --------------------------------------------
# Validity check function for objects of the abcdPar class
#
# @inheritParams overview
#
# @return Returns a \code{TRUE}, if the settings of the object are valid.
validateabcdPar <- 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 abcdPar
# --------------------------------------------
# Randomization parameters generic
setClass("abcdPar",
slots = c(a = "numeric"),
contains = "randPar",
validity = validateabcdPar)
# --------------------------------------------
# Constructor function for abcdPar
# --------------------------------------------
#' Representing Accelerated Biased Coin Design
#'
#' Represents the randomization procedure Accelerated Biased Coin Design.
#'
#' @details
#' This is a class of 'biased coins' where the probability of selecting the under-represented
#' treatment is dependent from the absolute difference between the two treatment allocations
#' up to the current step.
#'
#' @family randomization procedures
#'
#' @inheritParams overview
#'
#' @references
#' A. B. Antognini and A. Giovagnoli (2004) A new 'biased coin design' for the sequential
#' allocation of two treatments.
#' \emph{Journal of the Royal Statistical Society. Series C (Applied Statistics)}
#' \strong{53}, No. 4, 651-664
#'
#' @return
#' \code{S4} object of the class \code{abcdPar}.
#'
#' @export
abcdPar <- function(N, a, groups = LETTERS[1:2]) {
new("abcdPar", N = N, a = a, K = 2, ratio = c(1, 1), groups = groups)
}
# --------------------------------------------
# Sampling algorithm for abcd
# --------------------------------------------
#' Sampling algorithm for abcd
#'
#' @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 A. Giovagnoli (2004) A new 'biased coin design' for the sequential
#' allocation of two treatments.
#' \emph{Journal of the Royal Statistical Society. Series C (Applied Statistics)}
#' \strong{53}, No. 4, 651-664
#'
abcdRand <- function(N, a, K = 2) {
stopifnot(round(N) == N)
if (!(K == 2)) stop("abcd: K > 2 not available yet.")
R <- numeric(N); reps <- 0; nA <- 0; nB <- 0; d <- 0
while(reps < N) {
# case analysis
if (abs(d) == 0) {
R[reps + 1] <- rbinom(1, 1, 0.5)
} else {
if(d>=1){
Fa <- 1/(abs(d)^a + 1)
} else {
Fa <- (abs(d)^a)/(abs(d)^a + 1)
}
R[reps + 1] <- rbinom(1, 1, 1 - Fa)
}
reps <- reps + 1
nB <- sum(R[1:reps])
nA <- reps - nB
d <- nA-nB
}
R
}
# --------------------------------------------
# Methods for abcdPar
# --------------------------------------------
#' @rdname generateAllSequences
setMethod("getAllSeq", signature(obj = "abcdPar"),
function(obj) {
new("abcdSeq",
M = compltSet(obj),
a = a(obj),
N = N(obj),
K = K(obj),
ratio = obj@ratio,
groups = obj@groups
)
}
)
#' @rdname generateRandomSequences
setMethod("genSeq", signature(obj = "abcdPar", r = "numeric", seed = "numeric"),
function(obj, r, seed) {
set.seed(seed)
new("rAbcdSeq",
M = t(sapply(1:r, function(x) {
abcdRand(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 = "abcdPar", r = "numeric", seed = "missing"),
function(obj, r, seed) {
seed <- sample(.Machine$integer.max, 1)
set.seed(seed)
new("rAbcdSeq",
M = t(sapply(1:r, function(x) {
abcdRand(N = N(obj), a = a(obj))
})),
N = N(obj),
a = a(obj),
K = K(obj),
groups = obj@groups,
ratio = obj@ratio,
seed = seed)
}
)
#' @rdname generateRandomSequences
setMethod("genSeq", signature(obj = "abcdPar", r = "missing", seed = "numeric"),
function(obj, r, seed) {
set.seed(seed)
new("rAbcdSeq",
M = t(abcdRand(N = N(obj), a = a(obj))),
a = a(obj),
N = N(obj),
K = K(obj),
groups = obj@groups,
ratio = obj@ratio,
seed = seed)
}
)
#' @rdname generateRandomSequences
setMethod("genSeq", signature(obj = "abcdPar", r = "missing", seed = "missing"),
function(obj, r, seed) {
seed <- sample(.Machine$integer.max, 1)
set.seed(seed)
new("rAbcdSeq",
M = t(abcdRand(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 = "abcdPar"),
function(obj) {
paste("ABCD(", obj@a, ")", sep = "")
}
)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.