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#' @include randPar.R
#' @include pbrPar.R
#' @include util.R
NULL
###############################################
# --------------------------------------------#
# Class pbrPar #
# --------------------------------------------#
###############################################
# --------------------------------------------
# Function for validity check
# --------------------------------------------
# Validity check function for objects of the pbrPar class
#
# @inheritParams overview
#
# @return Returns a \code{TRUE}, if the settings of the object are valid.
validaterpbrPar <- function(object) {
errors <- character()
rb <- randBlocks(object)
ratio <- object@ratio
filledBlock <- object@filledBlock
if(!all(rb > 0)) {
msg <- paste("At least one of the block lengths has value smaller or equal to zero.
Should be greater than zero.")
errors <- c(errors, msg)
}
if(!all(sapply(rb, function(x) x == round(x)))) {
msg <- paste("At least one of the block lengths is not an integer. Should be though.")
errors <- c(errors, msg)
}
if(!all(rb %% sum(ratio) == 0)) {
msg <- paste("One of the block length is not a multiple of sum(ratio) = "
, sum(ratio), ".", sep = "", collapse = "")
errors <- c(errors, msg)
}
if(length(filledBlock) > 1) {
msg <- paste("filledBlock has length ", length(filledBlock), ". Should be one.",
sep = "", collapse = "")
errors <- c(errors, msg)
}
if(length(errors) == 0) TRUE else errors
}
# --------------------------------------------
# Class definition for pbrPar
# --------------------------------------------
# Randomization parameters class
setClass("rpbrPar",
slots = c(rb = "numeric", filledBlock = "logical"),
contains = "randPar",
validity = validaterpbrPar)
#
# --------------------------------------------
# Constructor function for pbrPar
# --------------------------------------------
#' Representing Randomized Permuted Block Randomization
#'
#' Represents the randomization procedure Randomized Permuted Block Randomization.
#'
#' @details
#' Fix the possible random block lengths \code{rb}, the number of treatment groups \code{K},
#' the sample size \code{N} and the vector of the \code{ratio}. Afterwards, one block length is
#' randomly selected of the random block lengths. The patients are assigned
#' according to the ratio to the corresponding treatment groups. This procedure is repeated
#' until \code{N} patients are assigned. Within each block all possible
#' randomization sequences are equiprobable.
#'
#' @family randomization procedures
#'
#' @inheritParams overview
#'
#' @return
#' \code{S4} object of the class \code{rpbrPar}.
#'
#' @export
#'
#' @references
#' W. F. Rosenberger and J. M. Lachin (2002) \emph{Randomization in Clinical Trials}.
#' Wiley.
rpbrPar <- function(N, rb, K = 2, ratio = rep(1, K), groups = LETTERS[1:K],
filledBlock = FALSE) {
new("rpbrPar", rb = rb, N = N, K = K, ratio = ratio, groups = groups,
filledBlock = filledBlock)
}
# --------------------------------------------
# Methods for pbrPar
# --------------------------------------------
#' @rdname generateRandomSequences
setMethod("genSeq", signature(obj = "rpbrPar", r = "missing", seed = "numeric"),
function(obj, r, seed) {
set.seed(seed)
bc <- genBlockConst(N(obj), randBlocks(obj), obj@filledBlock)
new("rRpbrSeq",
M = t(blockRand(bc = bc, K = K(obj),
ratio = ratio(obj))[1:N(obj)]),
filledBlock = obj@filledBlock,
rb = randBlocks(obj),
bc = list(bc),
N = N(obj),
K = K(obj),
ratio = obj@ratio,
groups = obj@groups,
seed = seed)
}
)
#' @rdname generateRandomSequences
setMethod("genSeq", signature(obj = "rpbrPar", r = "numeric", seed = "numeric"),
function(obj, r, seed) {
set.seed(seed)
bc <- lapply(1:r, function(x) genBlockConst(N(obj),
randBlocks(obj), obj@filledBlock))
new("rRpbrSeq",
M = t(sapply(bc, function(x) (blockRand(bc = x, K = K(obj),
ratio = ratio(obj)))[1:N(obj)])),
filledBlock = obj@filledBlock,
rb = randBlocks(obj),
bc = bc,
N = N(obj),
K = K(obj),
ratio = obj@ratio,
groups = obj@groups,
seed = seed)
}
)
#' @rdname generateRandomSequences
setMethod("genSeq", signature(obj = "rpbrPar", r = "missing", seed = "missing"),
function(obj, r, seed) {
seed <- sample(.Machine$integer.max, 1)
set.seed(seed)
bc <- genBlockConst(N(obj), randBlocks(obj), obj@filledBlock)
new("rRpbrSeq",
M = t(blockRand(bc = bc, K = K(obj), ratio = ratio(obj))[1:N(obj)]),
filledBlock = obj@filledBlock,
rb = randBlocks(obj),
bc = list(bc),
N = N(obj),
K = K(obj),
ratio = obj@ratio,
groups = obj@groups,
seed = seed)
}
)
#' @rdname generateRandomSequences
setMethod("genSeq", signature(obj = "rpbrPar", r = "numeric", seed = "missing"),
function(obj, r, seed) {
seed <- sample(.Machine$integer.max, 1)
set.seed(seed)
bc <- lapply(1:r, function(x) genBlockConst(N(obj),
randBlocks(obj), obj@filledBlock))
new("rRpbrSeq",
M = t(sapply(bc, function(x) (blockRand(bc = x, K = K(obj),
ratio = ratio(obj)))[1:N(obj)])),
filledBlock = obj@filledBlock,
bc = bc,
rb = randBlocks(obj),
N = N(obj),
K = K(obj),
ratio = obj@ratio,
groups = obj@groups,
seed = seed)
}
)
#' @rdname getDesign
setMethod("getDesign",
signature(obj = "rpbrPar"),
function(obj) {
rb <- capture.output(cat(obj@rb, sep = ","))
if (obj@filledBlock) {
paste(c("RPBRFB(", rb, ")"), sep = "", collapse = "")
} else {
paste(c("RPBR(", rb, ")"), sep = "", collapse = "")
}
}
)
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