Nothing
#' @include randPar.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.
validatepbrPar <- function(object) {
errors <- character()
bc <- object@bc
ratio <- object@ratio
# if(!all(bc > 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(bc, 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(bc %% sum(ratio) == 0)) {
msg <- paste("One of the block lengths is not a multiple of sum(ratio) = "
, sum(ratio), ".", sep = "", collapse = "")
errors <- c(errors, msg)
}
if(length(errors) == 0) TRUE else errors
}
# --------------------------------------------
# Class definition for pbrPar
# --------------------------------------------
# Randomization parameters generic
setClass("pbrPar",
slots = c(bc = "numeric"),
contains = "randPar",
validity = validatepbrPar)
# --------------------------------------------
# Constructor function for pbrPar
# --------------------------------------------
#' Representing Permuted Block Randomization
#'
#' Represents the randomization procedure Permuted Block Randomization.
#'
#' @details
#' Fix the block constellation \code{bc}, the number of treatment groups \code{K},
#' and the vector of the \code{ratio}. Afterwards,
#' in each block the patients are assigned according to the ratio to the
#' corresponding treatment groups. All generated randomization sequences
#' are equiprobable.
#'
#' @family randomization procedures
#'
#' @inheritParams overview
#'
#' @return
#' \code{S4} object of the class \code{pbrPar}.
#'
#' @export
#'
#' @references
#' W. F. Rosenberger and J. M. Lachin (2002) \emph{Randomization in Clinical Trials}.
#' Wiley.
pbrPar <- function(bc, K = 2, ratio = rep(1, K), groups = LETTERS[1:K]) {
new("pbrPar", bc = bc, N = sum(bc), K = K, ratio = ratio, groups = groups)
}
# --------------------------------------------
# Sampling alogorithm for PBR
# --------------------------------------------
# Permuted block randomization
#
# Compute a permuted block randomization sequence for a clinical trial with
# several blocks.
#
# @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).
#
blockRand <- function(bc, K = 2, ratio = rep(1, K)) {
as.vector(unlist(sapply(bc, function(k) blockSeq(k, K, ratio))))
}
# Permuted block randomization
#
# Compute a permuted block randomization sequence for a clinical trial for
# one block.
#
# @inheritParams overview
#
# @return
# A vector with the allocation sequence for a clinical trial for one block.
#
blockSeq <- function(k, K = 2, ratio = rep(1, K)) {
ratio <- ratio/sum(ratio)
sample(rep(0:(K-1), times = ratio*k))
}
# --------------------------------------------
# Methods for pbrPar
# --------------------------------------------
#' @rdname generateAllSequences
setMethod("getAllSeq",
signature(obj = "pbrPar"),
function(obj) {
if(obj@K != 2 || !identical(obj@ratio, c(1,1))) {
stop("Only possible for K equals 2 and ratio corresponds to c(1,1).")
}
allSeqs <- compltSet(obj)
blockEnds <- cumsum(blocks(obj))
bal <- apply(allSeqs,1, function(x, blockEnds) {
all(cumsum(2*x-1)[blockEnds] == 0)
}, blockEnds = blockEnds)
new("pbrSeq",
M = allSeqs[bal, ],
bc = blocks(obj),
N = N(obj),
K = K(obj),
ratio = obj@ratio,
groups = obj@groups)
}
)
#' @rdname generateRandomSequences
setMethod("genSeq",
signature(obj = "pbrPar", r = "missing", seed = "numeric"),
function(obj, r, seed) {
set.seed(seed)
new("rPbrSeq",
M = t(blockRand(bc = blocks(obj), K = K(obj),
ratio = ratio(obj))),
bc = blocks(obj),
N = N(obj),
K = K(obj),
ratio = obj@ratio,
groups = obj@groups,
seed = seed)
}
)
#' @rdname generateRandomSequences
setMethod("genSeq",
signature(obj = "pbrPar", r = "numeric", seed = "numeric"),
function(obj, r, seed) {
set.seed(seed)
new("rPbrSeq",
M = t(sapply(1:r, function(x) {
blockRand(bc = blocks(obj), K = K(obj), ratio = ratio(obj))
})),
bc = blocks(obj),
N = N(obj),
K = K(obj),
ratio = obj@ratio,
groups = obj@groups,
seed = seed)
}
)
#' @rdname generateRandomSequences
setMethod("genSeq",
signature(obj = "pbrPar", r = "missing", seed = "missing"),
function(obj, r, seed) {
seed <- sample(.Machine$integer.max, 1)
set.seed(seed)
new("rPbrSeq",
M = t(blockRand(bc = blocks(obj), K = K(obj),
ratio = ratio(obj))),
bc = blocks(obj),
N = N(obj),
K = K(obj),
ratio = obj@ratio,
groups = obj@groups,
seed = seed)
}
)
#' @rdname generateRandomSequences
setMethod("genSeq",
signature(obj = "pbrPar", r = "numeric", seed = "missing"),
function(obj, r, seed) {
seed <- sample(.Machine$integer.max, 1)
set.seed(seed)
new("rPbrSeq",
M = t(sapply(1:r, function(x) {
blockRand(bc = blocks(obj), K = K(obj), ratio = ratio(obj))
})),
bc = blocks(obj),
N = N(obj),
K = K(obj),
ratio = obj@ratio,
groups = obj@groups,
seed = seed)
}
)
#' @rdname getDesign
setMethod("getDesign",
signature(obj = "pbrPar"),
function(obj) {
if (sum(!duplicated(obj@bc)) == 1) {
paste("PBR(", obj@bc[1], ")", sep = "")
} else {
bc <- capture.output(cat(obj@bc, sep = ","))
paste(c("PBR(", bc, ")"), sep = "", collapse = "")
}
}
)
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.