R/seq_fletcher.R
In mjg211/xover: Design and analysis of cross-over clinical trials
Defines functions
seq_fletcher
Documented in
seq_fletcher
#' Fletcher (1987) cross-over design specification
#'
#' Specifies cross-over designs from Fletcher (1987).
#'
#' \code{seq_fletcher()} supports the specification of designs from Fletcher
#' (1987). Deisgns for four, six, eight, and nine treatments (see
#' \code{D}) are supported, for any chosen treatment labels (see \code{labels}).
#' In addition, the designs can be returned in \code{\link[base]{matrix}} or
#' \code{\link[tibble]{tibble}} form (see \code{as_matrix}).
#'
#' Precisely, for \code{D} equal to four, six, eight, and nine, there are four,
#' three, 12, and nine designs available respectively (accessible by setting
#' \code{selection} equal to one through twelve asappropriate). Ultimately, the
#' \ifelse{html}{\out{(<i>k</i>,<i>j</i>)}}{\eqn{(k,j)}}th element of the
#' cross-over design matrix corresponds to the treatment a subject on the
#' \ifelse{html}{\out{<i>k</i>}}{\eqn{k}}th sequence would receive in the
#' \ifelse{html}{\out{<i>j</i>}}{\eqn{j}}th period.
#'
#' @param D The number of treatments. Must be either four, six, eight, or nine.
#' Defaults to \code{4}.
#' @param selection A single \code{\link[base]{numeric}} integer indicating
#' which design to return, for the chosen value of \code{D}. See
#' \strong{Details} for information on supported values.
#' @param labels A \code{\link[base]{vector}} of labels for the treatments.
#' Should be of \code{\link[base]{length}} \code{D}, containing unique elements.
#' Defaults to \code{0:(D - 1)}.
#' @param as_matrix A \code{\link[base]{logical}} variable indicating whether
#' the design should be returned as a \code{\link[base]{matrix}}, or a
#' \code{\link[tibble]{tibble}}. Defaults to \code{T}.
#' @param summary A \code{\link[base]{logical}} variable indicating whether a
#' summary of the function's progress should be printed to the console. Defaults
#' to \code{T}.
#' @return Either a \code{\link[base]{matrix}} if \code{as_matrix = T} (with
#' rows corresponding to sequences and columns to periods), or a
#' \code{\link[tibble]{tibble}} if \code{as_matrix = F} (with rows corresponding
#' to a particular period on a particular sequence). In either case, the
#' returned object will have class \code{xover_seq}.
#' @examples
#' # Fletcher (1987) designs for four treatments
#' fletcher1 <- seq_fletcher(D = 4)
#' fletcher2 <- seq_fletcher(D = 4, selection = 2)
#' fletcher3 <- seq_fletcher(D = 4, selection = 3)
#' fletcher4 <- seq_fletcher(D = 4, selection = 4)
#' # Using different labels
#' fletcher1_ABCD <- seq_fletcher(D = 4, labels = LETTERS[1:4])
#' fletcher2_ABCD <- seq_fletcher(D = 4, selection = 2, labels = LETTERS[1:4])
#' fletcher3_ABCD <- seq_fletcher(D = 4, selection = 3, labels = LETTERS[1:4])
#' fletcher4_ABCD <- seq_fletcher(D = 4, selection = 4, labels = LETTERS[1:4])
#' # Returning in tibble form
#' fletcher1_tibble <- seq_fletcher(D = 4, as_matrix = F)
#' fletcher2_tibble <- seq_fletcher(D = 4, selection = 2, as_matrix = F)
#' fletcher3_tibble <- seq_fletcher(D = 4, selection = 3, as_matrix = F)
#' fletcher4_tibble <- seq_fletcher(D = 4, selection = 4, as_matrix = F)
#' @references Fletcher DJ (1987) A new class of change-over designs for
#' factorial experiments. \emph{Biometrika} \strong{74:}649-54.
#' @author Based on data from the \code{\link[Crossover]{Crossover}} package by
#' Kornelius Rohmeyer.
#' @export
seq_fletcher <- function(D = 6, selection = 1, labels = 0:(D - 1),
as_matrix = T, summary = T) {
##### Input checking #########################################################
check_belong(D, "D", c(4, 6, 8, 9), 1)
check_selection(selection, c(NA, NA, NA, 4, NA, 3, NA, 12, 9), D)
check_labels(labels, D)
check_logical(as_matrix, "as_matrix")
check_logical(summary, "summary")
##### Main computations ######################################################
if (summary) {
message(" Beginning the design specification...")
}
if (all(D == 4, selection == 1)) {
sequences <- matrix(c(1, 2, 4, 2, 1, 3, 3, 4, 2, 4, 3, 1), 4, 3, byrow = T)
} else if (all(D == 4, selection == 2)) {
sequences <- matrix(c(1, 2, 4, 2, 1, 3, 3, 4, 2, 4, 3, 1, 1, 4, 2, 2, 3, 1,
3, 2, 4, 4, 1, 3), 8, 3, byrow = T)
} else if (all(D == 4, selection == 3)) {
sequences <- matrix(c(1, 2, 4, 3, 2, 1, 3, 4, 3, 4, 2, 1, 4, 3, 1, 2), 4, 4,
byrow = T)
} else if (all(D == 4, selection == 4)) {
sequences <- matrix(c(1, 2, 4, 3, 2, 1, 3, 4, 3, 4, 2, 1, 4, 3, 1, 2, 1, 3,
4, 2, 2, 4, 3, 1, 3, 1, 2, 4, 4, 2, 1, 3), 8, 4,
byrow = T)
} else if (all(D == 6, selection == 1)) {
sequences <- matrix(c(1, 5, 6, 2, 2, 6, 4, 3, 3, 4, 5, 1, 4, 2, 3, 5, 5, 3,
1, 6, 6, 1, 2, 4), 6, 4, byrow = T)
} else if (all(D == 6, selection == 2)) {
sequences <- matrix(c(1, 5, 6, 2, 2, 6, 4, 3, 3, 4, 5, 1, 4, 2, 3, 5, 5, 3,
1, 6, 6, 1, 2, 4, 1, 3, 5, 6, 2, 1, 6, 4, 3, 2, 4, 5,
4, 6, 2, 3, 5, 4, 3, 1, 6, 5, 1, 2), 12, 4, byrow = T)
} else if (all(D == 6, selection == 3)) {
sequences <- matrix(c(1, 3, 4, 5, 2, 2, 1, 5, 6, 3, 3, 2, 6, 4, 1, 4, 6, 1,
2, 5, 5, 4, 2, 3, 6, 6, 5, 3, 1, 4), 6, 5, byrow = T)
} else if (all(D == 6, selection == 4)) {
sequences <- matrix(c(1, 3, 4, 5, 2, 2, 1, 5, 6, 3, 3, 2, 6, 4, 1, 4, 6, 1,
2, 5, 5, 4, 2, 3, 6, 6, 5, 3, 1, 4, 1, 2, 4, 6, 3, 2,
3, 5, 4, 1, 3, 1, 6, 5, 2, 4, 5, 1, 3, 6, 5, 6, 2, 1,
4, 6, 4, 3, 2, 5), 12, 5, byrow = T)
} else if (all(D == 6, selection == 5)) {
sequences <- matrix(c(1, 2, 6, 3, 5, 4, 2, 3, 4, 1, 6, 5, 3, 1, 5, 2, 4, 6,
4, 5, 3, 6, 2, 1, 5, 6, 1, 4, 3, 2, 6, 4, 2, 5, 1, 3),
6, 6, byrow = T)
} else if (all(D == 6, selection == 6)) {
sequences <- matrix(c(1, 2, 6, 3, 5, 4, 2, 3, 4, 1, 6, 5, 3, 1, 5, 2, 4, 6,
4, 5, 3, 6, 2, 1, 5, 6, 1, 4, 3, 2, 6, 4, 2, 5, 1, 3,
1, 2, 5, 4, 6, 3, 2, 3, 6, 5, 4, 1, 3, 1, 4, 6, 5, 2,
4, 5, 2, 1, 3, 6, 5, 6, 3, 2, 1, 4, 6, 4, 1, 3, 2, 5),
12, 6, byrow = T)
} else if (all(D == 8, selection == 1)) {
sequences <- matrix(c(1, 2, 8, 7, 2, 3, 5, 8, 3, 4, 6, 5, 4, 1, 7, 6, 5, 6,
4, 3, 6, 7, 1, 4, 7, 8, 2, 1, 8, 5, 3, 2), 8, 4,
byrow = T)
} else if (all(D == 8, selection == 2)) {
sequences <- matrix(c(1, 2, 8, 7, 2, 3, 5, 8, 3, 4, 6, 5, 4, 1, 7, 6, 5, 6,
4, 3, 6, 7, 1, 4, 7, 8, 2, 1, 8, 5, 3, 2, 1, 6, 8, 3,
2, 7, 5, 4, 3, 8, 6, 1, 4, 5, 7, 2, 5, 2, 4, 7, 6, 3,
1, 8, 7, 4, 2, 5, 8, 1, 3, 6), 16, 4, byrow = T)
} else if (all(D == 8, selection == 3)) {
sequences <- matrix(c(1, 2, 8, 7, 3, 2, 3, 5, 8, 4, 3, 4, 6, 5, 1, 4, 1, 7,
6, 2, 5, 6, 4, 3, 7, 6, 7, 1, 4, 8, 7, 8, 2, 1, 5, 8,
5, 3, 2, 6), 8, 5, byrow = T)
} else if (all(D == 8, selection == 4)) {
sequences <- matrix(c(1, 2, 8, 7, 3, 2, 3, 5, 8, 4, 3, 4, 6, 5, 1, 4, 1, 7,
6, 2, 5, 6, 4, 3, 7, 6, 7, 1, 4, 8, 7, 8, 2, 1, 5, 8,
5, 3, 2, 6, 1, 4, 6, 7, 3, 2, 1, 7, 8, 4, 3, 2, 8, 5,
1, 4, 3, 5, 6, 2, 5, 8, 2, 3, 7, 6, 5, 3, 4, 8, 7, 6,
4, 1, 5, 8, 7, 1, 2, 6), 16, 5, byrow = T)
} else if (all(D == 8, selection == 5)) {
sequences <- matrix(c(1, 3, 8, 7, 2, 6, 2, 4, 5, 8, 3, 7, 3, 1, 6, 5, 4, 8,
4, 2, 7, 6, 1, 5, 5, 7, 4, 3, 6, 2, 6, 8, 1, 4, 7, 3,
7, 5, 2, 1, 8, 4, 8, 6, 3, 2, 5, 1), 8, 6, byrow = T)
} else if (all(D == 8, selection == 6)) {
sequences <- matrix(c(1, 3, 8, 7, 2, 6, 2, 4, 5, 8, 3, 7, 3, 1, 6, 5, 4, 8,
4, 2, 7, 6, 1, 5, 5, 7, 4, 3, 6, 2, 6, 8, 1, 4, 7, 3,
7, 5, 2, 1, 8, 4, 8, 6, 3, 2, 5, 1, 1, 3, 7, 4, 6, 5,
2, 4, 8, 1, 7, 6, 3, 1, 5, 2, 8, 7, 4, 2, 6, 3, 5, 8,
5, 7, 3, 8, 2, 1, 6, 8, 4, 5, 3, 2, 7, 5, 1, 6, 4, 3,
8, 6, 2, 7, 1, 4), 16, 6, byrow = T)
} else if (all(D == 9, selection == 1)) {
sequences <- matrix(c(1, 6, 8, 5, 2, 4, 9, 6, 3, 5, 7, 4, 4, 9, 2, 8, 5, 7,
3, 9, 6, 8, 1, 7, 7, 3, 5, 2, 8, 1, 6, 3, 9, 2, 4, 1),
9, 4, byrow = T)
} else if (all(D == 9, selection == 2)) {
sequences <- matrix(c(1, 6, 8, 5, 2, 4, 9, 6, 3, 5, 7, 4, 4, 9, 2, 8, 5, 7,
3, 9, 6, 8, 1, 7, 7, 3, 5, 2, 8, 1, 6, 3, 9, 2, 4, 1,
1, 8, 6, 9, 2, 9, 4, 7, 3, 7, 5, 8, 4, 2, 9, 3, 5, 3,
7, 1, 6, 1, 8, 2, 7, 5, 3, 6, 8, 6, 1, 4, 9, 4, 2, 5),
18, 4, byrow = T)
} else if (all(D == 9, selection == 3)) {
sequences <- matrix(c(1, 6, 8, 5, 2, 4, 9, 6, 3, 5, 7, 4, 4, 9, 2, 8, 5, 7,
3, 9, 6, 8, 1, 7, 7, 3, 5, 2, 8, 1, 6, 3, 9, 2, 4, 1,
1, 8, 6, 9, 2, 9, 4, 7, 3, 7, 5, 8, 4, 2, 9, 3, 5, 3,
7, 1, 6, 1, 8, 2, 7, 5, 3, 6, 8, 6, 1, 4, 9, 4, 2, 5,
1, 9, 5, 6, 2, 7, 6, 4, 3, 8, 4, 5, 4, 3, 8, 9, 5, 1,
9, 7, 6, 2, 7, 8, 7, 6, 2, 3, 8, 4, 3, 1, 9, 5, 1, 2),
27, 4, byrow = T)
} else if (all(D == 9, selection == 4)) {
sequences <- matrix(c(1, 2, 6, 9, 5, 2, 3, 4, 7, 6, 3, 1, 5, 8, 4, 4, 5, 9,
3, 8, 5, 6, 7, 1, 9, 6, 4, 8, 2, 7, 7, 8, 3, 6, 2, 8,
9, 1, 4, 3, 9, 7, 2, 5, 1), 9, 5, byrow = T)
} else if (all(D == 9, selection == 5)) {
sequences <- matrix(c(1, 2, 6, 9, 5, 2, 3, 4, 7, 6, 3, 1, 5, 8, 4, 4, 5, 9,
3, 8, 5, 6, 7, 1, 9, 6, 4, 8, 2, 7, 7, 8, 3, 6, 2, 8,
9, 1, 4, 3, 9, 7, 2, 5, 1, 1, 9, 6, 5, 8, 2, 7, 4, 6,
9, 3, 8, 5, 4, 7, 4, 3, 9, 8, 2, 5, 1, 7, 9, 3, 6, 2,
8, 7, 1, 7, 6, 3, 2, 5, 8, 4, 1, 3, 6, 9, 5, 2, 1, 4),
18, 5, byrow = T)
} else if (all(D == 9, selection == 6)) {
sequences <- matrix(c(1, 2, 6, 9, 5, 2, 3, 4, 7, 6, 3, 1, 5, 8, 4, 4, 5, 9,
3, 8, 5, 6, 7, 1, 9, 6, 4, 8, 2, 7, 7, 8, 3, 6, 2, 8,
9, 1, 4, 3, 9, 7, 2, 5, 1, 1, 9, 6, 5, 8, 2, 7, 4, 6,
9, 3, 8, 5, 4, 7, 4, 3, 9, 8, 2, 5, 1, 7, 9, 3, 6, 2,
8, 7, 1, 7, 6, 3, 2, 5, 8, 4, 1, 3, 6, 9, 5, 2, 1, 4,
1, 5, 6, 9, 8, 2, 6, 4, 7, 9, 3, 4, 5, 8, 7, 4, 8, 9,
3, 2, 5, 9, 7, 1, 3, 6, 7, 8, 2, 1, 7, 2, 3, 6, 5, 8,
3, 1, 4, 6, 9, 1, 2, 5, 4), 27, 5, byrow = T)
} else if (all(D == 9, selection == 7)) {
sequences <- matrix(c(1, 2, 6, 9, 8, 4, 2, 3, 4, 7, 9, 5, 3, 1, 5, 8, 7, 6,
4, 5, 9, 3, 2, 7, 5, 6, 7, 1, 3, 8, 6, 4, 8, 2, 1, 9,
7, 8, 3, 6, 5, 1, 8, 9, 1, 4, 6, 2, 9, 7, 2, 5, 4, 3),
9, 6, byrow = T)
} else if (all(D == 9, selection == 8)) {
sequences <- matrix(c(1, 2, 6, 9, 8, 4, 2, 3, 4, 7, 9, 5, 3, 1, 5, 8, 7, 6,
4, 5, 9, 3, 2, 7, 5, 6, 7, 1, 3, 8, 6, 4, 8, 2, 1, 9,
7, 8, 3, 6, 5, 1, 8, 9, 1, 4, 6, 2, 9, 7, 2, 5, 4, 3,
1, 6, 9, 7, 5, 2, 2, 4, 7, 8, 6, 3, 3, 5, 8, 9, 4, 1,
4, 9, 3, 1, 8, 5, 5, 7, 1, 2, 9, 6, 6, 8, 2, 3, 7, 4,
7, 3, 6, 4, 2, 8, 8, 1, 4, 5, 3, 9, 9, 2, 5, 6, 1, 7),
18, 6, byrow = T)
} else if (all(D == 9, selection == 9)) {
sequences <- matrix(c(1, 2, 6, 9, 8, 4, 2, 3, 4, 7, 9, 5, 3, 1, 5, 8, 7, 6,
4, 5, 9, 3, 2, 7, 5, 6, 7, 1, 3, 8, 6, 4, 8, 2, 1, 9,
7, 8, 3, 6, 5, 1, 8, 9, 1, 4, 6, 2, 9, 7, 2, 5, 4, 3,
1, 6, 9, 7, 5, 2, 2, 4, 7, 8, 6, 3, 3, 5, 8, 9, 4, 1,
4, 9, 3, 1, 8, 5, 5, 7, 1, 2, 9, 6, 6, 8, 2, 3, 7, 4,
7, 3, 6, 4, 2, 8, 8, 1, 4, 5, 3, 9, 9, 2, 5, 6, 1, 7,
1, 2, 8, 4, 6, 9, 2, 3, 9, 5, 4, 7, 3, 1, 7, 6, 5, 8,
4, 5, 2, 7, 9, 3, 5, 6, 3, 8, 7, 1, 6, 4, 1, 9, 8, 2,
7, 8, 5, 1, 3, 6, 8, 9, 6, 2, 1, 4, 9, 7, 4, 3, 2, 5),
27, 6, byrow = T)
} else if (all(D == 8, selection == 7)) {
sequences <- matrix(c(1, 6, 4, 7, 5, 2, 5, 3, 8, 6, 3, 8, 2, 5, 7, 4, 7, 1,
6, 8, 5, 2, 8, 3, 1, 6, 1, 7, 4, 2, 7, 4, 6, 1, 3, 8,
3, 5, 2, 4), 8, 5, byrow = T)
} else if (all(D == 8, selection == 8)) {
sequences <- matrix(c(1, 6, 4, 7, 5, 2, 5, 3, 8, 6, 3, 7, 2, 5, 7, 4, 8, 1,
6, 8, 5, 2, 8, 3, 1, 6, 1, 7, 4, 2, 7, 4, 6, 1, 3, 8,
3, 5, 2, 4, 1, 2, 8, 7, 5, 2, 1, 7, 8, 6, 3, 4, 6, 5,
7, 4, 3, 5, 6, 8, 5, 6, 4, 3, 1, 6, 5, 3, 4, 2, 7, 8,
2, 1, 3, 8, 7, 1, 2, 4), 16, 5, byrow = T)
} else if (all(D == 8, selection == 9)) {
sequences <- matrix(c(1, 6, 4, 7, 5, 2, 5, 3, 8, 6, 3, 7, 2, 5, 7, 4, 8, 1,
6, 8, 5, 2, 8, 3, 1, 6, 1, 7, 4, 2, 7, 4, 6, 1, 3, 8,
3, 5, 2, 4, 1, 2, 8, 7, 5, 2, 1, 7, 8, 6, 3, 4, 6, 5,
7, 4, 3, 5, 6, 8, 5, 6, 4, 3, 1, 6, 5, 3, 4, 2, 7, 8,
2, 1, 3, 8, 7, 1, 2, 4, 1, 7, 4, 6, 5, 2, 8, 3, 5, 6,
3, 5, 2, 8, 7, 4, 6, 1, 7, 8, 5, 3, 8, 2, 1, 6, 4, 7,
1, 2, 7, 1, 6, 4, 3, 8, 2, 5, 3, 4), 24, 5, byrow = T)
} else if (all(D == 8, selection == 10)) {
sequences <- matrix(c(1, 2, 7, 3, 6, 8, 2, 1, 8, 4, 5, 7, 3, 4, 5, 1, 8, 6,
4, 3, 6, 2, 7, 5, 5, 6, 3, 7, 2, 4, 6, 5, 4, 8, 1, 3,
7, 8, 1, 5, 4, 2, 8, 7, 2, 6, 3, 1), 8, 6, byrow = T)
} else if (all(D == 8, selection == 11)) {
sequences <- matrix(c(1, 2, 7, 3, 6, 8, 2, 1, 8, 4, 5, 7, 3, 4, 5, 1, 8, 6,
4, 3, 6, 2, 7, 5, 5, 6, 3, 7, 2, 4, 6, 5, 4, 8, 1, 3,
7, 8, 1, 5, 4, 2, 8, 7, 2, 6, 3, 1, 1, 2, 8, 4, 7, 5,
2, 1, 7, 3, 8, 6, 3, 4, 6, 2, 5, 7, 4, 3, 5, 1, 6, 8,
5, 6, 4, 8, 3, 1, 6, 5, 3, 7, 4, 2, 7, 8, 2, 6, 1, 3,
8, 7, 1, 5, 2, 4), 16, 6, byrow = T)
} else if (all(D == 8, selection == 12)) {
sequences <- matrix(c(1, 2, 7, 3, 6, 8, 2, 1, 8, 4, 5, 7, 3, 4, 5, 1, 8, 6,
4, 3, 6, 2, 7, 5, 5, 6, 3, 7, 2, 4, 6, 5, 4, 8, 1, 3,
7, 8, 1, 5, 4, 2, 8, 7, 2, 6, 3, 1, 1, 2, 8, 4, 7, 5,
2, 1, 7, 3, 8, 6, 3, 4, 6, 2, 5, 7, 4, 3, 5, 1, 6, 8,
5, 6, 4, 8, 3, 1, 6, 5, 3, 7, 4, 2, 7, 8, 2, 6, 1, 3,
8, 7, 1, 5, 2, 4, 1, 3, 6, 5, 8, 4, 2, 4, 5, 6, 7, 3,
3, 1, 8, 7, 6, 2, 4, 2, 7, 8, 5, 1, 5, 7, 2, 1, 4, 8,
6, 8, 1, 2, 3, 7, 7, 5, 4, 3, 2, 6, 8, 6, 3, 4, 1, 5),
24, 6, byrow = T)
}
if (summary) {
message("...completed the design specification. Preparing outputs...")
}
sequences <- convert_labels(sequences, D, labels, 1:D)
sequences <- transform_to_xover(sequences, labels, as_matrix)
##### Outputting #############################################################
if (summary) {
message("...outputting.")
}
return(sequences)
}
mjg211/xover documentation built on Oct. 16, 2019, 10:46 a.m.
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Defines functions seq_fletcher
Documented in seq_fletcher
#' Fletcher (1987) cross-over design specification
#'
#' Specifies cross-over designs from Fletcher (1987).
#'
#' \code{seq_fletcher()} supports the specification of designs from Fletcher
#' (1987). Deisgns for four, six, eight, and nine treatments (see
#' \code{D}) are supported, for any chosen treatment labels (see \code{labels}).
#' In addition, the designs can be returned in \code{\link[base]{matrix}} or
#' \code{\link[tibble]{tibble}} form (see \code{as_matrix}).
#'
#' Precisely, for \code{D} equal to four, six, eight, and nine, there are four,
#' three, 12, and nine designs available respectively (accessible by setting
#' \code{selection} equal to one through twelve asappropriate). Ultimately, the
#' \ifelse{html}{\out{(<i>k</i>,<i>j</i>)}}{\eqn{(k,j)}}th element of the
#' cross-over design matrix corresponds to the treatment a subject on the
#' \ifelse{html}{\out{<i>k</i>}}{\eqn{k}}th sequence would receive in the
#' \ifelse{html}{\out{<i>j</i>}}{\eqn{j}}th period.
#'
#' @param D The number of treatments. Must be either four, six, eight, or nine.
#' Defaults to \code{4}.
#' @param selection A single \code{\link[base]{numeric}} integer indicating
#' which design to return, for the chosen value of \code{D}. See
#' \strong{Details} for information on supported values.
#' @param labels A \code{\link[base]{vector}} of labels for the treatments.
#' Should be of \code{\link[base]{length}} \code{D}, containing unique elements.
#' Defaults to \code{0:(D - 1)}.
#' @param as_matrix A \code{\link[base]{logical}} variable indicating whether
#' the design should be returned as a \code{\link[base]{matrix}}, or a
#' \code{\link[tibble]{tibble}}. Defaults to \code{T}.
#' @param summary A \code{\link[base]{logical}} variable indicating whether a
#' summary of the function's progress should be printed to the console. Defaults
#' to \code{T}.
#' @return Either a \code{\link[base]{matrix}} if \code{as_matrix = T} (with
#' rows corresponding to sequences and columns to periods), or a
#' \code{\link[tibble]{tibble}} if \code{as_matrix = F} (with rows corresponding
#' to a particular period on a particular sequence). In either case, the
#' returned object will have class \code{xover_seq}.
#' @examples
#' # Fletcher (1987) designs for four treatments
#' fletcher1 <- seq_fletcher(D = 4)
#' fletcher2 <- seq_fletcher(D = 4, selection = 2)
#' fletcher3 <- seq_fletcher(D = 4, selection = 3)
#' fletcher4 <- seq_fletcher(D = 4, selection = 4)
#' # Using different labels
#' fletcher1_ABCD <- seq_fletcher(D = 4, labels = LETTERS[1:4])
#' fletcher2_ABCD <- seq_fletcher(D = 4, selection = 2, labels = LETTERS[1:4])
#' fletcher3_ABCD <- seq_fletcher(D = 4, selection = 3, labels = LETTERS[1:4])
#' fletcher4_ABCD <- seq_fletcher(D = 4, selection = 4, labels = LETTERS[1:4])
#' # Returning in tibble form
#' fletcher1_tibble <- seq_fletcher(D = 4, as_matrix = F)
#' fletcher2_tibble <- seq_fletcher(D = 4, selection = 2, as_matrix = F)
#' fletcher3_tibble <- seq_fletcher(D = 4, selection = 3, as_matrix = F)
#' fletcher4_tibble <- seq_fletcher(D = 4, selection = 4, as_matrix = F)
#' @references Fletcher DJ (1987) A new class of change-over designs for
#' factorial experiments. \emph{Biometrika} \strong{74:}649-54.
#' @author Based on data from the \code{\link[Crossover]{Crossover}} package by
#' Kornelius Rohmeyer.
#' @export
seq_fletcher <- function(D = 6, selection = 1, labels = 0:(D - 1),
as_matrix = T, summary = T) {
##### Input checking #########################################################
check_belong(D, "D", c(4, 6, 8, 9), 1)
check_selection(selection, c(NA, NA, NA, 4, NA, 3, NA, 12, 9), D)
check_labels(labels, D)
check_logical(as_matrix, "as_matrix")
check_logical(summary, "summary")
##### Main computations ######################################################
if (summary) {
message(" Beginning the design specification...")
}
if (all(D == 4, selection == 1)) {
sequences <- matrix(c(1, 2, 4, 2, 1, 3, 3, 4, 2, 4, 3, 1), 4, 3, byrow = T)
} else if (all(D == 4, selection == 2)) {
sequences <- matrix(c(1, 2, 4, 2, 1, 3, 3, 4, 2, 4, 3, 1, 1, 4, 2, 2, 3, 1,
3, 2, 4, 4, 1, 3), 8, 3, byrow = T)
} else if (all(D == 4, selection == 3)) {
sequences <- matrix(c(1, 2, 4, 3, 2, 1, 3, 4, 3, 4, 2, 1, 4, 3, 1, 2), 4, 4,
byrow = T)
} else if (all(D == 4, selection == 4)) {
sequences <- matrix(c(1, 2, 4, 3, 2, 1, 3, 4, 3, 4, 2, 1, 4, 3, 1, 2, 1, 3,
4, 2, 2, 4, 3, 1, 3, 1, 2, 4, 4, 2, 1, 3), 8, 4,
byrow = T)
} else if (all(D == 6, selection == 1)) {
sequences <- matrix(c(1, 5, 6, 2, 2, 6, 4, 3, 3, 4, 5, 1, 4, 2, 3, 5, 5, 3,
1, 6, 6, 1, 2, 4), 6, 4, byrow = T)
} else if (all(D == 6, selection == 2)) {
sequences <- matrix(c(1, 5, 6, 2, 2, 6, 4, 3, 3, 4, 5, 1, 4, 2, 3, 5, 5, 3,
1, 6, 6, 1, 2, 4, 1, 3, 5, 6, 2, 1, 6, 4, 3, 2, 4, 5,
4, 6, 2, 3, 5, 4, 3, 1, 6, 5, 1, 2), 12, 4, byrow = T)
} else if (all(D == 6, selection == 3)) {
sequences <- matrix(c(1, 3, 4, 5, 2, 2, 1, 5, 6, 3, 3, 2, 6, 4, 1, 4, 6, 1,
2, 5, 5, 4, 2, 3, 6, 6, 5, 3, 1, 4), 6, 5, byrow = T)
} else if (all(D == 6, selection == 4)) {
sequences <- matrix(c(1, 3, 4, 5, 2, 2, 1, 5, 6, 3, 3, 2, 6, 4, 1, 4, 6, 1,
2, 5, 5, 4, 2, 3, 6, 6, 5, 3, 1, 4, 1, 2, 4, 6, 3, 2,
3, 5, 4, 1, 3, 1, 6, 5, 2, 4, 5, 1, 3, 6, 5, 6, 2, 1,
4, 6, 4, 3, 2, 5), 12, 5, byrow = T)
} else if (all(D == 6, selection == 5)) {
sequences <- matrix(c(1, 2, 6, 3, 5, 4, 2, 3, 4, 1, 6, 5, 3, 1, 5, 2, 4, 6,
4, 5, 3, 6, 2, 1, 5, 6, 1, 4, 3, 2, 6, 4, 2, 5, 1, 3),
6, 6, byrow = T)
} else if (all(D == 6, selection == 6)) {
sequences <- matrix(c(1, 2, 6, 3, 5, 4, 2, 3, 4, 1, 6, 5, 3, 1, 5, 2, 4, 6,
4, 5, 3, 6, 2, 1, 5, 6, 1, 4, 3, 2, 6, 4, 2, 5, 1, 3,
1, 2, 5, 4, 6, 3, 2, 3, 6, 5, 4, 1, 3, 1, 4, 6, 5, 2,
4, 5, 2, 1, 3, 6, 5, 6, 3, 2, 1, 4, 6, 4, 1, 3, 2, 5),
12, 6, byrow = T)
} else if (all(D == 8, selection == 1)) {
sequences <- matrix(c(1, 2, 8, 7, 2, 3, 5, 8, 3, 4, 6, 5, 4, 1, 7, 6, 5, 6,
4, 3, 6, 7, 1, 4, 7, 8, 2, 1, 8, 5, 3, 2), 8, 4,
byrow = T)
} else if (all(D == 8, selection == 2)) {
sequences <- matrix(c(1, 2, 8, 7, 2, 3, 5, 8, 3, 4, 6, 5, 4, 1, 7, 6, 5, 6,
4, 3, 6, 7, 1, 4, 7, 8, 2, 1, 8, 5, 3, 2, 1, 6, 8, 3,
2, 7, 5, 4, 3, 8, 6, 1, 4, 5, 7, 2, 5, 2, 4, 7, 6, 3,
1, 8, 7, 4, 2, 5, 8, 1, 3, 6), 16, 4, byrow = T)
} else if (all(D == 8, selection == 3)) {
sequences <- matrix(c(1, 2, 8, 7, 3, 2, 3, 5, 8, 4, 3, 4, 6, 5, 1, 4, 1, 7,
6, 2, 5, 6, 4, 3, 7, 6, 7, 1, 4, 8, 7, 8, 2, 1, 5, 8,
5, 3, 2, 6), 8, 5, byrow = T)
} else if (all(D == 8, selection == 4)) {
sequences <- matrix(c(1, 2, 8, 7, 3, 2, 3, 5, 8, 4, 3, 4, 6, 5, 1, 4, 1, 7,
6, 2, 5, 6, 4, 3, 7, 6, 7, 1, 4, 8, 7, 8, 2, 1, 5, 8,
5, 3, 2, 6, 1, 4, 6, 7, 3, 2, 1, 7, 8, 4, 3, 2, 8, 5,
1, 4, 3, 5, 6, 2, 5, 8, 2, 3, 7, 6, 5, 3, 4, 8, 7, 6,
4, 1, 5, 8, 7, 1, 2, 6), 16, 5, byrow = T)
} else if (all(D == 8, selection == 5)) {
sequences <- matrix(c(1, 3, 8, 7, 2, 6, 2, 4, 5, 8, 3, 7, 3, 1, 6, 5, 4, 8,
4, 2, 7, 6, 1, 5, 5, 7, 4, 3, 6, 2, 6, 8, 1, 4, 7, 3,
7, 5, 2, 1, 8, 4, 8, 6, 3, 2, 5, 1), 8, 6, byrow = T)
} else if (all(D == 8, selection == 6)) {
sequences <- matrix(c(1, 3, 8, 7, 2, 6, 2, 4, 5, 8, 3, 7, 3, 1, 6, 5, 4, 8,
4, 2, 7, 6, 1, 5, 5, 7, 4, 3, 6, 2, 6, 8, 1, 4, 7, 3,
7, 5, 2, 1, 8, 4, 8, 6, 3, 2, 5, 1, 1, 3, 7, 4, 6, 5,
2, 4, 8, 1, 7, 6, 3, 1, 5, 2, 8, 7, 4, 2, 6, 3, 5, 8,
5, 7, 3, 8, 2, 1, 6, 8, 4, 5, 3, 2, 7, 5, 1, 6, 4, 3,
8, 6, 2, 7, 1, 4), 16, 6, byrow = T)
} else if (all(D == 9, selection == 1)) {
sequences <- matrix(c(1, 6, 8, 5, 2, 4, 9, 6, 3, 5, 7, 4, 4, 9, 2, 8, 5, 7,
3, 9, 6, 8, 1, 7, 7, 3, 5, 2, 8, 1, 6, 3, 9, 2, 4, 1),
9, 4, byrow = T)
} else if (all(D == 9, selection == 2)) {
sequences <- matrix(c(1, 6, 8, 5, 2, 4, 9, 6, 3, 5, 7, 4, 4, 9, 2, 8, 5, 7,
3, 9, 6, 8, 1, 7, 7, 3, 5, 2, 8, 1, 6, 3, 9, 2, 4, 1,
1, 8, 6, 9, 2, 9, 4, 7, 3, 7, 5, 8, 4, 2, 9, 3, 5, 3,
7, 1, 6, 1, 8, 2, 7, 5, 3, 6, 8, 6, 1, 4, 9, 4, 2, 5),
18, 4, byrow = T)
} else if (all(D == 9, selection == 3)) {
sequences <- matrix(c(1, 6, 8, 5, 2, 4, 9, 6, 3, 5, 7, 4, 4, 9, 2, 8, 5, 7,
3, 9, 6, 8, 1, 7, 7, 3, 5, 2, 8, 1, 6, 3, 9, 2, 4, 1,
1, 8, 6, 9, 2, 9, 4, 7, 3, 7, 5, 8, 4, 2, 9, 3, 5, 3,
7, 1, 6, 1, 8, 2, 7, 5, 3, 6, 8, 6, 1, 4, 9, 4, 2, 5,
1, 9, 5, 6, 2, 7, 6, 4, 3, 8, 4, 5, 4, 3, 8, 9, 5, 1,
9, 7, 6, 2, 7, 8, 7, 6, 2, 3, 8, 4, 3, 1, 9, 5, 1, 2),
27, 4, byrow = T)
} else if (all(D == 9, selection == 4)) {
sequences <- matrix(c(1, 2, 6, 9, 5, 2, 3, 4, 7, 6, 3, 1, 5, 8, 4, 4, 5, 9,
3, 8, 5, 6, 7, 1, 9, 6, 4, 8, 2, 7, 7, 8, 3, 6, 2, 8,
9, 1, 4, 3, 9, 7, 2, 5, 1), 9, 5, byrow = T)
} else if (all(D == 9, selection == 5)) {
sequences <- matrix(c(1, 2, 6, 9, 5, 2, 3, 4, 7, 6, 3, 1, 5, 8, 4, 4, 5, 9,
3, 8, 5, 6, 7, 1, 9, 6, 4, 8, 2, 7, 7, 8, 3, 6, 2, 8,
9, 1, 4, 3, 9, 7, 2, 5, 1, 1, 9, 6, 5, 8, 2, 7, 4, 6,
9, 3, 8, 5, 4, 7, 4, 3, 9, 8, 2, 5, 1, 7, 9, 3, 6, 2,
8, 7, 1, 7, 6, 3, 2, 5, 8, 4, 1, 3, 6, 9, 5, 2, 1, 4),
18, 5, byrow = T)
} else if (all(D == 9, selection == 6)) {
sequences <- matrix(c(1, 2, 6, 9, 5, 2, 3, 4, 7, 6, 3, 1, 5, 8, 4, 4, 5, 9,
3, 8, 5, 6, 7, 1, 9, 6, 4, 8, 2, 7, 7, 8, 3, 6, 2, 8,
9, 1, 4, 3, 9, 7, 2, 5, 1, 1, 9, 6, 5, 8, 2, 7, 4, 6,
9, 3, 8, 5, 4, 7, 4, 3, 9, 8, 2, 5, 1, 7, 9, 3, 6, 2,
8, 7, 1, 7, 6, 3, 2, 5, 8, 4, 1, 3, 6, 9, 5, 2, 1, 4,
1, 5, 6, 9, 8, 2, 6, 4, 7, 9, 3, 4, 5, 8, 7, 4, 8, 9,
3, 2, 5, 9, 7, 1, 3, 6, 7, 8, 2, 1, 7, 2, 3, 6, 5, 8,
3, 1, 4, 6, 9, 1, 2, 5, 4), 27, 5, byrow = T)
} else if (all(D == 9, selection == 7)) {
sequences <- matrix(c(1, 2, 6, 9, 8, 4, 2, 3, 4, 7, 9, 5, 3, 1, 5, 8, 7, 6,
4, 5, 9, 3, 2, 7, 5, 6, 7, 1, 3, 8, 6, 4, 8, 2, 1, 9,
7, 8, 3, 6, 5, 1, 8, 9, 1, 4, 6, 2, 9, 7, 2, 5, 4, 3),
9, 6, byrow = T)
} else if (all(D == 9, selection == 8)) {
sequences <- matrix(c(1, 2, 6, 9, 8, 4, 2, 3, 4, 7, 9, 5, 3, 1, 5, 8, 7, 6,
4, 5, 9, 3, 2, 7, 5, 6, 7, 1, 3, 8, 6, 4, 8, 2, 1, 9,
7, 8, 3, 6, 5, 1, 8, 9, 1, 4, 6, 2, 9, 7, 2, 5, 4, 3,
1, 6, 9, 7, 5, 2, 2, 4, 7, 8, 6, 3, 3, 5, 8, 9, 4, 1,
4, 9, 3, 1, 8, 5, 5, 7, 1, 2, 9, 6, 6, 8, 2, 3, 7, 4,
7, 3, 6, 4, 2, 8, 8, 1, 4, 5, 3, 9, 9, 2, 5, 6, 1, 7),
18, 6, byrow = T)
} else if (all(D == 9, selection == 9)) {
sequences <- matrix(c(1, 2, 6, 9, 8, 4, 2, 3, 4, 7, 9, 5, 3, 1, 5, 8, 7, 6,
4, 5, 9, 3, 2, 7, 5, 6, 7, 1, 3, 8, 6, 4, 8, 2, 1, 9,
7, 8, 3, 6, 5, 1, 8, 9, 1, 4, 6, 2, 9, 7, 2, 5, 4, 3,
1, 6, 9, 7, 5, 2, 2, 4, 7, 8, 6, 3, 3, 5, 8, 9, 4, 1,
4, 9, 3, 1, 8, 5, 5, 7, 1, 2, 9, 6, 6, 8, 2, 3, 7, 4,
7, 3, 6, 4, 2, 8, 8, 1, 4, 5, 3, 9, 9, 2, 5, 6, 1, 7,
1, 2, 8, 4, 6, 9, 2, 3, 9, 5, 4, 7, 3, 1, 7, 6, 5, 8,
4, 5, 2, 7, 9, 3, 5, 6, 3, 8, 7, 1, 6, 4, 1, 9, 8, 2,
7, 8, 5, 1, 3, 6, 8, 9, 6, 2, 1, 4, 9, 7, 4, 3, 2, 5),
27, 6, byrow = T)
} else if (all(D == 8, selection == 7)) {
sequences <- matrix(c(1, 6, 4, 7, 5, 2, 5, 3, 8, 6, 3, 8, 2, 5, 7, 4, 7, 1,
6, 8, 5, 2, 8, 3, 1, 6, 1, 7, 4, 2, 7, 4, 6, 1, 3, 8,
3, 5, 2, 4), 8, 5, byrow = T)
} else if (all(D == 8, selection == 8)) {
sequences <- matrix(c(1, 6, 4, 7, 5, 2, 5, 3, 8, 6, 3, 7, 2, 5, 7, 4, 8, 1,
6, 8, 5, 2, 8, 3, 1, 6, 1, 7, 4, 2, 7, 4, 6, 1, 3, 8,
3, 5, 2, 4, 1, 2, 8, 7, 5, 2, 1, 7, 8, 6, 3, 4, 6, 5,
7, 4, 3, 5, 6, 8, 5, 6, 4, 3, 1, 6, 5, 3, 4, 2, 7, 8,
2, 1, 3, 8, 7, 1, 2, 4), 16, 5, byrow = T)
} else if (all(D == 8, selection == 9)) {
sequences <- matrix(c(1, 6, 4, 7, 5, 2, 5, 3, 8, 6, 3, 7, 2, 5, 7, 4, 8, 1,
6, 8, 5, 2, 8, 3, 1, 6, 1, 7, 4, 2, 7, 4, 6, 1, 3, 8,
3, 5, 2, 4, 1, 2, 8, 7, 5, 2, 1, 7, 8, 6, 3, 4, 6, 5,
7, 4, 3, 5, 6, 8, 5, 6, 4, 3, 1, 6, 5, 3, 4, 2, 7, 8,
2, 1, 3, 8, 7, 1, 2, 4, 1, 7, 4, 6, 5, 2, 8, 3, 5, 6,
3, 5, 2, 8, 7, 4, 6, 1, 7, 8, 5, 3, 8, 2, 1, 6, 4, 7,
1, 2, 7, 1, 6, 4, 3, 8, 2, 5, 3, 4), 24, 5, byrow = T)
} else if (all(D == 8, selection == 10)) {
sequences <- matrix(c(1, 2, 7, 3, 6, 8, 2, 1, 8, 4, 5, 7, 3, 4, 5, 1, 8, 6,
4, 3, 6, 2, 7, 5, 5, 6, 3, 7, 2, 4, 6, 5, 4, 8, 1, 3,
7, 8, 1, 5, 4, 2, 8, 7, 2, 6, 3, 1), 8, 6, byrow = T)
} else if (all(D == 8, selection == 11)) {
sequences <- matrix(c(1, 2, 7, 3, 6, 8, 2, 1, 8, 4, 5, 7, 3, 4, 5, 1, 8, 6,
4, 3, 6, 2, 7, 5, 5, 6, 3, 7, 2, 4, 6, 5, 4, 8, 1, 3,
7, 8, 1, 5, 4, 2, 8, 7, 2, 6, 3, 1, 1, 2, 8, 4, 7, 5,
2, 1, 7, 3, 8, 6, 3, 4, 6, 2, 5, 7, 4, 3, 5, 1, 6, 8,
5, 6, 4, 8, 3, 1, 6, 5, 3, 7, 4, 2, 7, 8, 2, 6, 1, 3,
8, 7, 1, 5, 2, 4), 16, 6, byrow = T)
} else if (all(D == 8, selection == 12)) {
sequences <- matrix(c(1, 2, 7, 3, 6, 8, 2, 1, 8, 4, 5, 7, 3, 4, 5, 1, 8, 6,
4, 3, 6, 2, 7, 5, 5, 6, 3, 7, 2, 4, 6, 5, 4, 8, 1, 3,
7, 8, 1, 5, 4, 2, 8, 7, 2, 6, 3, 1, 1, 2, 8, 4, 7, 5,
2, 1, 7, 3, 8, 6, 3, 4, 6, 2, 5, 7, 4, 3, 5, 1, 6, 8,
5, 6, 4, 8, 3, 1, 6, 5, 3, 7, 4, 2, 7, 8, 2, 6, 1, 3,
8, 7, 1, 5, 2, 4, 1, 3, 6, 5, 8, 4, 2, 4, 5, 6, 7, 3,
3, 1, 8, 7, 6, 2, 4, 2, 7, 8, 5, 1, 5, 7, 2, 1, 4, 8,
6, 8, 1, 2, 3, 7, 7, 5, 4, 3, 2, 6, 8, 6, 3, 4, 1, 5),
24, 6, byrow = T)
}
if (summary) {
message("...completed the design specification. Preparing outputs...")
}
sequences <- convert_labels(sequences, D, labels, 1:D)
sequences <- transform_to_xover(sequences, labels, as_matrix)
##### Outputting #############################################################
if (summary) {
message("...outputting.")
}
return(sequences)
}
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