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Commit 913472a3 authored by Walmes Zeviani's avatar Walmes Zeviani
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Add 'apcMatrix', all pairwise comparisons matrices.

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#' @title All pairwise comparisons matrix (Tukey contrasts)
#'
#' @name apcMatrix
#'
#' @description This function takes a matrix where each line defines a
#' linear function of the parameters to estimate a marginal mean
#' (aka least squares means) and return the matrix that define the
#' contrasts among these means. All pairwise contrasts are returned
#' (aka Tukey contrasts). The matrix with these contrasts can be
#' passed to \code{multcomp::glht()} to estimate them or used in
#' explicit matricial calculus.
#'
#' @param lfm a \eqn{k\times p} matrix where each line defines a linear
#' function to estimate a lsmean (or any linear function). In
#' general, these matrices are obtained using
#' \code{doBy::LSmatrix()}.
#'
#' @param lev a character vector with dimension equals to the numbers of
#' lines of \code{lfm} matrix (\eqn{k}). Default is \code{NULL} and
#' the row names of code{lfm} is used. If row names is also
#' \code{NULL}, an integer sequence is used to identify the
#' comparisons.
#'
#' @return a \eqn{K\times p} matrix with the linear functions that
#' define all pairwise contrasts. \eqn{K} is \eqn{\binom{k}{2}}.
#'
#' @seealso \link[doBy]{LSmatrix}.
#'
#' @author Walmes Zeviani, \email{walmes@@ufpr.br}
#'
#' @export
#'
#' @examples
#'
#' ## A matrix of linear functions corresponding to the cell means
#' ## parametrization.
#' X <- diag(4)
#'
#' ## If no rownames an integer sequence is used.
#' rownames(X)
#' apcMatrix(X)
#'
#' ## With rownames, those are used.
#' rownames(X) <- letters[nrow(X):1]
#' apcMatrix(X)
#'
#' ## Passing names by the argument `lev=`.
#' apcMatrix(X, lev=LETTERS[1:nrow(X)])
#'
#' ## Using the special case with attribute "grid" present in matrices
#' ## returned by doBy::LSmeans() and doBy::LSmatrix().
#' attr(X, "grid") <- data.frame(n=LETTERS[1:nrow(X)])
#' apcMatrix(X)
#'
apcMatrix <- function(lfm, lev=NULL){
nlev <- nrow(lfm)
rn <- rownames(lfm)
a <- attr(lfm, "grid")
if(is.null(lev)){
if(!is.null(a)){
lev <- apply(a, 1, paste, collapse=":")
} else if(!is.null(rn)){
lev <- rn
} else {
lev <- as.character(1:nlev)
}
}
cbn <- combn(seq_along(lev), 2)
M <- lfm[cbn[1,],]-lfm[cbn[2,],]
if (is.vector(M)){
dim(M) <- c(1, length(M))
}
rownames(M) <- paste(lev[cbn[1,]], lev[cbn[2,]], sep="-")
return(M)
}
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