R/rowMads.R

In Bioconductor/MatrixGenerics: S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects

#' Calculates the median absolute deviation for each row (column) of a
#' matrix-like object
#'
#' Calculates the median absolute deviation for each row (column) of a
#' matrix-like object.
#'
#' @include MatrixGenerics-package.R
#'
#' @export
#' @name rowMads
#'
#' @templateVar rowName rowMads
#' @templateVar colName colMads
#'
#' @template matrixStatsLink
#'
#' @template standardParameters
#' @template na_rmParameter
#' @param center (optional) the center, defaults to the row means
#' @param constant A scale factor. See \code{stats::\link[stats]{mad}()} for
#'   details.
#' @template dimParameter
#' @template useNamesParameter
#'
#' @template returnVector
#'
#' @seealso
#' \itemize{
#' \item \code{matrixStats::\link[matrixStats:rowSds]{rowMads}()} and
#'   \code{matrixStats::\link[matrixStats:rowSds]{colMads}()} which are used
#'   when  the input is a \code{matrix} or \code{numeric} vector.
#' \item For mean estimates, see \code{\link{rowMeans2}()} and
#'   \code{\link[base:colSums]{rowMeans}()}.
#' \item For non-robust standard deviation estimates, see
#'   \code{\link{rowSds}()}.
#' }
#'
#' @template standardExamples
#'
#' @keywords array iteration robust univar
setGeneric("rowMads", function(x, rows = NULL, cols = NULL, center = NULL, constant = 1.4826, na.rm = FALSE, ..., useNames = TRUE) standardGeneric("rowMads"),
           signature = "x"
)

.matrixStats_rowMads <- function(x, rows = NULL, cols = NULL, center = NULL, constant = 1.4826, na.rm = FALSE, dim. = dim(x), ..., useNames = TRUE){
  center <- normarg_center(center, nrow(x), "nrow(x)")
  matrixStats::rowMads(x, rows = rows, cols = cols, center = center, constant = constant, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
}

#' @export
#' @rdname rowMads
setMethod("rowMads", "matrix_OR_array_OR_table_OR_numeric", .matrixStats_rowMads)

#' @export
#' @rdname rowMads
## Default method with user-friendly fallback mechanism.
setMethod("rowMads", "ANY", make_default_method_def("rowMads"))



#' @export
#' @rdname rowMads
setGeneric("colMads", function(x, rows = NULL, cols = NULL, center = NULL, constant = 1.4826, na.rm = FALSE, ..., useNames = TRUE) standardGeneric("colMads"),
           signature = "x"
)

.matrixStats_colMads <- function(x, rows = NULL, cols = NULL, center = NULL, constant = 1.4826, na.rm = FALSE, dim. = dim(x), ..., useNames = TRUE){
  center <- normarg_center(center, ncol(x), "ncol(x)")
  matrixStats::colMads(x, rows = rows, cols = cols, center = center, constant = constant, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
}

#' @export
#' @rdname rowMads
setMethod("colMads", "matrix_OR_array_OR_table_OR_numeric", .matrixStats_colMads)

#' @export
#' @rdname rowMads
## Default method with user-friendly fallback mechanism.
setMethod("colMads", "ANY", make_default_method_def("colMads"))