# R/indTab.R In robCompositions: Compositional Data Analysis

#' Independence table
#'
#' Estimates the expected frequencies from an m-way table under the
#' null hypotheses of independence.
#'
#' @param x an object of class table
#' @param margin determines how the margins of the table should be estimated (default via geometric mean margins)
#' @param frequency indicates whether absolute or relative frequencies should be computed.
#' @param pTabMethod to estimate the propability table. Default is \sQuote{dirichlet}. Other available methods:
#' \sQuote{classical} that is function \code{prop.table()} from package base or method \dQuote{half} that add 1/2 to each cell
#' to avoid zero problems.
#' @details Because of the compositional nature of probability tables, the independence tables should
#' be estimated using geometric marginals.
#' @author Matthias Templ
#' @return The independence table(s) with either relative or absolute frequencies.
#' @references
#' Egozcue, J.J., Pawlowsky-Glahn, V., Templ, M., Hron, K. (2015)
#' Independence in contingency tables using simplicial geometry.
#' \emph{Communications in Statistics - Theory and Methods}, 44 (18), 3978--3996.
#'
#' @export
#' @examples
#' data(precipitation)
#' tab1 <- indTab(precipitation)
#' tab1
#' sum(tab1)
#'
#' \dontrun{
#' data("PreSex", package = "vcd")
#' indTab(PreSex)
#' }
indTab <-
function (x, margin = c("gmean_sum", "sum"), frequency = c("relative", "absolute"),
pTabMethod = c("dirichlet", "half", "classical"))
{
margin <- match.arg(margin)
frequency <- match.arg(frequency)
pTabMethod <- match.arg(pTabMethod)
n <- sum(x)
#	x <- x/n
x <- pTab(x, method=pTabMethod)
d <- dim(x)
margins <- lapply(1:length(d), function(i) apply(x, i, margin))
tab <- array(apply(expand.grid(margins), 1, prod), d, dimnames = dimnames(x))
if (frequency == "relative")
res <- tab/sum(tab)
else res <- tab*n
res
}


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robCompositions documentation built on Jan. 13, 2021, 10:07 p.m.