R/F_heq_nb.R

In CenterForStatistics-UGent/RCM: Fit row-column association models with the negative binomial distribution for the microbiome

#' Define linear equality constraints for env. gradient
#'
#' @param Alpha the current estimate of the environmental gradient
#' @param alphaK a matrix with the environmental gradients
#'  of the lower dimensions
#' @param d an integer, the number of environmental variables, including dummies
#' @param k an integer, the current dimension
#' @param centMat a centering matrix
#' @param ... further arguments for other methods, not needed in this one
#'
#' The centering matrix centMat ensures that the parameters of the dummies
#' of the same categorical variable sum to zero
#'
#' @return a vector of with current values of the constraints,
#'  should evolve to zeroes only
heq_nb = function(Alpha, alphaK, d, k, centMat, 
    ...) {
    centerFactors = centMat %*% Alpha  #Includes overal centering
    size = sum(Alpha^2) - 1
    if (k == 1) {
        return(c(centerFactors, size))
    }
    ortho = crossprod(alphaK, Alpha)
    c(centerFactors, size, ortho)
}