R/F_getInt.R

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

#' Integrate the spline of an vgam object
#'
#' @param coef A vector of coefficients
#' @param spline The cubic smoothing spline
#' @param sampleScore the observed environmental scores
#' @param stop.on.error see ?integrate
#' @param ... additional arguments passed on to integrate()
#'
#' @return a scalar, the value of the integral
getInt = function(coef, spline, sampleScore, 
    stop.on.error = FALSE, ...) {
    # Absolute values assure positive
    # outcomes
    integrate(f = function(y, coef, spline) {
        if (!is.null(spline)) {
            abs(getRowMat(sampleScore = y, 
                taxonCoef = coef, spline = spline, 
                responseFun = "nonparametric"))
        } else {
            # If GAM fails, GLM fit (or independence
            # model)
            abs(getModelMat(y, degree = length(coef) - 
                1) %*% coef)
        }
    }, lower = min(sampleScore), upper = max(sampleScore), 
        coef = coef, spline = spline, stop.on.error = stop.on.error, 
        ...)$value
}