R/F_estNBparams.R

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

#' A function to estimate the taxon-wise NB-params
#'
#' @param design an n-by-v design matrix
#' @param thetas a vector of dispersion parameters of length p
#' @param muMarg an offset matrix
#' @param psi a scalar, the importance parameter
#' @param X the data matrix
#' @param nleqslv.control a list of control elements, passed on to nleqslv()
#' @param ncols an integer, the number of columns of X
#' @param initParam a v-by-p matrix of initial parameter estimates
#' @param v an integer, the number of parameters per taxon
#' @param dynamic a boolean, should response function be determined dynamically?
#'  See details
#' @param envRange a vector of length 2, giving the range of observed
#' environmental scores
#' @param allowMissingness A boolean, are missing values present
#' @param naId The numeric index of the missing values in X
#'
#' If dynamic is TRUE, quadratic response functions are fitted for every taxon.
#' If the optimum falls outside of the observed range of environmental scores,
#' a linear response function is fitted instead
#'
#' @return a v-by-p matrix of parameters of the response function
estNBparams = function(design, thetas, muMarg,
    psi, X, nleqslv.control, ncols, initParam,
    v, dynamic = FALSE, envRange, allowMissingness, naId) {
    vapply(seq_len(ncols), FUN.VALUE = vector("numeric",
        v), function(i) {
        nleq = nleqslv(initParam[, i], reg = design,
            fn = dNBllcol_constr, theta = thetas[i],
            muMarg = muMarg[, i], psi = psi,
            X = X[, i], control = nleqslv.control,
            jac = JacCol_constr, allowMissingness = allowMissingness,
            naId = is.na(X[, i]))$x
        if (dynamic && ((-nleq[2]/(2 * nleq[3]) <
            envRange[1]) || (-nleq[2]/(2 *
            nleq[3]) > envRange[2]))) {
            # If out of observed range, fit a linear
            # model
            nleq = c(
            nleqslv(
                initParam[-3, i],
                reg = design[, -3],
                fn = dNBllcol_constr,
                theta = thetas[i],
                muMarg = muMarg[, i],
                psi = psi,
                X = X[, i],
                control = nleqslv.control,
                jac = JacCol_constr,
                allowMissingness = allowMissingness,
                naId = is.na(X[, i])
                )$x,0)
        }
        return(nleq)
    })
}