R/print_summary_bbdml.R

In corncob: Count Regression for Correlated Observations with the Beta-Binomial

#' Print summary function
#'
#' @param x Object of class \code{bbdml}
#' @param digits the number of significant digits to use when printing.
#' @param signif.stars logical. If \code{TRUE}, `significance stars' are printed for each coefficient.
#' @param ... No optional arguments are accepted at this time.
#'
#'
#' @return \code{NULL}. Displays printed model summary.
#'
#' @examples
#' data(soil_phylum_small)
#' mod <- bbdml(formula = OTU.1 ~ DayAmdmt,
#' phi.formula = ~ DayAmdmt,
#' data = soil_phylum_small)
#' print(summary(mod))
#' @export
print.summary.bbdml <- function(x, digits = max(3L, getOption("digits") - 3L),
                                signif.stars = getOption("show.signif.stars"), ...) {
  cat("\nCall:\n",
      paste(deparse(x$call), sep = "\n", collapse = "\n"), "\n\n", sep = "")

  cat("\nCoefficients associated with abundance:\n")
  coefs.mu <- x$coefficients[1:x$np.mu,, drop = FALSE]
  rownames(coefs.mu) <- substring(rownames(coefs.mu), 4)
  stats::printCoefmat(coefs.mu, digits = digits, signif.stars = signif.stars,
                 na.print = "NA", ...)

  cat("\n")

  cat("\nCoefficients associated with dispersion:\n")
  coefs.phi <- x$coefficients[(x$np.mu + 1):nrow(x$coefficients),, drop = FALSE]
  rownames(coefs.phi) <- substring(rownames(coefs.phi), 5)
  stats::printCoefmat(coefs.phi, digits = digits, signif.stars = signif.stars,
                      na.print = "NA", ...)

  cat("\n\nLog-likelihood: ", format(x$logL, digits = max(4L, digits + 1L)),
      "\n", sep = "")

  if (x$sep_da || x$sep_dv) {
    warning("This model is based on a discriminant taxa.
You may see NAs in the model summary because Wald testing is invalid.
Likelihood ratio testing can be used, but valid standard errors cannot be calculated.",
            immediate. = TRUE)
  }
}