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# Modification of print.summary.glm from the stats package for R.
#
# Copyright (C) 1995-2006 The R Core Team
# Copyright (C) 2006, 2008, 2009, 2015 Heather Turner
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 or 3 of the License
# (at your option).
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# A copy of the GNU General Public License is available at
# http://www.r-project.org/Licenses/
print.summary.gnm <- function (x, digits = max(3, getOption("digits") - 3),
signif.stars = getOption("show.signif.stars"),
symbolic.cor = x$symbolic.cor, ...)
{
cat("\nCall:\n", deparse(x$call), "\n", sep = "", fill = TRUE)
cat("Deviance Residuals: \n")
if (length(x$deviance.resid) > 5) {
x$deviance.resid <- quantile(x$deviance.resid, na.rm = TRUE)
names(x$deviance.resid) <- c("Min", "1Q", "Median", "3Q",
"Max")
}
print.default(x$deviance.resid, digits = digits, na.print = "",
print.gap = 2)
tidy.zeros <- function(vec)
ifelse(abs(vec) < 100 * .Machine$double.eps, 0, vec)
coefs <- tidy.zeros(coef(x))
if (length(ofInterest(x)) > 0)
coefs <- coefs[ofInterest(x), , drop = FALSE]
non.elim <- length(coefs)
elim <- length(x$eliminated)
if (non.elim | elim) {
cat("\nCoefficients", " of interest"[!is.null(ofInterest(x))], ":\n",
sep = "")
printCoefmat(coefs, digits = digits, signif.stars = signif.stars,
signif.legend = !elim, na.print = "NA", ...)
if (elim){
cat("\nEliminated coefficients:\n", sep = "")
printCoefmat(x$eliminated, digits = digits,
signif.stars = signif.stars, na.print = "NA", ...)
}
coefs <- c(coefs[,2], x$eliminated[,2])
if (any(!is.na(coefs)))
cat("\n(Dispersion parameter for ", x$family$family,
" family taken to be ", format(x$dispersion), ")\n", sep = "")
if (any(is.na(coefs)))
cat("\nStd. Error is NA where coefficient has been constrained or",
"is unidentified\n")
}
else cat("\nNo coefficients", " of interest"[!is.null(ofInterest(x))],
". \n\n", sep = "")
cat("\nResidual deviance: ", format(x$deviance,
digits = max(5, digits + 1)),
" on ", format(x$df.residual, digits = max(5, digits + 1)),
" degrees of freedom\n",
"AIC: ", format(x$aic, digits = max(4, digits + 1)), "\n\n",
"Number of iterations: ", x$iter, "\n", sep = "")
correl <- x$correlation
if (!is.null(correl)) {
if (attr(x$cov.scaled, "eliminate")) {
eliminate <- seq(attr(x$cov.scaled, "eliminate"))
correl <- correl[-eliminate, -eliminate]
}
p <- NCOL(correl)
if (p > 1) {
cat("\nCorrelation of Coefficients:\n")
if (is.logical(symbolic.cor) && symbolic.cor) {
print(symnum(correl, abbr.colnames = NULL))
}
else {
correl <- format(round(correl, 2), nsmall = 2, digits = digits)
correl[!lower.tri(correl)] <- ""
print(correl[-1, -p, drop = FALSE], quote = FALSE)
}
}
}
cat("\n")
invisible(x)
}
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