Nothing
print.summary.coxph <-
function(x, digits = max(getOption('digits')-3, 3),
signif.stars = getOption("show.signif.stars"), expand=FALSE, ...) {
if (!is.null(x$call)) {
cat("Call:\n")
dput(x$call)
cat("\n")
}
if (!is.null(x$fail)) {
cat(" Coxreg failed.", x$fail, "\n")
return()
}
savedig <- options(digits = digits)
on.exit(options(savedig))
omit <- x$na.action
cat(" n=", x$n)
if (!is.null(x$nevent)) cat(", number of events=", x$nevent, "\n")
else cat("\n")
if (length(omit))
cat(" (", naprint(omit), ")\n", sep="")
if (nrow(x$coefficients)==0) { # Null model
cat (" Null model\n")
return()
}
if (expand && !is.null(x$cmap)) { # this was a coxphms object
signif.stars <- FALSE #work around issue with printCoefmat
# print it group by group
tmap <- x$cmap
cname <- colnames(tmap)
printed <- rep(FALSE, length(cname))
for (i in 1:length(cname)) {
# if multiple colums of tmat are identical, only print that
# set of coefficients once
if (!printed[i]) { # this column hasn't been printed
j <- apply(tmap, 2, function(x) all(x == tmap[,i]))
printed[j] <- TRUE # mark all that match as 'printed'
tmp2 <- x$coefficients[tmap[,i],, drop=FALSE]
names(dimnames(tmp2)) <- c(paste(cname[j], collapse=", "), "")
# restore character row names
rownames(tmp2) <- rownames(tmap)[tmap[,i]>0]
printCoefmat(tmp2, digits=digits, P.values=TRUE,
has.Pvalue=TRUE, signif.legend=FALSE,
signif.stars = signif.stars, ...)
if (!is.null(x$conf.int)) {
tmp2 <- x$conf.int[tmap[,i],, drop=FALSE]
rownames(tmp2) <- rownames(tmap)[tmap[,i] >0]
names(dimnames(tmp2)) <- c(paste(cname[j], collapse=", "),"")
print(tmp2, digits=digits, ...)
}
}
}
cat("\n States:", paste(paste(seq(along.with =x$states), x$states, sep='= '),
collapse=", "), '\n')
} else {
if(!is.null(x$coefficients)) {
cat("\n")
printCoefmat(x$coefficients, digits=digits,
signif.stars=signif.stars, ...)
}
if(!is.null(x$conf.int)) {
cat("\n")
print(x$conf.int)
}
}
cat("\n")
if (!is.null(x$concordance)) {
cat("Concordance=", format(round(x$concordance[1],3)),
" (se =", format(round(x$concordance[2], 3)),")\n")
}
# cat("Rsquare=", format(round(x$rsq["rsq"],3)),
# " (max possible=", format(round(x$rsq["maxrsq"],3)),
# ")\n" )
pdig <- max(1, getOption("digits")-4) # default it too high IMO
cat("Likelihood ratio test= ", format(round(x$logtest["test"], 2)), " on ",
x$logtest["df"], " df,", " p=",
format.pval(x$logtest["pvalue"], digits=pdig),
"\n", sep = "")
cat("Wald test = ", format(round(x$waldtest["test"], 2)), " on ",
x$waldtest["df"], " df,", " p=",
format.pval(x$waldtest["pvalue"], digits=pdig),
"\n", sep = "")
cat("Score (logrank) test = ", format(round(x$sctest["test"], 2)), " on ",
x$sctest["df"]," df,", " p=",
format.pval(x$sctest["pvalue"], digits=pdig), sep ="")
if (is.null(x$robscore))
cat("\n\n")
else cat(", Robust = ", format(round(x$robscore["test"], 2)),
" p=",
format.pval(x$robscore["pvalue"], digits=pdig), "\n\n", sep="")
if (x$used.robust)
cat(" (Note: the likelihood ratio and score tests",
"assume independence of\n observations within a cluster,",
"the Wald and robust score tests do not).\n")
invisible()
}
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