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summary.coxph <- function(object, conf.int = 0.95, scale = 1, ...) {
cox<-object
beta <- cox$coefficients * scale
if (is.null(cox$coefficients)) { # Null model
return(object) #The summary method is the same as print in this case
}
nabeta <- !(is.na(beta)) #non-missing coefs
beta2 <- beta[nabeta]
if(is.null(beta) | is.null(cox$var))
stop("Input is not valid")
se <- sqrt(diag(cox$var)) * scale
if (!is.null(cox$naive.var)) nse <- sqrt(diag(cox$naive.var))
rval<-list(call=cox$call,fail=cox$fail, na.action=cox$na.action,
n=cox$n, loglik=cox$loglik)
if (!is.null(cox$nevent)) rval$nevent <- cox$nevent
if (is.null(cox$naive.var)) {
tmp <- cbind(beta, exp(beta), se, beta/se,
pchisq((beta/ se)^2, 1, lower.tail=FALSE))
dimnames(tmp) <- list(names(beta), c("coef", "exp(coef)",
"se(coef)", "z", "Pr(>|z|)"))
}
else {
tmp <- cbind(beta, exp(beta), nse, se, beta/se,
pchisq((beta/ se)^2, 1, lower.tail=FALSE))
dimnames(tmp) <- list(names(beta), c("coef", "exp(coef)",
"se(coef)", "robust se", "z", "Pr(>|z|)"))
}
rval$coefficients <- tmp
if (conf.int) {
z <- qnorm((1 + conf.int)/2, 0, 1)
tmp <- cbind(exp(beta), exp(-beta), exp(beta - z * se),
exp(beta + z * se))
dimnames(tmp) <- list(names(beta), c("exp(coef)", "exp(-coef)",
paste("lower .", round(100 * conf.int, 2), sep = ""),
paste("upper .", round(100 * conf.int, 2), sep = "")))
rval$conf.int <- tmp
}
df <- length(beta2)
logtest <- -2 * (cox$loglik[1] - cox$loglik[2])
rval$logtest <- c(test=logtest,
df=df,
pvalue= pchisq(logtest, df, lower.tail=FALSE))
rval$sctest <- c(test=cox$score,
df=df,
pvalue= pchisq(cox$score, df, lower.tail=FALSE))
rval$rsq<-c(rsq=1-exp(-logtest/cox$n),
maxrsq=1-exp(2*cox$loglik[1]/cox$n))
if (!is.null(cox$wald.test)) { # a model with no covariates is missing this
rval$waldtest<-c(test=as.vector(round(cox$wald.test, 2)),
df=df,
pvalue= pchisq(as.vector(cox$wald.test), df,
lower.tail=FALSE))
}
if (!is.null(cox$rscore))
rval$robscore<-c(test=cox$rscore,
df=df,
pvalue= pchisq(cox$rscore, df, lower.tail=FALSE))
rval$used.robust<-!is.null(cox$naive.var)
if (!is.null(cox$concordance)) {
# throw away the extra info, in the name of backwards compatability
rval$concordance <- cox$concordance[6:7]
names(rval$concordance) <- c("C", "se(C)")
}
if (inherits(cox, "coxphms")) {
rval$cmap <- cox$cmap
rval$states <- cox$states
}
class(rval) <-"summary.coxph"
rval
}
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