R/print.coxph.R

In survival: Survival Analysis

print.coxph <-
 function(x, digits=max(1L, getOption("digits") - 3L), signif.stars=FALSE, ...)
    {
    if (!is.null(cl<- x$call)) {
	cat("Call:\n")
	dput(cl)
	cat("\n")
	}
    if (!is.null(x$fail)) {
	cat(" Coxph failed.", x$fail, "\n")
	return()
	}
    savedig <- options(digits = digits)
    on.exit(options(savedig))

    coef <- x$coefficients
    se <- sqrt(diag(x$var))
    if(is.null(coef) | is.null(se))
        stop("Input is not valid")

    if (is.null(x$naive.var)) {
	tmp <- cbind(coef, exp(coef), se, coef/se,
               pchisq((coef/se)^2, 1, lower.tail=FALSE))
	dimnames(tmp) <- list(names(coef), c("coef", "exp(coef)",
	    "se(coef)", "z", "p"))
	}
    else {
	nse <- sqrt(diag(x$naive.var))
	tmp <- cbind(coef, exp(coef), nse, se, coef/se,
	       pchisq((coef/se)^2, 1, lower.tail=FALSE))
	dimnames(tmp) <- list(names(coef), c("coef", "exp(coef)",
	    "se(coef)", "robust se", "z", "p"))
	}
    
    if (inherits(x, "coxphms")) {
        # print it group by group
        # lazy: I don't want to type x$cmap many times
        #  remove transitions with no covariates
        cmap <- x$cmap[, colSums(x$cmap) > 0, drop=FALSE]
        cname <- colnames(cmap)
        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]) {
                j <- apply(cmap, 2, function(x) all(x == cmap[,i])) 
                printed[j] <- TRUE

                tmp2 <- tmp[cmap[,i],, drop=FALSE]
                names(dimnames(tmp2)) <- c(paste(cname[j], collapse=", "), "")
                # restore character row names
                rownames(tmp2) <- rownames(cmap)[cmap[,i]>0]
                printCoefmat(tmp2, digits=digits, P.values=TRUE, 
                             has.Pvalue=TRUE,
                             signif.stars = signif.stars, ...)
                cat("\n")   
            }       
        }

        cat(" States: ", paste(paste(seq(along.with=x$states), x$states, sep='= '), 
                               collapse=", "), '\n')
        # cat(" States: ", paste(x$states, collapse=", "), '\n')
        if (FALSE) { # alternate forms, still deciding which I like
            stemp <- x$states
            names(stemp) <- 1:length(stemp)
            print(stemp, quote=FALSE)
        }
    }
    else printCoefmat(tmp, digits=digits, P.values=TRUE, has.Pvalue=TRUE,
                 signif.stars = signif.stars, ...)

    logtest <- -2 * (x$loglik[1] - x$loglik[2])
    if (is.null(x$df)) df <- sum(!is.na(coef))
    else  df <- round(sum(x$df),2)
    cat("\n")
    cat("Likelihood ratio test=", format(round(logtest, 2)), "  on ",
	df, " df,", " p=", 
        format.pval(pchisq(logtest, df, lower.tail=FALSE), digits=digits), 
        "\n",  sep="")
    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="")
    invisible(x)
    }

coef.coxphms <- function(object, matrix=FALSE, ...){
    cmap <- object$cmap
    if (matrix) {
        cmap[cmap>0] <- object$coefficients[cmap]
        attr(cmap, "states") <- object$states
        cmap
    }
    else NextMethod(object, ...)
}