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#' summary of parameter estimates of a joint frailty model
#'
#' This function returns hazard rations (HR) and its confidence intervals.
#'
#'
#' @aliases summary.jointPenal print.summary.jointPenal
#' @usage \method{summary}{jointPenal}(object, level = 0.95, len = 6, d = 2,
#' lab="hr", ...)
#' @param object output from a call to frailtyPenal for joint models
#' @param level significance level of confidence interval. Default is 95\%.
#' @param d the desired number of digits after the decimal point. Default of 6
#' digits is used.
#' @param len the total field width. Default is 6.
#' @param lab label of printed results.
#' @param \dots other unused arguments.
#' @return Prints HR and its confidence intervals for each covariate.
#' Confidence level is allowed (level argument).
#' @seealso \code{\link{frailtyPenal}}
#' @keywords methods
##' @export
#' @examples
#'
#'
#' \dontrun{
#'
#' data(readmission)
#'
#' #-- gap-time
#' modJoint.gap <- frailtyPenal(Surv(time,event)~cluster(id)+sex+dukes+
#' charlson+terminal(death),formula.terminalEvent=~sex+dukes+charlson,
#' data=readmission,n.knots=14,kappa=c(9.55e+9,1.41e+12))
#'
#' #-- calendar time
#' modJoint.calendar <- frailtyPenal(Surv(t.start,t.stop,event)~cluster(id)+
#' sex+dukes+charlson+terminal(death),formula.terminalEvent=~sex+dukes+charlson,
#' data=readmission,n.knots=10,kappa=c(9.55e+9,1.41e+12),recurrentAG=TRUE)
#'
#' #-- It takes around 1 minute to converge
#'
#' summary(modJoint.gap)
#' summary(modJoint.calendar)
#'
#' }
#'
#'
"summary.jointPenal"<-
function(object,level=.95, len=6, d=2, lab="hr", ...)
{
if(is.null(object$family)){
x <- object
if (!inherits(x, "jointPenal"))
stop("Object must be of class 'frailtyPenal'")
z<-abs(qnorm((1-level)/2))
co <- x$coef
se <- sqrt(diag(x$varH))[-c(1:(1+x$indic_alpha))]
or <- exp(co)
li <- exp(co-z * se)
ls <- exp(co+z * se)
r <- cbind(or, li, ls)
dimnames(r) <- list(names(co), c(lab, paste(level*100,"%",sep=""), "C.I."))
n<-r
dd <- dim(n)
n[n > 999.99] <- Inf
a <- formatC(n, d, len,format="f")
dim(a) <- dd
if(length(dd) == 1){
dd<-c(1,dd)
dim(a)<-dd
lab<-" "
}
else
lab <- dimnames(n)[[1]]
mx <- max(nchar(lab)) + 1
cat("Recurrences:\n")
cat("------------- \n")
cat(paste(rep(" ",mx),collapse=""),paste(" ",dimnames(n)[[2]]),"\n")
for(i in 1:x$nvarnotdep[1])
{
lab[i] <- paste(c(rep(" ", mx - nchar(lab[i])), lab[i]),collapse = "")
cat(lab[i], a[i, 1], "(", a[i, 2], "-", a[i, 3], ") \n")
}
cat("\n")
cat("Terminal event:\n")
cat("--------------- \n")
cat(paste(rep(" ",mx),collapse=""),paste(" ",dimnames(n)[[2]]),"\n")
for(i in (x$nvarnotdep[1]+1):dd[1])
{
lab[i] <- paste(c(rep(" ", mx - nchar(lab[i])), lab[i]),collapse = "")
cat(lab[i], a[i, 1], "(", a[i, 2], "-", a[i, 3], ") \n")
}
}
else{
x <- object
if (!inherits(x, "jointPenal"))
stop("Object must be of class 'frailtyPenal'")
z<-abs(qnorm((1-level)/2))
co <- x$coef
se <- sqrt(diag(x$varH))[-c(1:(1+x$indic_alpha))]
or <- co
li <- co - z*se
ls <- co + z*se
r <- cbind(or, li, ls)
dimnames(r) <- list(names(co), c("coefs", paste(level*100,"%",sep=""), "C.I."))
n<-r
dd <- dim(n)
n[n > 999.99] <- Inf
a <- formatC(n, d, len,format="f")
dim(a) <- dd
if(length(dd) == 1){
dd<-c(1,dd)
dim(a)<-dd
lab<-" "
}
else
lab <- dimnames(n)[[1]]
mx <- max(nchar(lab)) + 1
cat("Recurrences:\n")
cat("------------- \n")
cat(
paste(rep(" ",mx-2),collapse=""),
paste(" ",dimnames(n)[[2]][1]),
paste("",dimnames(n)[[2]][2]),
paste("",dimnames(n)[[2]][3]),
"\n"
)
#cat(paste(rep(" ",mx),collapse=""),paste(" ",dimnames(n)[[2]]),"\n")
for(i in 1:x$nvarnotdep[1])
{
lab[i] <- paste(c(rep(" ", mx - nchar(lab[i])), lab[i]),collapse = "")
cat( lab[i], " " ,a[i,1], " (", a[i,2], ",", a[i,3], " )", sep="")
cat("\n")
#cat(lab[i], a[i, 1], "(", a[i, 2], "-", a[i, 3], ") \n")
}
cat("\n")
cat("Terminal event:\n")
cat("--------------- \n")
cat(
paste(rep(" ",mx-2),collapse=""),
paste(" ",dimnames(n)[[2]][1]),
paste("",dimnames(n)[[2]][2]),
paste("",dimnames(n)[[2]][3]),
"\n"
)
#cat(paste(rep(" ",mx),collapse=""),paste(" ",dimnames(n)[[2]]),"\n")
for(i in (x$nvarnotdep[1]+1):dd[1])
{
lab[i] <- paste(c(rep(" ", mx - nchar(lab[i])), lab[i]),collapse = "")
cat( lab[i], " " ,a[i,1], " (", a[i,2], ",", a[i,3], " )", sep="")
cat("\n")
#cat(lab[i], a[i, 1], "(", a[i, 2], "-", a[i, 3], ") \n")
}
}
}
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