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#' Prints aftreg objects
#'
#' The hazard, the cumulative hazard, the density, and the survivor baseline
#' functions are plotted.
#'
#'
#' @param x A \code{aftreg} object
#' @param digits Precision in printing
#' @param \dots Not used.
#' @return No value is returned.
#' @note Doesn't work for threeway or higher order interactions. Use
#' \code{\link[survival]{print.coxph}} in that case.
#' @author Göran Broström
#' @seealso \code{\link{phreg}}, \code{\link[survival]{print.coxph}}
#' @keywords survival regression
#' @export
print.aftreg <- function(x, digits=max(options()$digits - 4, 3), ...){
if (!is.null(cl<- x$call)) {
cat("Call:\n")
dput(cl)
cat("\n")
}
if (!is.null(x$fail)) {
cat(" aftreg failed.\n")
return()
}
savedig <- options(digits = digits)
on.exit(options(savedig))
if (x$pfixed){
n.slsh <- 1
}else{
n.slsh <- 2 * x$n.strata
}
coef <- x$coefficients
se <- sqrt(diag(x$var))
wald.p <- formatC(1 - pchisq((coef/ se)^2, 1),
digits = 3,
width = 9, format = "f")
if (is.null(coef) || is.null(se))
stop("Input is not valid")
#####################################
if (x$param == "lifeAcc"){
cat("Covariate W.mean Coef Time-Accn se(Coef) Wald p\n")
}else{
cat("Covariate W.mean Coef Life-Expn se(Coef) Wald p\n")
}
e.coef <- formatC(exp(coef), width = 9, digits = 3, format = "f")
coef <- formatC(coef, width = 9, digits = 3, format = "f")
se <- formatC(se, width = 9, digits = 3, format = "f")
ett <- formatC(1, width = 9, digits = 0, format = "f")
noll <- formatC(0, width = 5, digits = 0, format = "f")
factors <- attr(x$terms, "factors")
resp <- attr(x$terms, "response")
row.strata <- attr(x$terms, "specials")$strata
if (!is.null(row.strata))
col.strata <- which(factors[row.strata, ] == 1)
else col.strata <- NULL
if (!is.null(x$covars)){
if (!is.null(col.strata)){
factors <-
attr(x$terms, "factors")[-c(resp, row.strata), -col.strata,
drop = FALSE]
}else{
factors <-
attr(x$terms, "factors")[-c(resp, row.strata), ,
drop = FALSE]
}
covar.names <- c(x$covars,
names(coef)[(length(coef)-n.slsh + 1):
length(coef)])
term.names <- colnames(factors)
isF <- x$isF
}
ord <- attr(x$terms, "order")
if (!is.null(col.strata)) ord <- ord[-col.strata]
index <- 0
if (!is.null(x$covars)){
n.rows <- length(term.names)
for (term.no in 1:n.rows){
if (ord[term.no] == 1){
covar.no <- which(factors[, term.no] == 1)
if (isF[covar.no]){ ## Factors:
cat(covar.names[covar.no], "\n")
no.lev <- length(x$levels[[covar.no]])
cat(formatC(x$levels[[covar.no]][1], width = 16, flag =
"+"),
formatC(x$w.means[[covar.no]][1],
width = 8, digits = 3, format = "f"),
noll,
ett,
" (reference)\n")
for (lev in 2:no.lev){
index <- index + 1
cat(formatC(x$levels[[covar.no]][lev], width = 16,
flag = "+"),
formatC(x$w.means[[covar.no]][lev],
width = 8, digits = 3, format = "f"),
coef[index],
e.coef[index],
se[index],
#formatC(" ", width = 1),
#formatC(" ", width = 9),
formatC(wald.p[index],
digits = 3,
width = digits + 2,
format = "f"),
##signif(1 - pchisq((coef/ se)^2, 1), digits - 1),
"\n")
}
}else{ ## Covariates:
index <- index + 1
cat(formatC(covar.names[covar.no], width = 16, flag = "-"),
formatC(x$w.means[[covar.no]],
width = 8, digits = 3, format = "f"),
coef[index],
e.coef[index],
#exp(coef[index]),
se[index],
#formatC(" ", width = 1),
formatC(wald.p[index],
digits = 3,
width = digits + 2,
format = "f"),
##signif(1 - pchisq((coef/ se)^2, 1), digits - 1),
"\n")
}
}else if (ord[term.no] > 1){ ## Interactions:
cat(format(term.names[term.no], width = 16), "\n")
niv <- numeric(ord[term.no])
covar.no <- which(factors[, term.no] == 1)
for (i in 1:ord[term.no]){
if (isF[covar.no[i]]){
niv[i] <- length(x$levels[[covar.no[i]]]) - 1
}else{
niv[i] <- 1
}
}
stt <- index + 1
for (index in stt:(stt + prod(niv) - 1)){
vn <- sub(covar.names[covar.no[1]], "", names(coef)[index])
for (i in 1:ord[term.no]){
vn <- sub(covar.names[covar.no[i]], "", vn)
}
cat(formatC(" ", width = 2),
formatC(substring(vn, 1, 22), width = 22, flag = "-"),
## format(" ", 8),
coef[index],
e.coef[index],
se[index],
#formatC(" ", width = 1),
formatC(wald.p[index],
digits = 3,
width = digits + 2,
format = "f"),
##signif(1 - pchisq((coef[index]/ se[index])^2, 1), digits - 1),
"\n")
}
}
}
cat("\n")
}
cat("Baseline parameters:\n")
for (i in 1:n.slsh){
jup <- length(coef)
ss.names <- names(coef[(jup - n.slsh + 1):jup])
index <- index + 1
## covar.no <- covar.no + 1
cat(formatC(ss.names[i], width = 16, flag = "-"),
formatC(" ",
width = 8, digits = 3, format = "c"),
coef[index],
formatC(" ", width = 9), # Changed 2.4-3
##e.coef[index],
#exp(coef[index]),
se[index],
#formatC(" ", width = 1),
formatC(wald.p[index],
digits = 3,
width = digits + 2,
format = "f"),
##signif(1 - pchisq((coef/ se)^2, 1), digits - 1),
"\n")
}
cat("Baseline life expectancy: ", x$baselineMean, "\n")
#####################################
if(FALSE){
tmp <- cbind(coef, exp(coef), se,
signif(1 - pchisq((coef/ se)^2, 1), digits - 1))
dimnames(tmp) <- list(names(coef), c("coef", "rel. risk",
"se(coef)", "p"))
cat("\n")
prmatrix(tmp)
}
logtest <- -2 * (x$loglik[1] - x$loglik[2])
if (is.null(x$df)) df <- sum(!is.na(coef)) - n.slsh
else df <- round(sum(x$df), 2)
cat("\n")
if (x$pfixed) {
cat(" Shape is fixed at ", x$shape, "\n\n")
}
cat(formatC("Events", width = 25, flag = "-"), x$n.events, "\n")
cat(formatC("Total time at risk", width = 25, flag = "-"),
formatC(x$ttr, digits = 5, format = "fg"), "\n")
cat(formatC("Max. log. likelihood", width = 25, flag = "-"),
formatC(x$loglik[2], digits = 5, format = "fg"), "\n")
if (df > 0.5){
cat(formatC("LR test statistic", width = 25, flag = "-"),
format(round(logtest, 2)), "\n")
cat(formatC("Degrees of freedom", width = 25, flag = "-"),
formatC(df, digits = 0, format = "f"), "\n")
cat(formatC("Overall p-value", width = 25, flag = "-"),
format.pval(1 - pchisq(logtest, df), digits = 6, "\n"))
}
cat("\n")
if (length(x$icc))
cat(" number of clusters=", x$icc[1],
" ICC=", format(x$icc[2:3]), "\n")
invisible(x)
}
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