Nothing
## summary method
summary.npcure <- function(object, ...) {
dots <- list(...)
cat(paste("An object of class '", class(object), "'\n\n", sep = ""))
if (is.null(dots$give.attr))
str(object, give.attr = FALSE, ...)
else
str(object, ...)
}
## print method
print.npcure <- function(x, how, head = FALSE, ...) {
dots <- list(...)
if (is.null(dots$digits))
dots$digits <- getOption("digits")
if (head && is.null(dots$n))
dots$n <- 6
if (length(x$type) == 1) {
if (!missing(how)) {
if (how == "wide" && !is.null(x$conf))
warning("The option 'how = 'long'' is the only available for 'npcure' objects with 'type' component equal to 'cure', 'latency' or 'survival' and a 'conf' component")
if (how == "long" && x$local && x$type == "cure")
warning("The option 'how = 'wide'' is the only available for 'npcure' objets with components 'local' and 'type' equal to 'TRUE' and 'cure', respectively")
}
cat("\nBandwidth type: ")
if (x$local)
cat("local\n\n")
else
cat("global\n\n")
if (x$type == "cure") {
cat("Conditional", x$type, "estimate:\n")
if (head && length(x$x0) < dots$n)
head <- FALSE
if (x$local) { ## local
if (is.null(x$conf)) { ## without CI
df <- as.data.frame(x[c("h", "x0", "q")])
dimnames(df)[[2]][3] <- x$type
}
else { ## with CI
df <- as.data.frame(x[c("h", "x0", "q", "conf")])
dimnames(df)[[2]][3:5] <- c(x$type, sprintf("lower %s%% CI", formatC(x$conflevel*100)), sprintf("upper %s%% CI", formatC(x$conflevel*100)))
}
if (head) {
print(df[1:dots$n, ], row.names = FALSE, digits = dots$digits)
cat("...\n")
}
else {
print(df, row.names = FALSE, digits = dots$digits)
}
}
else { ## cure, global
if (is.null(x$conf)) { ## without CI
if (!missing(how) && how == "long") {## long
for (i in 1:length(x$h)) {
cat("\nh =", format(x$h[i], digits = dots$digits), "\n")
df <- data.frame(x["x0"], x$q[i])
dimnames(df)[[2]][2] <- x$type
if (head) {
print(df[1:dots$n, ], row.names = FALSE, digits = dots$digits)
cat("...\n")
}
else {
print(df, row.names = FALSE, digits = dots$digits)
}
}
}
else { ## wide
df <- data.frame(x["x0"])
for (i in 1:length(x$h))
df <- cbind(df, x$q[i])
dimnames(df)[[2]] <- c("x0", formatC(paste("h = ", x$h, sep = ""), getOption("digits") + 1))
if (head) {
print(df[1:dots$n, ], row.names = FALSE, digits = dots$digits)
cat("...\n")
}
else {
print(df, row.names = FALSE, digits = dots$digits)
}
}
}
else { ## long by default
for (i in 1:length(x$h)) {
cat("\nh =", format(x$h[i], digits = dots$digits), "\n")
df <- data.frame(x["x0"], x$q[i], x$conf[[i]])
dimnames(df)[[2]] <- c("x0", x$type, sprintf("lower %s%% CI", formatC(x$conflevel*100)), sprintf("upper %s%% CI", formatC(x$conflevel*100)))
if (head) {
print(df[1:dots$n, ], row.names = FALSE, digits = dots$digits)
cat("...\n")
}
else {
print(df, row.names = FALSE, digits = dots$digits)
}
}
}
}
}
else { ## latency or beran
cat("Covariate (x0):", format(x$x0, digits = dots$digits))
cat("\nBandwidth (h): ", format(x$h, digits = dots$digits), "\n\n")
if (x$type == "latency")
cat("Conditional ")
else
cat("Beran's conditional ")
cat(x$type, "estimate:\n")
if (head && length(x$testim) < dots$n)
head <- FALSE
if (x$local) { ## latency or beran, local
if (is.null(x$conf)) {
if (!missing(how) && how == "long") { ## long
for (i in 1:length(x$h)) {
cat("\nx0 =", format(x$x0[i], digits = dots$digits))
cat("\nh =", format(x$h[i], digits = dots$digits), "\n")
if (length(x$h) == 1)
df <- data.frame(x["testim"], x$S)
else
df <- data.frame(x["testim"], x$S[i])
dimnames(df)[[2]] <- c("time", x$type)
if (head) {
print(df[1:dots$n, ], row.names = FALSE, digits = dots$digits)
cat("...\n")
}
else {
print(df, row.names = FALSE, digits = dots$digits)
}
}
}
else { ## wide
df <- data.frame(x["testim"])
for (i in 1:length(x$h))
df <- cbind(df, x$S[i])
dimnames(df)[[2]] <- c("time", formatC(paste("x0 = ", x$x0, sep = ""), getOption("digits") + 1))
cat("\n")
if (head) {
print(df[1:dots$n, ], row.names = FALSE, digits = dots$digits)
cat("...\n")
}
else {
print(df, row.names = FALSE, digits = dots$digits)
}
}
}
else { ## latency or beran, local, with CI, only long by default
for (i in 1:length(x$h)) {
cat("\nx0 =", format(x$x0[i], digits = dots$digits), "\n")
if (length(x$h) == 1)
df <- data.frame(x["testim"], x$S, x$conf)
else
df <- data.frame(x["testim"], x$S[i], x$conf[[i]])
dimnames(df)[[2]] <- c("time", x$type, sprintf("lower %s%% CI", formatC(x$conflevel*100)), sprintf("upper %s%% CI", formatC(x$conflevel*100)))
if (head) {
print(df[1:dots$n, ], row.names = FALSE, digits = dots$digits)
cat("...\n")
}
else {
print(df, row.names = FALSE, digits = dots$digits)
}
}
}
}
else { ## latency or beran, global
if (is.null(x$conf)) { ## without CI
if (!missing(how) && how == "long") { ## long
for (i in 1:length(x$x0)) {
for (j in 1:length(x$h)) {
cat("\nx0 =", format(x$x0[i], digits = dots$digits))
cat("\nh =", format(x$h[j], digits = dots$digits), "\n")
df <- data.frame(x["testim"], x$S[[j]][i])
dimnames(df)[[2]] <- c("time", x$type)
if (head) {
print(df[1:dots$n, ], row.names = FALSE, digits = dots$digits)
cat("...\n")
}
else {
print(df, row.names = FALSE, digits = dots$digits)
}
}
}
}
else { ## wide
for (i in 1:length(x$x0)) {
cat("\nx0 =", format(x$x0[i], digits = dots$digits), "\n")
df <- data.frame(x["testim"])
for (j in 1:length(x$h))
df <- cbind(df, x$S[[j]][i])
dimnames(df)[[2]] <- c("time", formatC(paste("h = ", x$h, sep = ""), dots$digits + 1))
if (head) {
print(df[1:dots$n, ], row.names = FALSE, digits = dots$digits)
cat("...\n")
}
else {
print(df, row.names = FALSE, digits = dots$digits)
}
}
}
}
else { ## latency or beran, global, with CI
for (i in 1:length(x$x0)) { ## only long (default)
for (j in 1:length(x$h)) {
cat("\nx0 =", format(x$x0[i], digits = dots$digits), "\n")
cat("h =", format(x$h[j], digits = dots$digits), "\n")
df <- data.frame(x["testim"])
df <- cbind(df, x$S[[j]][i], x$conf[[j]][i])
dimnames(df)[[2]] <- c("time", x$type, sprintf("lower %s%% CI", formatC(x$conflevel*100)), sprintf("upper %s%% CI", formatC(x$conflevel*100)))
if (head) {
print(df[1:dots$n, ], row.names = FALSE, digits = dots$digits)
cat("...\n")
}
else {
print(df, row.names = FALSE, digits = dots$digits)
}
}
}
}
}
}
}
else { ## of if (length(x$type) == 1)
if (!missing(how))
warning("The option 'how' is ignored for 'npcure' objects with 'type' component of length 2")
if (x$type[1] == "test") { ## test
cat(x$type[2], x$type[1], "\n\n")
if (x$type[2] == "Covariate") {
cat("Covariate: ", x$x, "\n")
df <- data.frame(test = c("Cramer-von Mises", "Kolmogorov-Smirnov"), statistic = c(x$CM$statistic, x$KS$statistic), p.value = c(x$CM$pvalue, x$KS$pvalue))
}
else {
df <- data.frame(statistic = x$aux$statistic, n = x$aux$n, p.value = x$pvalue)
}
print(df, row.names = FALSE, digits = dots$digits)
}
else { ## bandwidth
cat(x$type[1], "(h) for", if (x$type[2] == "survival") "Beran's", x$type[2], "estimator conditional on covariate x0:\n")
if (head && length(x$x0) < dots$n)
head <- FALSE
if (is.null(x$hsmooth)) {
df <- data.frame(x[c("x0", "h")])
dimnames(df)[[2]] <- c("x0", "h")
}
else {
df <- data.frame(x[c("x0", "h", "hsmooth")])
dimnames(df)[[2]] <- c("x0", "h", "h.smooth")
}
cat("\n")
if (head) {
print(df[1:dots$n, ], row.names = FALSE, digits = dots$digits)
cat("...\n")
}
else {
print(df, row.names = FALSE, digits = dots$digits)
}
}
}
}
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