##
## intsurv: Integrative Survival Models
## Copyright (C) 2017-2021 Wenjie Wang <wang@wwenjie.org>
##
## This file is part of the R package intsurv.
##
## The R package intsurv is free software: You can redistribute it and/or
## modify it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version 3 of the License, or any later
## version (at your option). See the GNU General Public License at
## <https://www.gnu.org/licenses/> for details.
##
## The R package intsurv is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
##
##' @method print cox_cure
##' @export
print.cox_cure <- function(x, ...)
{
## function call
cat("Call:\n", paste(deparse(x$call), sep = "\n", collapse = "\n"),
"\n", sep = "")
## get the coef matrix
obj <- summary.cox_cure(x)
## survival part
cat("\nCoefficient estimates from the survival part:\n\n")
printCoefmat(obj$surv_coef_mat)
## cure rate part
cat("\nCoefficient estimates from the cure rate part:\n\n")
printCoefmat(obj$cure_coef_mat)
## return
invisible(x)
}
##' @method print cox_cure_uncer
##' @export
print.cox_cure_uncer <- function(x, ...)
{
## function call
cat("Call:\n", paste(deparse(x$call), sep = "\n", collapse = "\n"),
"\n", sep = "")
## get the coef matrix
obj <- summary.cox_cure_uncer(x)
## survival part
cat("\nCoefficient estimates from the survival part:\n\n")
printCoefmat(obj$surv_coef_mat)
## cure rate part
cat("\nCoefficient estimates from the cure rate part:\n\n")
printCoefmat(obj$cure_coef_mat)
## return
invisible(x)
}
##' @method print summary_cox_cure
##' @export
print.summary_cox_cure <- function(x, ...)
{
## function call
cat("Call:\n", paste(deparse(x$call), sep = "\n", collapse = "\n"),
"\n", sep = "")
## survival coef
cat("\nCoefficient estimates from the survival part:\n\n")
printCoefmat(x$surv_coef_mat)
## cure coef
cat("\nCoefficient estimates from the cure rate part:\n\n")
printCoefmat(x$cure_coef_mat)
## misc
cat(sprintf("\nNumber of observations: %d\n", x$model$nObs))
cat(sprintf("Number of events: %d\n", x$model$nEvent))
cat(sprintf("Weighted concordance index: %2.2f%s\n",
100 * x$model$c_index, "%"))
cat(sprintf("Observed data log-likelihood: %.3f\n",
- x$model$negLogL))
## return
invisible(x)
}
## TODO: customize more for cox_cure_uncer
##' @method print summary_cox_cure_uncer
##' @export
print.summary_cox_cure_uncer <- print.summary_cox_cure
##' @method print cox_cure_net
##' @export
print.cox_cure_net <- function(x, ...)
{
## function call
cat("Call:\n", paste(deparse(x$call), sep = "\n", collapse = "\n"),
"\n\n", sep = "")
bic_dat <- BIC.cox_cure_net(x)
digits <- max(3, getOption("digits") - 3)
lambda_dat <- as.data.frame(signif(x$penalty$lambda_mat, digits))
colnames(lambda_dat) <- c("surv_l1", "surv_l2", "cure_l1", "cure_l2")
print_dat <- cbind(bic_dat, lambda_dat)
print(print_dat)
## return nothing
invisible(NULL)
}
##' @method print cox_cure_net_uncer
##' @export
print.cox_cure_net_uncer <- print.cox_cure_net
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