R/show.R

In wenjie2wang/intsurv: Integrative Survival Modeling

##
## 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.
##

## collation after class.R
##' @include class.R
NULL

##' Show Methods
##'
##' S4 class methods that display or summarize certain objects.
##'
##' \itemize{
##'
##' \item For \code{\link{iCoxph-class}} object, it prints out a brief summary
##'     of the fitted model.
##'
##' \item For \code{\link{summary.iCoxph-class}} object, it prints out summary
##'       of a fitted model.
##'
##' }
##'
##' @param object An object used to dispatch a method.
##' @return object input (invisibly).
##' @name show-method
##' @importFrom methods show
NULL


##' @rdname show-method
##' @aliases show,iCoxph-method
##' @importFrom stats printCoefmat
##' @export
setMethod(
    f = "show", signature = "iCoxph",
    definition = function(object)
    {
        ## function call
        cat("Call:\n", paste(deparse(object@call), sep = "\n", collapse = "\n"),
            "\n\n", sep = "")
        ## coefficient estimates
        cat("Coefficients of covariates: \n")
        printCoefmat(object@estimates$beta)
        ## return
        invisible(object)
    }
)


##' @rdname show-method
##' @aliases show,summary.iCoxph-method
##' @importFrom stats printCoefmat
##' @export
setMethod(
    f = "show", signature = "summary.iCoxph",
    definition = function(object)
    {
        ## function call
        if (attr(object@call, "show")) {
            Call <- object@call
            attr(Call, "show") <- NULL
            cat("Call:\n",
                paste(deparse(Call), sep = "\n",
                      collapse = "\n"),
                "\n\n", sep = "")
        }
        ## coefficient estimates
        cat("Coefficients of covariates: \n")
        printCoefmat(object@coefMat)
        ## log-likelihood after convergence
        cat("\nLog-likelihood under observed data:", object@logL, "\n")
        ## return
        invisible(object)
    }
)