Nothing
##
## 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
##' Estimated Covariates Coefficients
##'
##' \code{coef,iCoxph-method} is an S4 class method that extracts covariate
##' coefficient estimates from \code{\link{iCoxph-class}} object from function
##' \code{\link{iCoxph}}.
##'
##' @param object \code{\link{iCoxph-class}} object.
##' @param ... Other arguments for future usage.
##' @return A named numeric vector.
##' @aliases coef,iCoxph-method coef.iCoxph
##' @seealso
##' \code{\link{iCoxph}} for fitting integrative Cox model;
##' \code{\link{summary,iCoxph-method}} for summary of a fitted model.
##' @examples
##' ## See examples of function iCoxph.
##' @importFrom stats coef
##' @export
setMethod(
f = "coef", signature = "iCoxph",
definition = function(object, ...)
{
object@estimates$beta[, "coef"]
})
##' Estimated Covariate Coefficients
##'
##' Extract the covariate coefficient estimates from a fitted Cox cure rate
##' model with possible uncertain event status.
##'
##' @param object Object representing a fitted model.
##' @param part A character string specifying the coefficient estimates from a
##' particular model part. The available options are \code{"both"} for the
##' coefficient estimates from both model parts, \code{"survival"} for the
##' coefficient estimates from the survival model part, and \code{"cure"}
##' for the coefficient estimates from the cure rate model part. The
##' default option is \code{"all"}.
##' @param ... Other arguments for future usage.
##'
##' @return If \code{part = "both"}, this function returns a list that consists
##' of the following named elements \itemize{
##'
##' \item \code{surv}: the coefficient estimates of survival model part.
##'
##' \item \code{cure}: the coefficient estimates of cure rate model part.
##'
##' }
##'
##' Otherwise, a named numeric vector representing the coefficient estimates of
##' the specified model part will be returned.
##'
##' @importFrom stats coef
##' @method coef cox_cure
##' @export
coef.cox_cure <- function(object, part = c("both", "survival", "cure"), ...)
{
part <- match.arg(part)
if (part != "both") {
coef_name <- sprintf(
"%s_coef", switch(part, "survival" = "surv", "cure" = "cure")
)
return(object[[coef_name]])
}
## else return both
list(surv = object$surv_coef,
cure = object$cure_coef)
}
##' @rdname coef.cox_cure
##' @method coef cox_cure_uncer
##' @export
coef.cox_cure_uncer <- coef.cox_cure
##' Estimated Covariate Coefficients
##'
##' Extract the covariate coefficient estimates from a solution path of
##' regularized Cox cure rate model.
##'
##' @param object Object representing a fitted solution path.
##' @param naive_en A logical value specifying whether to return naive elastic
##' net estimates. If \code{FALSE} by default, the elastic net estimates
##' will be returned instead of the naive elastic net estimates.
##' @param selection A character string for specifying the criterion for
##' selection of coefficient estimates. The available options are
##' \code{"bic1"} for selecting coefficient estimates by regular BIC
##' criterion based on the number of observations, \code{"bic2"} for a
##' variant BIC criterion based on the effective sample size, and
##' \code{"all"} for returning the whole solution path. See
##' \code{\link{BIC.cox_cure_net}} for details of selection by BIC.
##' @param ... Other arguments for future usage.
##'
##' @return A list that consists of the following named elements:
##' \itemize{
##'
##' \item \code{surv}: the selected coefficient estimates of survival model
##' part.
##'
##' \item \code{cure}: the selected coefficient estimates of cure rate model
##' part.
##'
##' }
##'
##' @examples
##' ## see examples of function `cox_cure_net`
##'
##' @importFrom stats coef
##' @method coef cox_cure_net
##' @export
coef.cox_cure_net <- function(object, naive_en = FALSE,
selection = c("bic1", "bic2", "all"), ...)
{
bic <- match.arg(selection)
surv_coef_name <- paste0("surv_", ifelse(naive_en, "", "en_"), "coef")
cure_coef_name <- paste0("cure_", ifelse(naive_en, "", "en_"), "coef")
if (bic != "all") {
idx <- which.min(object$model[[bic]])
out <- list(surv = object[[surv_coef_name]][idx, ],
cure = object[[cure_coef_name]][idx, ])
} else {
out <- list(surv = object[[surv_coef_name]],
cure = object[[cure_coef_name]])
}
## return
out
}
##' @rdname coef.cox_cure_net
##' @importFrom stats coef
##' @method coef cox_cure_net_uncer
##' @export
coef.cox_cure_net_uncer <- coef.cox_cure_net
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.