R/multisurvival.h.R

In sbalci/ClinicoPath: Analysis for Clinicopathological Research

# This file is automatically generated, you probably don't want to edit this

multisurvivalOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
    "multisurvivalOptions",
    inherit = jmvcore::Options,
    public = list(
        initialize = function(
            explanatory = NULL,
            outcome = NULL,
            overalltime = NULL,
            sty = "t1",
            ac = FALSE,
            adjexplanatory = NULL, ...) {

            super$initialize(
                package='ClinicoPath',
                name='multisurvival',
                requiresData=TRUE,
                ...)

            private$..explanatory <- jmvcore::OptionVariables$new(
                "explanatory",
                explanatory)
            private$..outcome <- jmvcore::OptionVariable$new(
                "outcome",
                outcome,
                suggested=list(
                    "continuous"),
                permitted=list(
                    "numeric"))
            private$..overalltime <- jmvcore::OptionVariable$new(
                "overalltime",
                overalltime,
                suggested=list(
                    "continuous"),
                permitted=list(
                    "numeric"))
            private$..sty <- jmvcore::OptionList$new(
                "sty",
                sty,
                options=list(
                    "t1",
                    "t3"),
                default="t1")
            private$..ac <- jmvcore::OptionBool$new(
                "ac",
                ac,
                default=FALSE)
            private$..adjexplanatory <- jmvcore::OptionVariable$new(
                "adjexplanatory",
                adjexplanatory)

            self$.addOption(private$..explanatory)
            self$.addOption(private$..outcome)
            self$.addOption(private$..overalltime)
            self$.addOption(private$..sty)
            self$.addOption(private$..ac)
            self$.addOption(private$..adjexplanatory)
        }),
    active = list(
        explanatory = function() private$..explanatory$value,
        outcome = function() private$..outcome$value,
        overalltime = function() private$..overalltime$value,
        sty = function() private$..sty$value,
        ac = function() private$..ac$value,
        adjexplanatory = function() private$..adjexplanatory$value),
    private = list(
        ..explanatory = NA,
        ..outcome = NA,
        ..overalltime = NA,
        ..sty = NA,
        ..ac = NA,
        ..adjexplanatory = NA)
)

multisurvivalResults <- if (requireNamespace('jmvcore')) R6::R6Class(
    inherit = jmvcore::Group,
    active = list(
        todo = function() private$.items[["todo"]],
        text = function() private$.items[["text"]],
        plot = function() private$.items[["plot"]],
        plot3 = function() private$.items[["plot3"]],
        plot4 = function() private$.items[["plot4"]]),
    private = list(),
    public=list(
        initialize=function(options) {
            super$initialize(
                options=options,
                name="",
                title="Multivariate Survival Analysis")
            self$add(jmvcore::Html$new(
                options=options,
                name="todo",
                title="To Do",
                clearWith=list(
                    "explanatory",
                    "outcome",
                    "overalltime")))
            self$add(jmvcore::Html$new(
                options=options,
                name="text",
                title="Multivariate Survival",
                clearWith=list(
                    "explanatory",
                    "outcome",
                    "overalltime"),
                refs="finalfit"))
            self$add(jmvcore::Image$new(
                options=options,
                name="plot",
                title="Hazards Regression Plot",
                width=600,
                height=450,
                renderFun=".plot",
                requiresData=TRUE,
                clearWith=list(
                    "explanatory",
                    "outcome",
                    "overalltime"),
                visible="(sty:t1)",
                refs="finalfit"))
            self$add(jmvcore::Image$new(
                options=options,
                name="plot3",
                title="Hazards Regression (Forest) Plot",
                width=800,
                height=600,
                renderFun=".plot3",
                requiresData=TRUE,
                clearWith=list(
                    "explanatory",
                    "outcome",
                    "overalltime"),
                visible="(sty:t3)",
                refs="survminer"))
            self$add(jmvcore::Image$new(
                options=options,
                name="plot4",
                title="Show Adjusted Survival Curve",
                width=800,
                height=600,
                renderFun=".plot4",
                requiresData=TRUE,
                clearWith=list(
                    "explanatory",
                    "outcome",
                    "overalltime",
                    "adjexplanatory"),
                visible="(ac)",
                refs="survminer"))}))

multisurvivalBase <- if (requireNamespace('jmvcore')) R6::R6Class(
    "multisurvivalBase",
    inherit = jmvcore::Analysis,
    public = list(
        initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
            super$initialize(
                package = 'ClinicoPath',
                name = 'multisurvival',
                version = c(1,0,0),
                options = options,
                results = multisurvivalResults$new(options=options),
                data = data,
                datasetId = datasetId,
                analysisId = analysisId,
                revision = revision,
                pause = NULL,
                completeWhenFilled = FALSE,
                requiresMissings = FALSE)
        }))

#' Multivariate Survival Analysis
#'
#' Function for Multivariate Survival Analysis using Cox-regression.
#'
#' @examples
#' \dontrun{
#' # example will be added
#'}
#' @param data The data as a data frame.
#' @param explanatory .
#' @param outcome .
#' @param overalltime .
#' @param sty .
#' @param ac .
#' @param adjexplanatory .
#' @return A results object containing:
#' \tabular{llllll}{
#'   \code{results$todo} \tab \tab \tab \tab \tab a html \cr
#'   \code{results$text} \tab \tab \tab \tab \tab a html \cr
#'   \code{results$plot} \tab \tab \tab \tab \tab an image \cr
#'   \code{results$plot3} \tab \tab \tab \tab \tab an image \cr
#'   \code{results$plot4} \tab \tab \tab \tab \tab an image \cr
#' }
#'
#' @export
multisurvival <- function(
    data,
    explanatory,
    outcome,
    overalltime,
    sty = "t1",
    ac = FALSE,
    adjexplanatory) {

    if ( ! requireNamespace('jmvcore'))
        stop('multisurvival requires jmvcore to be installed (restart may be required)')

    if ( ! missing(explanatory)) explanatory <- jmvcore::resolveQuo(jmvcore::enquo(explanatory))
    if ( ! missing(outcome)) outcome <- jmvcore::resolveQuo(jmvcore::enquo(outcome))
    if ( ! missing(overalltime)) overalltime <- jmvcore::resolveQuo(jmvcore::enquo(overalltime))
    if ( ! missing(adjexplanatory)) adjexplanatory <- jmvcore::resolveQuo(jmvcore::enquo(adjexplanatory))
    if (missing(data))
        data <- jmvcore::marshalData(
            parent.frame(),
            `if`( ! missing(explanatory), explanatory, NULL),
            `if`( ! missing(outcome), outcome, NULL),
            `if`( ! missing(overalltime), overalltime, NULL),
            `if`( ! missing(adjexplanatory), adjexplanatory, NULL))


    options <- multisurvivalOptions$new(
        explanatory = explanatory,
        outcome = outcome,
        overalltime = overalltime,
        sty = sty,
        ac = ac,
        adjexplanatory = adjexplanatory)

    analysis <- multisurvivalClass$new(
        options = options,
        data = data)

    analysis$run()

    analysis$results
}