ClinicoPath: Analysis for Clinicopathological Research

Documented in survival

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

survivalOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
    "survivalOptions",
    inherit = jmvcore::Options,
    public = list(
        initialize = function(
            explanatory = NULL,
            overalltime = NULL,
            outcome = NULL,
            cutp = "12, 36, 60",
            sc = FALSE,
            ce = FALSE,
            ch = FALSE, ...) {

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

            private$..explanatory <- jmvcore::OptionVariable$new(
                "explanatory",
                explanatory,
                suggested=list(
                    "ordinal",
                    "nominal"),
                permitted=list(
                    "factor"))
            private$..overalltime <- jmvcore::OptionVariable$new(
                "overalltime",
                overalltime,
                suggested=list(
                    "continuous"),
                permitted=list(
                    "numeric"))
            private$..outcome <- jmvcore::OptionVariable$new(
                "outcome",
                outcome,
                suggested=list(
                    "continuous"),
                permitted=list(
                    "numeric"))
            private$..cutp <- jmvcore::OptionString$new(
                "cutp",
                cutp,
                default="12, 36, 60")
            private$..sc <- jmvcore::OptionBool$new(
                "sc",
                sc,
                default=FALSE)
            private$..ce <- jmvcore::OptionBool$new(
                "ce",
                ce,
                default=FALSE)
            private$..ch <- jmvcore::OptionBool$new(
                "ch",
                ch,
                default=FALSE)

            self$.addOption(private$..explanatory)
            self$.addOption(private$..overalltime)
            self$.addOption(private$..outcome)
            self$.addOption(private$..cutp)
            self$.addOption(private$..sc)
            self$.addOption(private$..ce)
            self$.addOption(private$..ch)
        }),
    active = list(
        explanatory = function() private$..explanatory$value,
        overalltime = function() private$..overalltime$value,
        outcome = function() private$..outcome$value,
        cutp = function() private$..cutp$value,
        sc = function() private$..sc$value,
        ce = function() private$..ce$value,
        ch = function() private$..ch$value),
    private = list(
        ..explanatory = NA,
        ..overalltime = NA,
        ..outcome = NA,
        ..cutp = NA,
        ..sc = NA,
        ..ce = NA,
        ..ch = NA)
)

survivalResults <- if (requireNamespace('jmvcore')) R6::R6Class(
    inherit = jmvcore::Group,
    active = list(
        todo = function() private$.items[["todo"]],
        text2 = function() private$.items[["text2"]],
        text1html = function() private$.items[["text1html"]],
        text5 = function() private$.items[["text5"]],
        text4 = function() private$.items[["text4"]],
        text7 = function() private$.items[["text7"]],
        text6 = function() private$.items[["text6"]],
        text8 = function() private$.items[["text8"]],
        text9 = function() private$.items[["text9"]],
        plot = function() private$.items[["plot"]],
        plot2 = function() private$.items[["plot2"]],
        plot3 = function() private$.items[["plot3"]]),
    private = list(),
    public=list(
        initialize=function(options) {
            super$initialize(
                options=options,
                name="",
                title="`Survival Analysis - ${explanatory}`",
                refs=list(
                    "finalfit",
                    "survival",
                    "survminer"))
            self$add(jmvcore::Html$new(
                options=options,
                name="todo",
                title="To Do",
                clearWith=list(
                    "explanatory",
                    "outcome",
                    "overalltime")))
            self$add(jmvcore::Preformatted$new(
                options=options,
                name="text2",
                title="`Median Survival Summary and Table - ${explanatory}`",
                clearWith=list(
                    "explanatory",
                    "outcome",
                    "overalltime")))
            self$add(jmvcore::Html$new(
                options=options,
                name="text1html",
                title="`Median Survival Table  - ${explanatory}`",
                clearWith=list(
                    "explanatory",
                    "outcome",
                    "overalltime")))
            self$add(jmvcore::Preformatted$new(
                options=options,
                name="text5",
                title="`Cox Regression Summary and Table - ${explanatory}`",
                clearWith=list(
                    "explanatory",
                    "outcome",
                    "overalltime")))
            self$add(jmvcore::Html$new(
                options=options,
                name="text4",
                title="`Cox Table- ${explanatory}`",
                clearWith=list(
                    "explanatory",
                    "outcome",
                    "overalltime")))
            self$add(jmvcore::Preformatted$new(
                options=options,
                name="text7",
                title="`1, 3, 5-yr Survival Summary and Table  - ${explanatory}`",
                clearWith=list(
                    "explanatory",
                    "outcome",
                    "overalltime")))
            self$add(jmvcore::Html$new(
                options=options,
                name="text6",
                title="`1, 3, 5-yr Survival  - ${explanatory}`",
                clearWith=list(
                    "explanatory",
                    "outcome",
                    "overalltime")))
            self$add(jmvcore::Preformatted$new(
                options=options,
                name="text8",
                title="`Pairwise Comparison - ${explanatory}`",
                clearWith=list(
                    "explanatory",
                    "outcome",
                    "overalltime")))
            self$add(jmvcore::Preformatted$new(
                options=options,
                name="text9",
                title="`Pairwise Comparison Summary - ${explanatory}`",
                clearWith=list(
                    "explanatory",
                    "outcome",
                    "overalltime")))
            self$add(jmvcore::Image$new(
                options=options,
                name="plot",
                title="`Survival Plot  - ${explanatory}`",
                width=600,
                height=450,
                renderFun=".plot",
                visible="(sc)",
                requiresData=TRUE,
                clearWith=list(
                    "sc",
                    "explanatory",
                    "outcome",
                    "overalltime")))
            self$add(jmvcore::Image$new(
                options=options,
                name="plot2",
                title="`Cumulative Events  - ${explanatory}`",
                width=600,
                height=450,
                renderFun=".plot2",
                visible="(ce)",
                requiresData=TRUE,
                clearWith=list(
                    "ce",
                    "explanatory",
                    "outcome",
                    "overalltime")))
            self$add(jmvcore::Image$new(
                options=options,
                name="plot3",
                title="`Cumulative Hazard  - ${explanatory}`",
                width=600,
                height=450,
                renderFun=".plot3",
                visible="(ch)",
                requiresData=TRUE,
                clearWith=list(
                    "ch",
                    "explanatory",
                    "outcome",
                    "overalltime")))}))

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

#' Survival Analysis
#'
#' Function for Generating Summaries for Survival Analysis.
#'
#' @examples
#' \dontrun{
#' # example will be added
#'}
#' @param data The data as a data frame.
#' @param explanatory .
#' @param overalltime .
#' @param outcome .
#' @param cutp .
#' @param sc .
#' @param ce .
#' @param ch .
#' @return A results object containing:
#' \tabular{llllll}{
#'   \code{results$todo} \tab \tab \tab \tab \tab a html \cr
#'   \code{results$text2} \tab \tab \tab \tab \tab a preformatted \cr
#'   \code{results$text1html} \tab \tab \tab \tab \tab a html \cr
#'   \code{results$text5} \tab \tab \tab \tab \tab a preformatted \cr
#'   \code{results$text4} \tab \tab \tab \tab \tab a html \cr
#'   \code{results$text7} \tab \tab \tab \tab \tab a preformatted \cr
#'   \code{results$text6} \tab \tab \tab \tab \tab a html \cr
#'   \code{results$text8} \tab \tab \tab \tab \tab a preformatted \cr
#'   \code{results$text9} \tab \tab \tab \tab \tab a preformatted \cr
#'   \code{results$plot} \tab \tab \tab \tab \tab an image \cr
#'   \code{results$plot2} \tab \tab \tab \tab \tab an image \cr
#'   \code{results$plot3} \tab \tab \tab \tab \tab an image \cr
#' }
#'
#' @export
survival <- function(
    data,
    explanatory,
    overalltime,
    outcome,
    cutp = "12, 36, 60",
    sc = FALSE,
    ce = FALSE,
    ch = FALSE) {

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

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

    for (v in explanatory) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])

    options <- survivalOptions$new(
        explanatory = explanatory,
        overalltime = overalltime,
        outcome = outcome,
        cutp = cutp,
        sc = sc,
        ce = ce,
        ch = ch)

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

    analysis$run()

    analysis$results
}