R/oddsratio.h.R

In sbalci/ClinicoPath: Analysis for Clinicopathological Research

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

oddsratioOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
    "oddsratioOptions",
    inherit = jmvcore::Options,
    public = list(
        initialize = function(
            explanatory = NULL,
            outcome = NULL, ...) {

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

            private$..explanatory <- jmvcore::OptionVariables$new(
                "explanatory",
                explanatory)
            private$..outcome <- jmvcore::OptionVariable$new(
                "outcome",
                outcome,
                suggested=list(
                    "ordinal",
                    "nominal"),
                permitted=list(
                    "factor"))

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

oddsratioResults <- if (requireNamespace('jmvcore')) R6::R6Class(
    inherit = jmvcore::Group,
    active = list(
        todo = function() private$.items[["todo"]],
        text = function() private$.items[["text"]],
        plot = function() private$.items[["plot"]]),
    private = list(),
    public=list(
        initialize=function(options) {
            super$initialize(
                options=options,
                name="",
                title="Odds Ratio Table and Plot",
                refs=list(
                    "finalfit"))
            self$add(jmvcore::Html$new(
                options=options,
                name="todo",
                title="To Do",
                clearWith=list(
                    "explanatory",
                    "outcome")))
            self$add(jmvcore::Html$new(
                options=options,
                name="text",
                title="Odds Ratio Table",
                clearWith=list(
                    "explanatory",
                    "outcome")))
            self$add(jmvcore::Image$new(
                options=options,
                name="plot",
                title="Odds Ratio Plot",
                width=600,
                height=450,
                renderFun=".plot",
                requiresData=TRUE,
                clearWith=list(
                    "explanatory",
                    "outcome")))}))

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

#' Odds Ratio Table and Plot
#'
#' Function for Odds Ratio Table and Plot.
#'
#' @examples
#' \dontrun{
#' # example will be added
#'}
#' @param data The data as a data frame.
#' @param explanatory .
#' @param outcome .
#' @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
#' }
#'
#' @export
oddsratio <- function(
    data,
    explanatory,
    outcome) {

    if ( ! requireNamespace('jmvcore'))
        stop('oddsratio 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(data))
        data <- jmvcore::marshalData(
            parent.frame(),
            `if`( ! missing(explanatory), explanatory, NULL),
            `if`( ! missing(outcome), outcome, NULL))

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

    options <- oddsratioOptions$new(
        explanatory = explanatory,
        outcome = outcome)

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

    analysis$run()

    analysis$results
}