R/decision.h.R

In sbalci/ClinicoPath: Analysis for Clinicopathological Research

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

decisionOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
    "decisionOptions",
    inherit = jmvcore::Options,
    public = list(
        initialize = function(
            gold = NULL,
            goldPositive = NULL,
            newtest = NULL,
            testPositive = NULL, ...) {

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

            private$..gold <- jmvcore::OptionVariable$new(
                "gold",
                gold,
                suggested=list(
                    "nominal"),
                permitted=list(
                    "factor"))
            private$..goldPositive <- jmvcore::OptionLevel$new(
                "goldPositive",
                goldPositive,
                variable="(gold)")
            private$..newtest <- jmvcore::OptionVariable$new(
                "newtest",
                newtest,
                suggested=list(
                    "nominal"),
                permitted=list(
                    "factor"))
            private$..testPositive <- jmvcore::OptionLevel$new(
                "testPositive",
                testPositive,
                variable="(newtest)")

            self$.addOption(private$..gold)
            self$.addOption(private$..goldPositive)
            self$.addOption(private$..newtest)
            self$.addOption(private$..testPositive)
        }),
    active = list(
        gold = function() private$..gold$value,
        goldPositive = function() private$..goldPositive$value,
        newtest = function() private$..newtest$value,
        testPositive = function() private$..testPositive$value),
    private = list(
        ..gold = NA,
        ..goldPositive = NA,
        ..newtest = NA,
        ..testPositive = NA)
)

decisionResults <- if (requireNamespace('jmvcore')) R6::R6Class(
    inherit = jmvcore::Group,
    active = list(
        text1 = function() private$.items[["text1"]],
        text2 = function() private$.items[["text2"]]),
    private = list(),
    public=list(
        initialize=function(options) {
            super$initialize(
                options=options,
                name="",
                title="Medical Decision",
                refs="caret")
            self$add(jmvcore::Preformatted$new(
                options=options,
                name="text1",
                title="Original Data"))
            self$add(jmvcore::Preformatted$new(
                options=options,
                name="text2",
                title="Decision Tests"))}))

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

#' Medical Decision
#'
#' Function for Medical Decision Analysis. Sensitivity, specificity, positive 
#' predictive value, negative predictive value.
#' 
#'
#' @examples
#' \dontrun{
#' # example will be added
#'}
#' @param data The data as a data frame.
#' @param gold .
#' @param goldPositive .
#' @param newtest .
#' @param testPositive .
#' @return A results object containing:
#' \tabular{llllll}{
#'   \code{results$text1} \tab \tab \tab \tab \tab a preformatted \cr
#'   \code{results$text2} \tab \tab \tab \tab \tab a preformatted \cr
#' }
#'
#' @export
decision <- function(
    data,
    gold,
    goldPositive,
    newtest,
    testPositive) {

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

    if ( ! missing(gold)) gold <- jmvcore::resolveQuo(jmvcore::enquo(gold))
    if ( ! missing(newtest)) newtest <- jmvcore::resolveQuo(jmvcore::enquo(newtest))
    if (missing(data))
        data <- jmvcore::marshalData(
            parent.frame(),
            `if`( ! missing(gold), gold, NULL),
            `if`( ! missing(newtest), newtest, NULL))

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

    options <- decisionOptions$new(
        gold = gold,
        goldPositive = goldPositive,
        newtest = newtest,
        testPositive = testPositive)

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

    analysis$run()

    analysis$results
}