R/tree.h.R

In sbalci/ClinicoPathJamoviModule: Analysis for Clinicopathological Research

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

treeOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
    "treeOptions",
    inherit = jmvcore::Options,
    public = list(
        initialize = function(
            vars = NULL,
            facs = NULL,
            target = NULL,
            targetLevel = NULL,
            train = NULL,
            trainLevel = NULL,
            showPlot = FALSE, ...) {

            super$initialize(
                package="ClinicoPath",
                name="tree",
                requiresData=TRUE,
                ...)

            private$..vars <- jmvcore::OptionVariables$new(
                "vars",
                vars,
                suggested=list(
                    "continuous"),
                permitted=list(
                    "numeric"))
            private$..facs <- jmvcore::OptionVariables$new(
                "facs",
                facs,
                suggested=list(
                    "ordinal",
                    "nominal"),
                permitted=list(
                    "factor"))
            private$..target <- jmvcore::OptionVariable$new(
                "target",
                target,
                suggested=list(
                    "ordinal",
                    "nominal"),
                permitted=list(
                    "factor"))
            private$..targetLevel <- jmvcore::OptionLevel$new(
                "targetLevel",
                targetLevel,
                variable="(target)")
            private$..train <- jmvcore::OptionVariable$new(
                "train",
                train,
                suggested=list(
                    "ordinal",
                    "nominal"),
                permitted=list(
                    "factor"))
            private$..trainLevel <- jmvcore::OptionLevel$new(
                "trainLevel",
                trainLevel,
                variable="(train)")
            private$..showPlot <- jmvcore::OptionBool$new(
                "showPlot",
                showPlot,
                default=FALSE)

            self$.addOption(private$..vars)
            self$.addOption(private$..facs)
            self$.addOption(private$..target)
            self$.addOption(private$..targetLevel)
            self$.addOption(private$..train)
            self$.addOption(private$..trainLevel)
            self$.addOption(private$..showPlot)
        }),
    active = list(
        vars = function() private$..vars$value,
        facs = function() private$..facs$value,
        target = function() private$..target$value,
        targetLevel = function() private$..targetLevel$value,
        train = function() private$..train$value,
        trainLevel = function() private$..trainLevel$value,
        showPlot = function() private$..showPlot$value),
    private = list(
        ..vars = NA,
        ..facs = NA,
        ..target = NA,
        ..targetLevel = NA,
        ..train = NA,
        ..trainLevel = NA,
        ..showPlot = NA)
)

treeResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
    "treeResults",
    inherit = jmvcore::Group,
    active = list(
        todo = function() private$.items[["todo"]],
        text1 = function() private$.items[["text1"]],
        text2 = function() private$.items[["text2"]],
        text2a = function() private$.items[["text2a"]],
        text2b = function() private$.items[["text2b"]],
        text3 = function() private$.items[["text3"]],
        text4 = function() private$.items[["text4"]]),
    private = list(),
    public=list(
        initialize=function(options) {
            super$initialize(
                options=options,
                name="",
                title="Decision Tree",
                refs=list(
                    "ClinicoPathJamoviModule"))
            self$add(jmvcore::Html$new(
                options=options,
                name="todo",
                title="To Do",
                clearWith=list(
                    "vars",
                    "facs",
                    "target",
                    "targetLevel",
                    "train",
                    "trainLevel")))
            self$add(jmvcore::Preformatted$new(
                options=options,
                name="text1",
                title="Data View 1",
                clearWith=list(
                    "vars",
                    "facs",
                    "target",
                    "targetLevel",
                    "train",
                    "trainLevel")))
            self$add(jmvcore::Preformatted$new(
                options=options,
                name="text2",
                title="Data View 2",
                clearWith=list(
                    "vars",
                    "facs",
                    "target",
                    "targetLevel",
                    "train",
                    "trainLevel")))
            self$add(jmvcore::Preformatted$new(
                options=options,
                name="text2a",
                title="Data View 2a",
                clearWith=list(
                    "vars",
                    "facs",
                    "target",
                    "targetLevel",
                    "train",
                    "trainLevel")))
            self$add(jmvcore::Preformatted$new(
                options=options,
                name="text2b",
                title="Data View 2b",
                clearWith=list(
                    "vars",
                    "facs",
                    "target",
                    "targetLevel",
                    "train",
                    "trainLevel")))
            self$add(jmvcore::Preformatted$new(
                options=options,
                name="text3",
                title="Decision Tree 3",
                clearWith=list(
                    "vars",
                    "facs",
                    "target",
                    "targetLevel",
                    "train",
                    "trainLevel")))
            self$add(jmvcore::Html$new(
                options=options,
                name="text4",
                title="Decision Tree 4",
                clearWith=list(
                    "vars",
                    "facs",
                    "target",
                    "targetLevel",
                    "train",
                    "trainLevel")))}))

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

#' Decision Tree
#'
#' Function for making Decision Trees.
#'
#' @examples
#' \donttest{
#' # example will be added
#'}
#' @param data The data as a data frame.
#' @param vars continuous explanatory variables
#' @param facs categorical explanatory variables
#' @param target target variable
#' @param targetLevel .
#' @param train Variable containing Test/Train information
#' @param trainLevel .
#' @param showPlot .
#' @return A results object containing:
#' \tabular{llllll}{
#'   \code{results$todo} \tab \tab \tab \tab \tab a html \cr
#'   \code{results$text1} \tab \tab \tab \tab \tab a preformatted \cr
#'   \code{results$text2} \tab \tab \tab \tab \tab a preformatted \cr
#'   \code{results$text2a} \tab \tab \tab \tab \tab a preformatted \cr
#'   \code{results$text2b} \tab \tab \tab \tab \tab a preformatted \cr
#'   \code{results$text3} \tab \tab \tab \tab \tab a preformatted \cr
#'   \code{results$text4} \tab \tab \tab \tab \tab a html \cr
#' }
#'
#' @export
tree <- function(
    data,
    vars,
    facs,
    target,
    targetLevel,
    train,
    trainLevel,
    showPlot = FALSE) {

    if ( ! requireNamespace("jmvcore", quietly=TRUE))
        stop("tree requires jmvcore to be installed (restart may be required)")

    if ( ! missing(vars)) vars <- jmvcore::resolveQuo(jmvcore::enquo(vars))
    if ( ! missing(facs)) facs <- jmvcore::resolveQuo(jmvcore::enquo(facs))
    if ( ! missing(target)) target <- jmvcore::resolveQuo(jmvcore::enquo(target))
    if ( ! missing(train)) train <- jmvcore::resolveQuo(jmvcore::enquo(train))
    if (missing(data))
        data <- jmvcore::marshalData(
            parent.frame(),
            `if`( ! missing(vars), vars, NULL),
            `if`( ! missing(facs), facs, NULL),
            `if`( ! missing(target), target, NULL),
            `if`( ! missing(train), train, NULL))

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

    options <- treeOptions$new(
        vars = vars,
        facs = facs,
        target = target,
        targetLevel = targetLevel,
        train = train,
        trainLevel = trainLevel,
        showPlot = showPlot)

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

    analysis$run()

    analysis$results
}