ClinicoPathJamoviModule: Analysis for Clinicopathological Research

Documented in vartree3

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

vartree3Options <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
    "vartree3Options",
    inherit = jmvcore::Options,
    public = list(
        initialize = function(
            vars = NULL,
            percvar = NULL,
            percvarLevel = NULL,
            summaryvar = NULL,
            prunebelow = NULL,
            pruneLevel1 = NULL,
            pruneLevel2 = NULL,
            follow = NULL,
            followLevel1 = NULL,
            followLevel2 = NULL,
            excl = FALSE,
            vp = TRUE,
            horizontal = FALSE,
            sline = TRUE,
            varnames = FALSE,
            nodelabel = TRUE,
            pct = FALSE,
            showcount = TRUE,
            legend = FALSE,
            pattern = FALSE,
            sequence = FALSE,
            ptable = FALSE,
            mytitle = "",
            useprunesmaller = FALSE,
            prunesmaller = 5,
            summarylocation = "leafonly",
            style = "default",
            showInterpretation = TRUE,
            survival = FALSE,
            labs = FALSE,
            response = FALSE, ...) {

            super$initialize(
                package="ClinicoPath",
                name="vartree3",
                requiresData=TRUE,
                ...)

            private$..vars <- jmvcore::OptionVariables$new(
                "vars",
                vars,
                suggested=list(
                    "ordinal",
                    "nominal"),
                permitted=list(
                    "factor"))
            private$..percvar <- jmvcore::OptionVariable$new(
                "percvar",
                percvar,
                suggested=list(
                    "ordinal",
                    "nominal"),
                permitted=list(
                    "factor"))
            private$..percvarLevel <- jmvcore::OptionLevel$new(
                "percvarLevel",
                percvarLevel,
                variable="(percvar)")
            private$..summaryvar <- jmvcore::OptionVariable$new(
                "summaryvar",
                summaryvar,
                suggested=list(
                    "continuous"),
                permitted=list(
                    "numeric"))
            private$..prunebelow <- jmvcore::OptionVariable$new(
                "prunebelow",
                prunebelow,
                suggested=list(
                    "ordinal",
                    "nominal"),
                permitted=list(
                    "factor"))
            private$..pruneLevel1 <- jmvcore::OptionLevel$new(
                "pruneLevel1",
                pruneLevel1,
                variable="(prunebelow)",
                allowNone=TRUE)
            private$..pruneLevel2 <- jmvcore::OptionLevel$new(
                "pruneLevel2",
                pruneLevel2,
                variable="(prunebelow)",
                allowNone=TRUE)
            private$..follow <- jmvcore::OptionVariable$new(
                "follow",
                follow,
                suggested=list(
                    "ordinal",
                    "nominal"),
                permitted=list(
                    "factor"))
            private$..followLevel1 <- jmvcore::OptionLevel$new(
                "followLevel1",
                followLevel1,
                variable="(follow)",
                allowNone=TRUE)
            private$..followLevel2 <- jmvcore::OptionLevel$new(
                "followLevel2",
                followLevel2,
                variable="(follow)",
                allowNone=TRUE)
            private$..excl <- jmvcore::OptionBool$new(
                "excl",
                excl,
                default=FALSE)
            private$..vp <- jmvcore::OptionBool$new(
                "vp",
                vp,
                default=TRUE)
            private$..horizontal <- jmvcore::OptionBool$new(
                "horizontal",
                horizontal,
                default=FALSE)
            private$..sline <- jmvcore::OptionBool$new(
                "sline",
                sline,
                default=TRUE)
            private$..varnames <- jmvcore::OptionBool$new(
                "varnames",
                varnames,
                default=FALSE)
            private$..nodelabel <- jmvcore::OptionBool$new(
                "nodelabel",
                nodelabel,
                default=TRUE)
            private$..pct <- jmvcore::OptionBool$new(
                "pct",
                pct,
                default=FALSE)
            private$..showcount <- jmvcore::OptionBool$new(
                "showcount",
                showcount,
                default=TRUE)
            private$..legend <- jmvcore::OptionBool$new(
                "legend",
                legend,
                default=FALSE)
            private$..pattern <- jmvcore::OptionBool$new(
                "pattern",
                pattern,
                default=FALSE)
            private$..sequence <- jmvcore::OptionBool$new(
                "sequence",
                sequence,
                default=FALSE)
            private$..ptable <- jmvcore::OptionBool$new(
                "ptable",
                ptable,
                default=FALSE)
            private$..mytitle <- jmvcore::OptionString$new(
                "mytitle",
                mytitle,
                default="")
            private$..useprunesmaller <- jmvcore::OptionBool$new(
                "useprunesmaller",
                useprunesmaller,
                default=FALSE)
            private$..prunesmaller <- jmvcore::OptionInteger$new(
                "prunesmaller",
                prunesmaller,
                default=5)
            private$..summarylocation <- jmvcore::OptionList$new(
                "summarylocation",
                summarylocation,
                options=list(
                    "allnodes",
                    "leafonly"),
                default="leafonly")
            private$..style <- jmvcore::OptionList$new(
                "style",
                style,
                options=list(
                    "default",
                    "clean",
                    "minimal"),
                default="default")
            private$..showInterpretation <- jmvcore::OptionBool$new(
                "showInterpretation",
                showInterpretation,
                default=TRUE)
            private$..survival <- jmvcore::OptionBool$new(
                "survival",
                survival,
                default=FALSE)
            private$..labs <- jmvcore::OptionBool$new(
                "labs",
                labs,
                default=FALSE)
            private$..response <- jmvcore::OptionBool$new(
                "response",
                response,
                default=FALSE)

            self$.addOption(private$..vars)
            self$.addOption(private$..percvar)
            self$.addOption(private$..percvarLevel)
            self$.addOption(private$..summaryvar)
            self$.addOption(private$..prunebelow)
            self$.addOption(private$..pruneLevel1)
            self$.addOption(private$..pruneLevel2)
            self$.addOption(private$..follow)
            self$.addOption(private$..followLevel1)
            self$.addOption(private$..followLevel2)
            self$.addOption(private$..excl)
            self$.addOption(private$..vp)
            self$.addOption(private$..horizontal)
            self$.addOption(private$..sline)
            self$.addOption(private$..varnames)
            self$.addOption(private$..nodelabel)
            self$.addOption(private$..pct)
            self$.addOption(private$..showcount)
            self$.addOption(private$..legend)
            self$.addOption(private$..pattern)
            self$.addOption(private$..sequence)
            self$.addOption(private$..ptable)
            self$.addOption(private$..mytitle)
            self$.addOption(private$..useprunesmaller)
            self$.addOption(private$..prunesmaller)
            self$.addOption(private$..summarylocation)
            self$.addOption(private$..style)
            self$.addOption(private$..showInterpretation)
            self$.addOption(private$..survival)
            self$.addOption(private$..labs)
            self$.addOption(private$..response)
        }),
    active = list(
        vars = function() private$..vars$value,
        percvar = function() private$..percvar$value,
        percvarLevel = function() private$..percvarLevel$value,
        summaryvar = function() private$..summaryvar$value,
        prunebelow = function() private$..prunebelow$value,
        pruneLevel1 = function() private$..pruneLevel1$value,
        pruneLevel2 = function() private$..pruneLevel2$value,
        follow = function() private$..follow$value,
        followLevel1 = function() private$..followLevel1$value,
        followLevel2 = function() private$..followLevel2$value,
        excl = function() private$..excl$value,
        vp = function() private$..vp$value,
        horizontal = function() private$..horizontal$value,
        sline = function() private$..sline$value,
        varnames = function() private$..varnames$value,
        nodelabel = function() private$..nodelabel$value,
        pct = function() private$..pct$value,
        showcount = function() private$..showcount$value,
        legend = function() private$..legend$value,
        pattern = function() private$..pattern$value,
        sequence = function() private$..sequence$value,
        ptable = function() private$..ptable$value,
        mytitle = function() private$..mytitle$value,
        useprunesmaller = function() private$..useprunesmaller$value,
        prunesmaller = function() private$..prunesmaller$value,
        summarylocation = function() private$..summarylocation$value,
        style = function() private$..style$value,
        showInterpretation = function() private$..showInterpretation$value,
        survival = function() private$..survival$value,
        labs = function() private$..labs$value,
        response = function() private$..response$value),
    private = list(
        ..vars = NA,
        ..percvar = NA,
        ..percvarLevel = NA,
        ..summaryvar = NA,
        ..prunebelow = NA,
        ..pruneLevel1 = NA,
        ..pruneLevel2 = NA,
        ..follow = NA,
        ..followLevel1 = NA,
        ..followLevel2 = NA,
        ..excl = NA,
        ..vp = NA,
        ..horizontal = NA,
        ..sline = NA,
        ..varnames = NA,
        ..nodelabel = NA,
        ..pct = NA,
        ..showcount = NA,
        ..legend = NA,
        ..pattern = NA,
        ..sequence = NA,
        ..ptable = NA,
        ..mytitle = NA,
        ..useprunesmaller = NA,
        ..prunesmaller = NA,
        ..summarylocation = NA,
        ..style = NA,
        ..showInterpretation = NA,
        ..survival = NA,
        ..labs = NA,
        ..response = NA)
)

vartree3Results <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
    "vartree3Results",
    inherit = jmvcore::Group,
    active = list(
        todo = function() private$.items[["todo"]],
        text1 = function() private$.items[["text1"]],
        text2 = function() private$.items[["text2"]]),
    private = list(),
    public=list(
        initialize=function(options) {
            super$initialize(
                options=options,
                name="",
                title="Variable Tree V3",
                refs=list(
                    "vtree",
                    "ClinicoPathJamoviModule"))
            self$add(jmvcore::Html$new(
                options=options,
                name="todo",
                title="To Do"))
            self$add(jmvcore::Html$new(
                options=options,
                name="text1",
                title="Variable Tree V3"))
            self$add(jmvcore::Preformatted$new(
                options=options,
                name="text2",
                title="Pattern Table",
                visible="(ptable)"))}))

vartree3Base <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
    "vartree3Base",
    inherit = jmvcore::Analysis,
    public = list(
        initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
            super$initialize(
                package = "ClinicoPath",
                name = "vartree3",
                version = c(1,0,0),
                options = options,
                results = vartree3Results$new(options=options),
                data = data,
                datasetId = datasetId,
                analysisId = analysisId,
                revision = revision,
                pause = NULL,
                completeWhenFilled = FALSE,
                requiresMissings = FALSE,
                weightsSupport = 'auto')
        }))

#' Variable Tree V3
#'
#' Function for Generating Enhanced Tree Summaries of Variables
#'
#' @examples
#' \donttest{
#' # Example will be added
#'}
#' @param data The data as a data frame.
#' @param vars .
#' @param percvar .
#' @param percvarLevel .
#' @param summaryvar .
#' @param prunebelow .
#' @param pruneLevel1 .
#' @param pruneLevel2 .
#' @param follow .
#' @param followLevel1 .
#' @param followLevel2 .
#' @param excl .
#' @param vp .
#' @param horizontal .
#' @param sline .
#' @param varnames .
#' @param nodelabel .
#' @param pct .
#' @param showcount .
#' @param legend .
#' @param pattern .
#' @param sequence .
#' @param ptable .
#' @param mytitle .
#' @param useprunesmaller .
#' @param prunesmaller .
#' @param summarylocation .
#' @param style .
#' @param showInterpretation .
#' @param survival .
#' @param labs .
#' @param response .
#' @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 html \cr
#'   \code{results$text2} \tab \tab \tab \tab \tab a preformatted \cr
#' }
#'
#' @export
vartree3 <- function(
    data,
    vars,
    percvar,
    percvarLevel,
    summaryvar,
    prunebelow,
    pruneLevel1,
    pruneLevel2,
    follow,
    followLevel1,
    followLevel2,
    excl = FALSE,
    vp = TRUE,
    horizontal = FALSE,
    sline = TRUE,
    varnames = FALSE,
    nodelabel = TRUE,
    pct = FALSE,
    showcount = TRUE,
    legend = FALSE,
    pattern = FALSE,
    sequence = FALSE,
    ptable = FALSE,
    mytitle = "",
    useprunesmaller = FALSE,
    prunesmaller = 5,
    summarylocation = "leafonly",
    style = "default",
    showInterpretation = TRUE,
    survival = FALSE,
    labs = FALSE,
    response = FALSE) {

    if ( ! requireNamespace("jmvcore", quietly=TRUE))
        stop("vartree3 requires jmvcore to be installed (restart may be required)")

    if ( ! missing(vars)) vars <- jmvcore::resolveQuo(jmvcore::enquo(vars))
    if ( ! missing(percvar)) percvar <- jmvcore::resolveQuo(jmvcore::enquo(percvar))
    if ( ! missing(summaryvar)) summaryvar <- jmvcore::resolveQuo(jmvcore::enquo(summaryvar))
    if ( ! missing(prunebelow)) prunebelow <- jmvcore::resolveQuo(jmvcore::enquo(prunebelow))
    if ( ! missing(follow)) follow <- jmvcore::resolveQuo(jmvcore::enquo(follow))
    if (missing(data))
        data <- jmvcore::marshalData(
            parent.frame(),
            `if`( ! missing(vars), vars, NULL),
            `if`( ! missing(percvar), percvar, NULL),
            `if`( ! missing(summaryvar), summaryvar, NULL),
            `if`( ! missing(prunebelow), prunebelow, NULL),
            `if`( ! missing(follow), follow, NULL))

    for (v in vars) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
    for (v in percvar) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
    for (v in prunebelow) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
    for (v in follow) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])

    options <- vartree3Options$new(
        vars = vars,
        percvar = percvar,
        percvarLevel = percvarLevel,
        summaryvar = summaryvar,
        prunebelow = prunebelow,
        pruneLevel1 = pruneLevel1,
        pruneLevel2 = pruneLevel2,
        follow = follow,
        followLevel1 = followLevel1,
        followLevel2 = followLevel2,
        excl = excl,
        vp = vp,
        horizontal = horizontal,
        sline = sline,
        varnames = varnames,
        nodelabel = nodelabel,
        pct = pct,
        showcount = showcount,
        legend = legend,
        pattern = pattern,
        sequence = sequence,
        ptable = ptable,
        mytitle = mytitle,
        useprunesmaller = useprunesmaller,
        prunesmaller = prunesmaller,
        summarylocation = summarylocation,
        style = style,
        showInterpretation = showInterpretation,
        survival = survival,
        labs = labs,
        response = response)

    analysis <- vartree3Class$new(
        options = options,
        data = data)

    analysis$run()

    analysis$results
}