R/jjwithinstats.h.R

In sbalci/ClinicoPathJamoviModule: Analysis for Clinicopathological Research

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

jjwithinstatsOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
    "jjwithinstatsOptions",
    inherit = jmvcore::Options,
    public = list(
        initialize = function(
            dep1 = NULL,
            dep2 = NULL,
            dep3 = NULL,
            dep4 = NULL,
            pointpath = FALSE,
            centralitypath = FALSE,
            centralityplotting = FALSE,
            centralitytype = "parameteric",
            typestatistics = "parametric",
            pairwisecomparisons = FALSE,
            pairwisedisplay = "significant",
            padjustmethod = "holm",
            effsizetype = "biased",
            violin = TRUE,
            boxplot = TRUE,
            point = TRUE,
            mytitle = "Within Group Comparison",
            xtitle = "",
            ytitle = "",
            originaltheme = FALSE,
            resultssubtitle = TRUE, ...) {

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

            private$..dep1 <- jmvcore::OptionVariable$new(
                "dep1",
                dep1,
                suggested=list(
                    "continuous"),
                permitted=list(
                    "numeric"))
            private$..dep2 <- jmvcore::OptionVariable$new(
                "dep2",
                dep2,
                suggested=list(
                    "continuous"),
                permitted=list(
                    "numeric"))
            private$..dep3 <- jmvcore::OptionVariable$new(
                "dep3",
                dep3,
                suggested=list(
                    "continuous"),
                permitted=list(
                    "numeric"))
            private$..dep4 <- jmvcore::OptionVariable$new(
                "dep4",
                dep4,
                suggested=list(
                    "continuous"),
                permitted=list(
                    "numeric"))
            private$..pointpath <- jmvcore::OptionBool$new(
                "pointpath",
                pointpath,
                default=FALSE)
            private$..centralitypath <- jmvcore::OptionBool$new(
                "centralitypath",
                centralitypath,
                default=FALSE)
            private$..centralityplotting <- jmvcore::OptionBool$new(
                "centralityplotting",
                centralityplotting,
                default=FALSE)
            private$..centralitytype <- jmvcore::OptionList$new(
                "centralitytype",
                centralitytype,
                options=list(
                    "parameteric",
                    "nonparametric",
                    "robust",
                    "bayes"),
                default="parameteric")
            private$..typestatistics <- jmvcore::OptionList$new(
                "typestatistics",
                typestatistics,
                options=list(
                    "parametric",
                    "nonparametric",
                    "robust",
                    "bayes"),
                default="parametric")
            private$..pairwisecomparisons <- jmvcore::OptionBool$new(
                "pairwisecomparisons",
                pairwisecomparisons,
                default=FALSE)
            private$..pairwisedisplay <- jmvcore::OptionList$new(
                "pairwisedisplay",
                pairwisedisplay,
                options=list(
                    "significant",
                    "non-significant",
                    "everything"),
                default="significant")
            private$..padjustmethod <- jmvcore::OptionList$new(
                "padjustmethod",
                padjustmethod,
                options=list(
                    "holm",
                    "hochberg",
                    "hommel",
                    "bonferroni",
                    "BH",
                    "BY",
                    "fdr",
                    "none"),
                default="holm")
            private$..effsizetype <- jmvcore::OptionList$new(
                "effsizetype",
                effsizetype,
                options=list(
                    "biased",
                    "unbiased",
                    "eta",
                    "omega"),
                default="biased")
            private$..violin <- jmvcore::OptionBool$new(
                "violin",
                violin,
                default=TRUE)
            private$..boxplot <- jmvcore::OptionBool$new(
                "boxplot",
                boxplot,
                default=TRUE)
            private$..point <- jmvcore::OptionBool$new(
                "point",
                point,
                default=TRUE)
            private$..mytitle <- jmvcore::OptionString$new(
                "mytitle",
                mytitle,
                default="Within Group Comparison")
            private$..xtitle <- jmvcore::OptionString$new(
                "xtitle",
                xtitle,
                default="")
            private$..ytitle <- jmvcore::OptionString$new(
                "ytitle",
                ytitle,
                default="")
            private$..originaltheme <- jmvcore::OptionBool$new(
                "originaltheme",
                originaltheme,
                default=FALSE)
            private$..resultssubtitle <- jmvcore::OptionBool$new(
                "resultssubtitle",
                resultssubtitle,
                default=TRUE)

            self$.addOption(private$..dep1)
            self$.addOption(private$..dep2)
            self$.addOption(private$..dep3)
            self$.addOption(private$..dep4)
            self$.addOption(private$..pointpath)
            self$.addOption(private$..centralitypath)
            self$.addOption(private$..centralityplotting)
            self$.addOption(private$..centralitytype)
            self$.addOption(private$..typestatistics)
            self$.addOption(private$..pairwisecomparisons)
            self$.addOption(private$..pairwisedisplay)
            self$.addOption(private$..padjustmethod)
            self$.addOption(private$..effsizetype)
            self$.addOption(private$..violin)
            self$.addOption(private$..boxplot)
            self$.addOption(private$..point)
            self$.addOption(private$..mytitle)
            self$.addOption(private$..xtitle)
            self$.addOption(private$..ytitle)
            self$.addOption(private$..originaltheme)
            self$.addOption(private$..resultssubtitle)
        }),
    active = list(
        dep1 = function() private$..dep1$value,
        dep2 = function() private$..dep2$value,
        dep3 = function() private$..dep3$value,
        dep4 = function() private$..dep4$value,
        pointpath = function() private$..pointpath$value,
        centralitypath = function() private$..centralitypath$value,
        centralityplotting = function() private$..centralityplotting$value,
        centralitytype = function() private$..centralitytype$value,
        typestatistics = function() private$..typestatistics$value,
        pairwisecomparisons = function() private$..pairwisecomparisons$value,
        pairwisedisplay = function() private$..pairwisedisplay$value,
        padjustmethod = function() private$..padjustmethod$value,
        effsizetype = function() private$..effsizetype$value,
        violin = function() private$..violin$value,
        boxplot = function() private$..boxplot$value,
        point = function() private$..point$value,
        mytitle = function() private$..mytitle$value,
        xtitle = function() private$..xtitle$value,
        ytitle = function() private$..ytitle$value,
        originaltheme = function() private$..originaltheme$value,
        resultssubtitle = function() private$..resultssubtitle$value),
    private = list(
        ..dep1 = NA,
        ..dep2 = NA,
        ..dep3 = NA,
        ..dep4 = NA,
        ..pointpath = NA,
        ..centralitypath = NA,
        ..centralityplotting = NA,
        ..centralitytype = NA,
        ..typestatistics = NA,
        ..pairwisecomparisons = NA,
        ..pairwisedisplay = NA,
        ..padjustmethod = NA,
        ..effsizetype = NA,
        ..violin = NA,
        ..boxplot = NA,
        ..point = NA,
        ..mytitle = NA,
        ..xtitle = NA,
        ..ytitle = NA,
        ..originaltheme = NA,
        ..resultssubtitle = NA)
)

jjwithinstatsResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
    "jjwithinstatsResults",
    inherit = jmvcore::Group,
    active = list(
        todo = function() private$.items[["todo"]],
        plot = function() private$.items[["plot"]]),
    private = list(),
    public=list(
        initialize=function(options) {
            super$initialize(
                options=options,
                name="",
                title="Violin Plots to Compare Within Groups",
                refs=list(
                    "ggplot2",
                    "ggstatsplot",
                    "ClinicoPathJamoviModule"),
                clearWith=list(
                    "dep1",
                    "dep2",
                    "dep3",
                    "dep4",
                    "typestatistics",
                    "originaltheme",
                    "excl"))
            self$add(jmvcore::Html$new(
                options=options,
                name="todo",
                title="To Do"))
            self$add(jmvcore::Image$new(
                options=options,
                name="plot",
                title="Violin Plots",
                renderFun=".plot",
                requiresData=TRUE))}))

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

#' Box-Violin Plots to Compare Within Groups
#'
#' 
#'
#' @examples
#' \donttest{
#' # example will be added
#'}
#' @param data The data as a data frame.
#' @param dep1 .
#' @param dep2 .
#' @param dep3 .
#' @param dep4 .
#' @param pointpath .
#' @param centralitypath .
#' @param centralityplotting .
#' @param centralitytype .
#' @param typestatistics .
#' @param pairwisecomparisons .
#' @param pairwisedisplay .
#' @param padjustmethod .
#' @param effsizetype .
#' @param violin .
#' @param boxplot .
#' @param point .
#' @param mytitle .
#' @param xtitle .
#' @param ytitle .
#' @param originaltheme .
#' @param resultssubtitle .
#' @return A results object containing:
#' \tabular{llllll}{
#'   \code{results$todo} \tab \tab \tab \tab \tab a html \cr
#'   \code{results$plot} \tab \tab \tab \tab \tab an image \cr
#' }
#'
#' @export
jjwithinstats <- function(
    data,
    dep1,
    dep2,
    dep3,
    dep4,
    pointpath = FALSE,
    centralitypath = FALSE,
    centralityplotting = FALSE,
    centralitytype = "parameteric",
    typestatistics = "parametric",
    pairwisecomparisons = FALSE,
    pairwisedisplay = "significant",
    padjustmethod = "holm",
    effsizetype = "biased",
    violin = TRUE,
    boxplot = TRUE,
    point = TRUE,
    mytitle = "Within Group Comparison",
    xtitle = "",
    ytitle = "",
    originaltheme = FALSE,
    resultssubtitle = TRUE) {

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

    if ( ! missing(dep1)) dep1 <- jmvcore::resolveQuo(jmvcore::enquo(dep1))
    if ( ! missing(dep2)) dep2 <- jmvcore::resolveQuo(jmvcore::enquo(dep2))
    if ( ! missing(dep3)) dep3 <- jmvcore::resolveQuo(jmvcore::enquo(dep3))
    if ( ! missing(dep4)) dep4 <- jmvcore::resolveQuo(jmvcore::enquo(dep4))
    if (missing(data))
        data <- jmvcore::marshalData(
            parent.frame(),
            `if`( ! missing(dep1), dep1, NULL),
            `if`( ! missing(dep2), dep2, NULL),
            `if`( ! missing(dep3), dep3, NULL),
            `if`( ! missing(dep4), dep4, NULL))


    options <- jjwithinstatsOptions$new(
        dep1 = dep1,
        dep2 = dep2,
        dep3 = dep3,
        dep4 = dep4,
        pointpath = pointpath,
        centralitypath = centralitypath,
        centralityplotting = centralityplotting,
        centralitytype = centralitytype,
        typestatistics = typestatistics,
        pairwisecomparisons = pairwisecomparisons,
        pairwisedisplay = pairwisedisplay,
        padjustmethod = padjustmethod,
        effsizetype = effsizetype,
        violin = violin,
        boxplot = boxplot,
        point = point,
        mytitle = mytitle,
        xtitle = xtitle,
        ytitle = ytitle,
        originaltheme = originaltheme,
        resultssubtitle = resultssubtitle)

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

    analysis$run()

    analysis$results
}