R/summarydata.h.R

In sbalci/ClinicoPathDescriptives: Descriptive Analysis Tools for Clinicopathological Research

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

summarydataOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
    "summarydataOptions",
    inherit = jmvcore::Options,
    public = list(
        initialize = function(
            vars = NULL,
            date_vars = NULL,
            distr = FALSE,
            summary_format = "standard",
            grvar = NULL,
            pivot_layout = "clinical",
            include_confidence = TRUE,
            advanced_metrics = FALSE,
            pivot_export = FALSE,
            summarytools_graphs = TRUE,
            summarytools_round_digits = 2, ...) {

            super$initialize(
                package="ClinicoPathDescriptives",
                name="summarydata",
                requiresData=TRUE,
                ...)

            private$..vars <- jmvcore::OptionVariables$new(
                "vars",
                vars,
                suggested=list(
                    "continuous"),
                permitted=list(
                    "numeric"))
            private$..date_vars <- jmvcore::OptionVariables$new(
                "date_vars",
                date_vars,
                suggested=list(
                    "continuous"),
                permitted=list(
                    "numeric"),
                default=NULL)
            private$..distr <- jmvcore::OptionBool$new(
                "distr",
                distr,
                default=FALSE)
            private$..summary_format <- jmvcore::OptionList$new(
                "summary_format",
                summary_format,
                options=list(
                    "standard",
                    "sumvar",
                    "pivot",
                    "summarytools_df",
                    "summarytools_desc",
                    "summarytools_freq"),
                default="standard")
            private$..grvar <- jmvcore::OptionVariable$new(
                "grvar",
                grvar,
                suggested=list(
                    "ordinal",
                    "nominal"),
                permitted=list(
                    "factor"),
                default=NULL)
            private$..pivot_layout <- jmvcore::OptionList$new(
                "pivot_layout",
                pivot_layout,
                options=list(
                    "clinical",
                    "statistical",
                    "comparative"),
                default="clinical")
            private$..include_confidence <- jmvcore::OptionBool$new(
                "include_confidence",
                include_confidence,
                default=TRUE)
            private$..advanced_metrics <- jmvcore::OptionBool$new(
                "advanced_metrics",
                advanced_metrics,
                default=FALSE)
            private$..pivot_export <- jmvcore::OptionBool$new(
                "pivot_export",
                pivot_export,
                default=FALSE)
            private$..summarytools_graphs <- jmvcore::OptionBool$new(
                "summarytools_graphs",
                summarytools_graphs,
                default=TRUE)
            private$..summarytools_round_digits <- jmvcore::OptionInteger$new(
                "summarytools_round_digits",
                summarytools_round_digits,
                min=1,
                max=6,
                default=2)

            self$.addOption(private$..vars)
            self$.addOption(private$..date_vars)
            self$.addOption(private$..distr)
            self$.addOption(private$..summary_format)
            self$.addOption(private$..grvar)
            self$.addOption(private$..pivot_layout)
            self$.addOption(private$..include_confidence)
            self$.addOption(private$..advanced_metrics)
            self$.addOption(private$..pivot_export)
            self$.addOption(private$..summarytools_graphs)
            self$.addOption(private$..summarytools_round_digits)
        }),
    active = list(
        vars = function() private$..vars$value,
        date_vars = function() private$..date_vars$value,
        distr = function() private$..distr$value,
        summary_format = function() private$..summary_format$value,
        grvar = function() private$..grvar$value,
        pivot_layout = function() private$..pivot_layout$value,
        include_confidence = function() private$..include_confidence$value,
        advanced_metrics = function() private$..advanced_metrics$value,
        pivot_export = function() private$..pivot_export$value,
        summarytools_graphs = function() private$..summarytools_graphs$value,
        summarytools_round_digits = function() private$..summarytools_round_digits$value),
    private = list(
        ..vars = NA,
        ..date_vars = NA,
        ..distr = NA,
        ..summary_format = NA,
        ..grvar = NA,
        ..pivot_layout = NA,
        ..include_confidence = NA,
        ..advanced_metrics = NA,
        ..pivot_export = NA,
        ..summarytools_graphs = NA,
        ..summarytools_round_digits = NA)
)

summarydataResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
    "summarydataResults",
    inherit = jmvcore::Group,
    active = list(
        todo = function() private$.items[["todo"]],
        text = function() private$.items[["text"]],
        text1 = function() private$.items[["text1"]],
        pivot_summary = function() private$.items[["pivot_summary"]],
        pivot_export_info = function() private$.items[["pivot_export_info"]]),
    private = list(),
    public=list(
        initialize=function(options) {
            super$initialize(
                options=options,
                name="",
                title="Summary of Continuous Variables",
                refs=list(
                    "gtExtras",
                    "ClinicoPathJamoviModule"))
            self$add(jmvcore::Html$new(
                options=options,
                name="todo",
                title="To Do"))
            self$add(jmvcore::Html$new(
                options=options,
                name="text",
                title=""))
            self$add(jmvcore::Html$new(
                options=options,
                name="text1",
                title="Continuous Data Plots"))
            self$add(jmvcore::Html$new(
                options=options,
                name="pivot_summary",
                title="Enhanced Pivot Summary",
                visible="(summary_format:pivot)",
                clearWith=list(
                    "vars",
                    "summary_format",
                    "pivot_layout",
                    "include_confidence",
                    "advanced_metrics",
                    "grvar")))
            self$add(jmvcore::Html$new(
                options=options,
                name="pivot_export_info",
                title="Export Information",
                visible="(pivot_export && summary_format:pivot)"))}))

summarydataBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
    "summarydataBase",
    inherit = jmvcore::Analysis,
    public = list(
        initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
            super$initialize(
                package = "ClinicoPathDescriptives",
                name = "summarydata",
                version = c(0,0,3),
                options = options,
                results = summarydataResults$new(options=options),
                data = data,
                datasetId = datasetId,
                analysisId = analysisId,
                revision = revision,
                pause = NULL,
                completeWhenFilled = FALSE,
                requiresMissings = FALSE,
                weightsSupport = 'auto')
        }))

#' Summary of Continuous Variables
#'
#' This module generates descriptive statistics for continuous variables.
#' It provides both a textual summary and a visually appealing summary table.
#' Optionally, you can enable distribution diagnostics to examine normality, 
#' skewness, and kurtosis.
#' 
#'
#' @examples
#' \donttest{
#' # Example:
#' # 1. Load your data frame.
#' # 2. Select one or more continuous variables.
#' # 3. (Optional) Enable Distribution Diagnostics to view additional tests.
#' # 4. Run the summarydata module to see descriptive statistics and distribution characteristics.
#'}
#' @param data The data as a data frame.
#' @param vars a string naming the variables from \code{data} that contains
#'   the continuous values used for the report
#' @param date_vars Variables containing date/time data to be analyzed with
#'   date-specific statistics (similar to sumvar's dist_date function)
#' @param distr If TRUE, additional distribution diagnostics (Shapiro-Wilk
#'   test, skewness, and kurtosis) will be computed and explained.
#' @param summary_format Choose the format for summary statistics display. New
#'   summarytools options provide publication-ready automated EDA summaries with
#'   embedded visualizations.
#' @param grvar Optional grouping variable to stratify the summary statistics
#'   by categories.
#' @param pivot_layout Layout style for pivottabler enhanced summaries.
#' @param include_confidence Include confidence intervals in pivot summary
#'   tables.
#' @param advanced_metrics Include advanced metrics like IQR, MAD, and robust
#'   statistics.
#' @param pivot_export Enable enhanced export capabilities for pivot tables.
#' @param summarytools_graphs Include histograms and bar charts in
#'   summarytools dfSummary output.
#' @param summarytools_round_digits Number of decimal places for summarytools
#'   output.
#' @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$text1} \tab \tab \tab \tab \tab a html \cr
#'   \code{results$pivot_summary} \tab \tab \tab \tab \tab a html \cr
#'   \code{results$pivot_export_info} \tab \tab \tab \tab \tab a html \cr
#' }
#'
#' @export
summarydata <- function(
    data,
    vars,
    date_vars = NULL,
    distr = FALSE,
    summary_format = "standard",
    grvar = NULL,
    pivot_layout = "clinical",
    include_confidence = TRUE,
    advanced_metrics = FALSE,
    pivot_export = FALSE,
    summarytools_graphs = TRUE,
    summarytools_round_digits = 2) {

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

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

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

    options <- summarydataOptions$new(
        vars = vars,
        date_vars = date_vars,
        distr = distr,
        summary_format = summary_format,
        grvar = grvar,
        pivot_layout = pivot_layout,
        include_confidence = include_confidence,
        advanced_metrics = advanced_metrics,
        pivot_export = pivot_export,
        summarytools_graphs = summarytools_graphs,
        summarytools_round_digits = summarytools_round_digits)

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

    analysis$run()

    analysis$results
}