cogModels:

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

sdtOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
    "sdtOptions",
    inherit = jmvcore::Options,
    public = list(
        initialize = function(
            stim = NULL,
            sig = NULL,
            res = NULL,
            subj = NULL,
            group = NULL,
            ci = FALSE,
            ciWidth = 95,
            summary = FALSE,
            nSamples = 1000,
            nChains = 1,
            nBurnin = 0,
            nThin = 1, ...) {

            super$initialize(
                package='resWagner',
                name='sdt',
                requiresData=TRUE,
                ...)

            private$..stim <- jmvcore::OptionVariable$new(
                "stim",
                stim,
                suggested=list(
                    "nominal"),
                permitted=list(
                    "factor"))
            private$..sig <- jmvcore::OptionLevel$new(
                "sig",
                sig,
                variable="(stim)")
            private$..res <- jmvcore::OptionVariable$new(
                "res",
                res,
                suggested=list(
                    "nominal"),
                permitted=list(
                    "factor"))
            private$..subj <- jmvcore::OptionVariable$new(
                "subj",
                subj,
                default=NULL,
                suggested=list(
                    "nominal"),
                permitted=list(
                    "factor"))
            private$..group <- jmvcore::OptionVariable$new(
                "group",
                group,
                default=NULL,
                suggested=list(
                    "nominal"),
                permitted=list(
                    "factor"))
            private$..ci <- jmvcore::OptionBool$new(
                "ci",
                ci,
                default=FALSE)
            private$..ciWidth <- jmvcore::OptionNumber$new(
                "ciWidth",
                ciWidth,
                min=50,
                max=99.9,
                default=95)
            private$..summary <- jmvcore::OptionBool$new(
                "summary",
                summary,
                default=FALSE)
            private$..nSamples <- jmvcore::OptionNumber$new(
                "nSamples",
                nSamples,
                min=1,
                max=1000000,
                default=1000)
            private$..nChains <- jmvcore::OptionNumber$new(
                "nChains",
                nChains,
                min=1,
                max=10,
                default=1)
            private$..nBurnin <- jmvcore::OptionNumber$new(
                "nBurnin",
                nBurnin,
                min=0,
                max=1000000,
                default=0)
            private$..nThin <- jmvcore::OptionNumber$new(
                "nThin",
                nThin,
                min=1,
                max=100,
                default=1)

            self$.addOption(private$..stim)
            self$.addOption(private$..sig)
            self$.addOption(private$..res)
            self$.addOption(private$..subj)
            self$.addOption(private$..group)
            self$.addOption(private$..ci)
            self$.addOption(private$..ciWidth)
            self$.addOption(private$..summary)
            self$.addOption(private$..nSamples)
            self$.addOption(private$..nChains)
            self$.addOption(private$..nBurnin)
            self$.addOption(private$..nThin)
        }),
    active = list(
        stim = function() private$..stim$value,
        sig = function() private$..sig$value,
        res = function() private$..res$value,
        subj = function() private$..subj$value,
        group = function() private$..group$value,
        ci = function() private$..ci$value,
        ciWidth = function() private$..ciWidth$value,
        summary = function() private$..summary$value,
        nSamples = function() private$..nSamples$value,
        nChains = function() private$..nChains$value,
        nBurnin = function() private$..nBurnin$value,
        nThin = function() private$..nThin$value),
    private = list(
        ..stim = NA,
        ..sig = NA,
        ..res = NA,
        ..subj = NA,
        ..group = NA,
        ..ci = NA,
        ..ciWidth = NA,
        ..summary = NA,
        ..nSamples = NA,
        ..nChains = NA,
        ..nBurnin = NA,
        ..nThin = NA)
)

sdtResults <- if (requireNamespace('jmvcore')) R6::R6Class(
    inherit = jmvcore::Group,
    active = list(
        sdtGroup = function() private$.items[["sdtGroup"]],
        sdtSubj = function() private$.items[["sdtSubj"]],
        dPrimePlot = function() private$.items[["dPrimePlot"]],
        cPlot = function() private$.items[["cPlot"]]),
    private = list(),
    public=list(
        initialize=function(options) {
            super$initialize(
                options=options,
                name="",
                title="Signal Detection Theory")
            self$add(jmvcore::Table$new(
                options=options,
                name="sdtGroup",
                title="SDT Group Parameters",
                rows="(levels(group))",
                clearWith=list(
                    "stim",
                    "sig",
                    "res",
                    "subj",
                    "group",
                    "nSamples",
                    "nChains",
                    "nBurnin",
                    "nThin"),
                columns=list(
                    list(
                        `name`="group", 
                        `title`="Group", 
                        `type`="text", 
                        `content`="($key)"),
                    list(
                        `name`="dPrime", 
                        `title`="d'", 
                        `type`="number"),
                    list(
                        `name`="dPrimeLower", 
                        `title`="Lower", 
                        `type`="number", 
                        `visible`="(ci)"),
                    list(
                        `name`="dPrimeUpper", 
                        `title`="Upper", 
                        `type`="number", 
                        `visible`="(ci)"),
                    list(
                        `name`="c", 
                        `title`="Criterion", 
                        `type`="number"),
                    list(
                        `name`="cLower", 
                        `title`="Lower", 
                        `type`="number", 
                        `visible`="(ci)"),
                    list(
                        `name`="cUpper", 
                        `title`="Upper", 
                        `type`="number", 
                        `visible`="(ci)"))))
            self$add(jmvcore::Table$new(
                options=options,
                name="sdtSubj",
                title="SDT Subject Parameters",
                clearWith=list(
                    "stim",
                    "sig",
                    "res",
                    "subj",
                    "group",
                    "nSamples",
                    "nChains",
                    "nBurnin",
                    "nThin"),
                rows="(levels(subj))",
                columns=list(
                    list(
                        `name`="group", 
                        `title`="Group", 
                        `type`="text", 
                        `visible`="(group)", 
                        `combineBelow`=TRUE),
                    list(
                        `name`="subj", 
                        `title`="Subject", 
                        `type`="text", 
                        `visible`="(subj)", 
                        `content`="($key)"),
                    list(
                        `name`="dPrime", 
                        `title`="d'", 
                        `type`="number"),
                    list(
                        `name`="dPrimeLower", 
                        `title`="Lower", 
                        `type`="number", 
                        `visible`="(ci)"),
                    list(
                        `name`="dPrimeUpper", 
                        `title`="Upper", 
                        `type`="number", 
                        `visible`="(ci)"),
                    list(
                        `name`="c", 
                        `title`="Criterion", 
                        `type`="number"),
                    list(
                        `name`="cLower", 
                        `title`="Lower", 
                        `type`="number", 
                        `visible`="(ci)"),
                    list(
                        `name`="cUpper", 
                        `title`="Upper", 
                        `type`="number", 
                        `visible`="(ci)"),
                    list(
                        `name`="h", 
                        `title`="Hit", 
                        `type`="integer", 
                        `visible`="(summary)"),
                    list(
                        `name`="m", 
                        `title`="Miss", 
                        `type`="integer", 
                        `visible`="(summary)"),
                    list(
                        `name`="cr", 
                        `title`="Correct Rejection", 
                        `type`="integer", 
                        `visible`="(summary)"),
                    list(
                        `name`="fa", 
                        `title`="False Alarm", 
                        `type`="integer", 
                        `visible`="(summary)"))))
            self$add(jmvcore::Image$new(
                options=options,
                name="dPrimePlot",
                title="dPrime",
                renderFun=".dPrimePlot",
                clearWith=list(
                    "stim",
                    "sig",
                    "res",
                    "subj",
                    "group",
                    "nSamples",
                    "nChains",
                    "nBurnin",
                    "nThin")))
            self$add(jmvcore::Image$new(
                options=options,
                name="cPlot",
                title="Criterion",
                renderFun=".cPlot",
                clearWith=list(
                    "stim",
                    "sig",
                    "res",
                    "subj",
                    "group",
                    "nSamples",
                    "nChains",
                    "nBurnin",
                    "nThin")))}))

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

#' Signal Detection Theory
#'
#' 
#' @param data .
#' @param stim .
#' @param sig .
#' @param res .
#' @param subj .
#' @param group .
#' @param ci \code{TRUE} or \code{FALSE} (default), provide a credible
#'   interval for the model parameters
#' @param ciWidth a number between 50 and 99.9 (default: 95) specifying the
#'   credible interval width that is used as \code{'ci'}
#' @param summary .
#' @param nSamples a number between 1 and 1000000 (default: 1000) specifying
#'   the number of samples that need to be drawn from the posterior distribution
#' @param nChains a number between 1 and 10 (default: 3) specifying the number
#'   of MCMC chains that need to be drawn from the posterior distribution
#' @param nBurnin a number between 1 and 1000000 (default: 1000) specifying
#'   the number of burn-in samples that need to be drawn
#' @param nThin a number between 1 and 100 (default: 1) save the nth number of
#'   each chain
#' @return A results object containing:
#' \tabular{llllll}{
#'   \code{results$sdtGroup} \tab \tab \tab \tab \tab a table \cr
#'   \code{results$sdtSubj} \tab \tab \tab \tab \tab a table \cr
#'   \code{results$dPrimePlot} \tab \tab \tab \tab \tab plot of the d' parameter \cr
#'   \code{results$cPlot} \tab \tab \tab \tab \tab plot of the criterion parameter \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$sdtGroup$asDF}
#'
#' \code{as.data.frame(results$sdtGroup)}
#'
#' @export
sdt <- function(
    data,
    stim,
    sig,
    res,
    subj = NULL,
    group = NULL,
    ci = FALSE,
    ciWidth = 95,
    summary = FALSE,
    nSamples = 1000,
    nChains = 1,
    nBurnin = 0,
    nThin = 1) {

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

    options <- sdtOptions$new(
        stim = stim,
        sig = sig,
        res = res,
        subj = subj,
        group = group,
        ci = ci,
        ciWidth = ciWidth,
        summary = summary,
        nSamples = nSamples,
        nChains = nChains,
        nBurnin = nBurnin,
        nThin = nThin)

    results <- sdtResults$new(
        options = options)

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

    analysis$run()

    analysis$results
}