R/datatosttwo.h.R
In Lakens/TOSTER: Two One-Sided Tests (TOST) Equivalence Testing
Defines functions
dataTOSTtwo
Documented in
dataTOSTtwo
# This file is automatically generated, you probably don't want to edit this
dataTOSTtwoOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"dataTOSTtwoOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
deps = NULL,
group = NULL,
var_equal = FALSE,
hypothesis = "EQU",
low_eqbound = -0.5,
high_eqbound = 0.5,
eqbound_type = "raw",
alpha = 0.05,
desc = FALSE,
plots = FALSE,
descplots = FALSE,
low_eqbound_d = -999999999,
high_eqbound_d = -999999999,
smd_type = "g", ...) {
super$initialize(
package="TOSTER",
name="dataTOSTtwo",
requiresData=TRUE,
...)
private$..deps <- jmvcore::OptionVariable$new(
"deps",
deps,
permitted=list(
"numeric"),
suggested=list(
"continuous"))
private$..group <- jmvcore::OptionVariable$new(
"group",
group,
suggested=list(
"nominal",
"ordinal"))
private$..var_equal <- jmvcore::OptionBool$new(
"var_equal",
var_equal,
default=FALSE)
private$..hypothesis <- jmvcore::OptionList$new(
"hypothesis",
hypothesis,
options=list(
"EQU",
"MET"),
default="EQU")
private$..low_eqbound <- jmvcore::OptionNumber$new(
"low_eqbound",
low_eqbound,
default=-0.5)
private$..high_eqbound <- jmvcore::OptionNumber$new(
"high_eqbound",
high_eqbound,
default=0.5)
private$..eqbound_type <- jmvcore::OptionList$new(
"eqbound_type",
eqbound_type,
options=list(
"SMD",
"raw"),
default="raw")
private$..alpha <- jmvcore::OptionNumber$new(
"alpha",
alpha,
default=0.05)
private$..desc <- jmvcore::OptionBool$new(
"desc",
desc,
default=FALSE)
private$..plots <- jmvcore::OptionBool$new(
"plots",
plots,
default=FALSE)
private$..descplots <- jmvcore::OptionBool$new(
"descplots",
descplots,
default=FALSE)
private$..low_eqbound_d <- jmvcore::OptionNumber$new(
"low_eqbound_d",
low_eqbound_d,
default=-999999999,
hidden=TRUE)
private$..high_eqbound_d <- jmvcore::OptionNumber$new(
"high_eqbound_d",
high_eqbound_d,
default=-999999999,
hidden=TRUE)
private$..smd_type <- jmvcore::OptionList$new(
"smd_type",
smd_type,
options=list(
"d",
"g"),
default="g")
self$.addOption(private$..deps)
self$.addOption(private$..group)
self$.addOption(private$..var_equal)
self$.addOption(private$..hypothesis)
self$.addOption(private$..low_eqbound)
self$.addOption(private$..high_eqbound)
self$.addOption(private$..eqbound_type)
self$.addOption(private$..alpha)
self$.addOption(private$..desc)
self$.addOption(private$..plots)
self$.addOption(private$..descplots)
self$.addOption(private$..low_eqbound_d)
self$.addOption(private$..high_eqbound_d)
self$.addOption(private$..smd_type)
}),
active = list(
deps = function() private$..deps$value,
group = function() private$..group$value,
var_equal = function() private$..var_equal$value,
hypothesis = function() private$..hypothesis$value,
low_eqbound = function() private$..low_eqbound$value,
high_eqbound = function() private$..high_eqbound$value,
eqbound_type = function() private$..eqbound_type$value,
alpha = function() private$..alpha$value,
desc = function() private$..desc$value,
plots = function() private$..plots$value,
descplots = function() private$..descplots$value,
low_eqbound_d = function() private$..low_eqbound_d$value,
high_eqbound_d = function() private$..high_eqbound_d$value,
smd_type = function() private$..smd_type$value),
private = list(
..deps = NA,
..group = NA,
..var_equal = NA,
..hypothesis = NA,
..low_eqbound = NA,
..high_eqbound = NA,
..eqbound_type = NA,
..alpha = NA,
..desc = NA,
..plots = NA,
..descplots = NA,
..low_eqbound_d = NA,
..high_eqbound_d = NA,
..smd_type = NA)
)
dataTOSTtwoResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"dataTOSTtwoResults",
inherit = jmvcore::Group,
active = list(
text = function() private$.items[["text"]],
tost = function() private$.items[["tost"]],
eqb = function() private$.items[["eqb"]],
effsize = function() private$.items[["effsize"]],
desc = function() private$.items[["desc"]],
plots = function() private$.items[["plots"]],
descplots = function() private$.items[["descplots"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="TOST Independent Samples T-Test")
self$add(jmvcore::Html$new(
options=options,
name="text",
refs=list(
"TOSTER")))
self$add(jmvcore::Table$new(
options=options,
name="tost",
title="TOST Results",
rows="(deps)",
clearWith=list(
"group",
"alpha",
"hypothesis",
"low_eqbound",
"high_eqbound",
"eqbound_type",
"var_equal"),
columns=list(
list(
`name`="var",
`title`="",
`type`="text",
`content`="($key)"),
list(
`name`="b[0]",
`title`="",
`type`="text",
`content`="t-test"),
list(
`name`="t[0]",
`title`="t",
`type`="number"),
list(
`name`="df[0]",
`title`="df",
`type`="number"),
list(
`name`="p[0]",
`title`="p",
`type`="number",
`format`="zto,pvalue"),
list(
`name`="b[1]",
`title`="",
`type`="text",
`content`="TOST Upper"),
list(
`name`="t[1]",
`title`="t",
`type`="number"),
list(
`name`="df[1]",
`title`="df",
`type`="number"),
list(
`name`="p[1]",
`title`="p",
`type`="number",
`format`="zto,pvalue"),
list(
`name`="b[2]",
`title`="",
`type`="text",
`content`="TOST Lower"),
list(
`name`="t[2]",
`title`="t",
`type`="number"),
list(
`name`="df[2]",
`title`="df",
`type`="number"),
list(
`name`="p[2]",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="eqb",
title="Equivalence Bounds",
rows="(deps)",
clearWith=list(
"group",
"alpha",
"low_eqbound",
"high_eqbound",
"eqbound_type",
"var_equal"),
columns=list(
list(
`name`="var",
`title`="",
`type`="text",
`content`="($key)"),
list(
`name`="stat[cohen]",
`title`="",
`type`="text"),
list(
`name`="low[cohen]",
`title`="Low",
`type`="number"),
list(
`name`="high[cohen]",
`title`="High",
`type`="number"),
list(
`name`="stat[raw]",
`title`="",
`type`="text"),
list(
`name`="low[raw]",
`title`="Low",
`type`="number"),
list(
`name`="high[raw]",
`title`="High",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="effsize",
title="Effect Sizes",
rows="(deps)",
clearWith=list(
"group",
"alpha",
"low_eqbound",
"high_eqbound",
"eqbound_type",
"var_equal"),
columns=list(
list(
`name`="var",
`title`="",
`type`="text",
`content`="($key)"),
list(
`name`="stat[cohen]",
`title`="",
`type`="text"),
list(
`name`="est[cohen]",
`title`="Estimate",
`type`="number"),
list(
`name`="cil[cohen]",
`title`="Lower",
`superTitle`="Confidence Interval"),
list(
`name`="ciu[cohen]",
`title`="Upper",
`superTitle`="Confidence Interval"),
list(
`name`="stat[raw]",
`title`="",
`type`="text",
`content`="Raw"),
list(
`name`="est[raw]",
`title`="Estimate",
`type`="number"),
list(
`name`="cil[raw]",
`title`="Lower",
`superTitle`="Confidence Interval"),
list(
`name`="ciu[raw]",
`title`="Upper",
`superTitle`="Confidence Interval"))))
self$add(jmvcore::Table$new(
options=options,
name="desc",
title="Descriptives",
visible="(desc)",
rows="(deps)",
clearWith=list(
"group"),
columns=list(
list(
`name`="name[1]",
`title`="",
`type`="text"),
list(
`name`="n[1]",
`title`="N",
`type`="integer"),
list(
`name`="m[1]",
`title`="Mean",
`type`="number"),
list(
`name`="med[1]",
`title`="Median",
`type`="number"),
list(
`name`="sd[1]",
`title`="SD",
`type`="number"),
list(
`name`="se[1]",
`title`="SE",
`type`="number"),
list(
`name`="name[2]",
`title`="",
`type`="text"),
list(
`name`="n[2]",
`title`="N",
`type`="integer"),
list(
`name`="m[2]",
`title`="Mean",
`type`="number"),
list(
`name`="med[2]",
`title`="Median",
`type`="number"),
list(
`name`="sd[2]",
`title`="SD",
`type`="number"),
list(
`name`="se[2]",
`title`="SE",
`type`="number"))))
self$add(jmvcore::Array$new(
options=options,
name="plots",
title="Effect Size Plot",
items="(deps)",
visible="(plots)",
template=jmvcore::Image$new(
options=options,
title="$key",
renderFun=".plot",
width=500,
height=500,
clearWith=list(
"group",
"alpha",
"hypothesis",
"smd_type",
"low_eqbound",
"high_eqbound",
"eqbound_type",
"var_equal"))))
self$add(jmvcore::Array$new(
options=options,
name="descplots",
title="Data Plot",
items="(deps)",
visible="(descplots)",
template=jmvcore::Image$new(
options=options,
title="$key",
renderFun=".descplot",
width=400,
height=375,
clearWith=list(
"group",
"alpha",
"hypothesis",
"smd_type",
"low_eqbound",
"high_eqbound",
"eqbound_type",
"var_equal"))))}))
dataTOSTtwoBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"dataTOSTtwoBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "TOSTER",
name = "dataTOSTtwo",
version = c(1,0,0),
options = options,
results = dataTOSTtwoResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE)
}))
#' TOST Independent Samples T-Test
#'
#' TOST Independent Samples T-Test for jamovi. This function is not meant to
#' be utilized in R. See t_TOST function.
#'
#' @examples
#' library(TOSTER)
#'
#' ## Load iris dataset, remove one of the three groups so two are left
#'
#' data<-iris[which(iris$Species!="versicolor"),]
#'
#' ## TOST procedure on the raw data
#'
#' dataTOSTtwo(data, deps="Sepal.Width", group="Species", var_equal = TRUE, low_eqbound = -0.5,
#' high_eqbound = 0.5, alpha = 0.05, desc = TRUE, plots = TRUE)
#'
#' @section References:
#' Berger, R. L., & Hsu, J. C. (1996). Bioequivalence Trials, Intersection-Union Tests and Equivalence Confidence Sets. Statistical Science, 11(4), 283-302.
#'
#' Gruman, J. A., Cribbie, R. A., & Arpin-Cribbie, C. A. (2007). The effects of heteroscedasticity on tests of equivalence. Journal of Modern Applied Statistical Methods, 6(1), 133-140, formula for Welch's t-test on page 135
#'
#' @param data the data as a data frame
#' @param deps a vector of strings naming dependent variables in \code{data}
#' @param group a string naming the grouping variable in \code{data}; must
#' have two levels
#' @param var_equal \code{TRUE} or \code{FALSE} (default), assume equal
#' variances
#' @param hypothesis \code{'EQU'} for equivalence (default), or \code{'MET'}
#' for minimal effects test, the alternative hypothesis.
#' @param low_eqbound a number (default: -0.5) the lower equivalence/MET
#' bounds
#' @param high_eqbound a number (default: 0.5) the upper equivalence/MET
#' bounds
#' @param eqbound_type \code{'SMD'} (default) or \code{'raw'}; whether the
#' bounds are specified in Cohen's d or raw units respectively
#' @param alpha alpha level (default = 0.05)
#' @param desc \code{TRUE} or \code{FALSE} (default), provide descriptive
#' statistics
#' @param plots \code{TRUE} or \code{FALSE} (default), provide effect size
#' plots
#' @param descplots \code{TRUE} or \code{FALSE} (default), provide plots
#' @param low_eqbound_d deprecated
#' @param high_eqbound_d deprecated
#' @param smd_type \code{'d'} (default) or \code{'g'}; whether the calculated
#' effect size is biased (d) or bias-corrected (g).
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$text} \tab \tab \tab \tab \tab a html \cr
#' \code{results$tost} \tab \tab \tab \tab \tab a table \cr
#' \code{results$eqb} \tab \tab \tab \tab \tab a table \cr
#' \code{results$effsize} \tab \tab \tab \tab \tab a table \cr
#' \code{results$desc} \tab \tab \tab \tab \tab a table \cr
#' \code{results$plots} \tab \tab \tab \tab \tab an array of images \cr
#' \code{results$descplots} \tab \tab \tab \tab \tab an array of images \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$tost$asDF}
#'
#' \code{as.data.frame(results$tost)}
#'
#' @export
dataTOSTtwo <- function(
data,
deps,
group,
var_equal = FALSE,
hypothesis = "EQU",
low_eqbound = -0.5,
high_eqbound = 0.5,
eqbound_type = "raw",
alpha = 0.05,
desc = FALSE,
plots = FALSE,
descplots = FALSE,
low_eqbound_d = -999999999,
high_eqbound_d = -999999999,
smd_type = "g") {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("dataTOSTtwo requires jmvcore to be installed (restart may be required)")
if ( ! missing(deps)) deps <- jmvcore::resolveQuo(jmvcore::enquo(deps))
if ( ! missing(group)) group <- jmvcore::resolveQuo(jmvcore::enquo(group))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(deps), deps, NULL),
`if`( ! missing(group), group, NULL))
options <- dataTOSTtwoOptions$new(
deps = deps,
group = group,
var_equal = var_equal,
hypothesis = hypothesis,
low_eqbound = low_eqbound,
high_eqbound = high_eqbound,
eqbound_type = eqbound_type,
alpha = alpha,
desc = desc,
plots = plots,
descplots = descplots,
low_eqbound_d = low_eqbound_d,
high_eqbound_d = high_eqbound_d,
smd_type = smd_type)
analysis <- dataTOSTtwoClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
Lakens/TOSTER documentation built on April 27, 2024, 11:20 p.m.
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Defines functions dataTOSTtwo
Documented in dataTOSTtwo
# This file is automatically generated, you probably don't want to edit this
dataTOSTtwoOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"dataTOSTtwoOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
deps = NULL,
group = NULL,
var_equal = FALSE,
hypothesis = "EQU",
low_eqbound = -0.5,
high_eqbound = 0.5,
eqbound_type = "raw",
alpha = 0.05,
desc = FALSE,
plots = FALSE,
descplots = FALSE,
low_eqbound_d = -999999999,
high_eqbound_d = -999999999,
smd_type = "g", ...) {
super$initialize(
package="TOSTER",
name="dataTOSTtwo",
requiresData=TRUE,
...)
private$..deps <- jmvcore::OptionVariable$new(
"deps",
deps,
permitted=list(
"numeric"),
suggested=list(
"continuous"))
private$..group <- jmvcore::OptionVariable$new(
"group",
group,
suggested=list(
"nominal",
"ordinal"))
private$..var_equal <- jmvcore::OptionBool$new(
"var_equal",
var_equal,
default=FALSE)
private$..hypothesis <- jmvcore::OptionList$new(
"hypothesis",
hypothesis,
options=list(
"EQU",
"MET"),
default="EQU")
private$..low_eqbound <- jmvcore::OptionNumber$new(
"low_eqbound",
low_eqbound,
default=-0.5)
private$..high_eqbound <- jmvcore::OptionNumber$new(
"high_eqbound",
high_eqbound,
default=0.5)
private$..eqbound_type <- jmvcore::OptionList$new(
"eqbound_type",
eqbound_type,
options=list(
"SMD",
"raw"),
default="raw")
private$..alpha <- jmvcore::OptionNumber$new(
"alpha",
alpha,
default=0.05)
private$..desc <- jmvcore::OptionBool$new(
"desc",
desc,
default=FALSE)
private$..plots <- jmvcore::OptionBool$new(
"plots",
plots,
default=FALSE)
private$..descplots <- jmvcore::OptionBool$new(
"descplots",
descplots,
default=FALSE)
private$..low_eqbound_d <- jmvcore::OptionNumber$new(
"low_eqbound_d",
low_eqbound_d,
default=-999999999,
hidden=TRUE)
private$..high_eqbound_d <- jmvcore::OptionNumber$new(
"high_eqbound_d",
high_eqbound_d,
default=-999999999,
hidden=TRUE)
private$..smd_type <- jmvcore::OptionList$new(
"smd_type",
smd_type,
options=list(
"d",
"g"),
default="g")
self$.addOption(private$..deps)
self$.addOption(private$..group)
self$.addOption(private$..var_equal)
self$.addOption(private$..hypothesis)
self$.addOption(private$..low_eqbound)
self$.addOption(private$..high_eqbound)
self$.addOption(private$..eqbound_type)
self$.addOption(private$..alpha)
self$.addOption(private$..desc)
self$.addOption(private$..plots)
self$.addOption(private$..descplots)
self$.addOption(private$..low_eqbound_d)
self$.addOption(private$..high_eqbound_d)
self$.addOption(private$..smd_type)
}),
active = list(
deps = function() private$..deps$value,
group = function() private$..group$value,
var_equal = function() private$..var_equal$value,
hypothesis = function() private$..hypothesis$value,
low_eqbound = function() private$..low_eqbound$value,
high_eqbound = function() private$..high_eqbound$value,
eqbound_type = function() private$..eqbound_type$value,
alpha = function() private$..alpha$value,
desc = function() private$..desc$value,
plots = function() private$..plots$value,
descplots = function() private$..descplots$value,
low_eqbound_d = function() private$..low_eqbound_d$value,
high_eqbound_d = function() private$..high_eqbound_d$value,
smd_type = function() private$..smd_type$value),
private = list(
..deps = NA,
..group = NA,
..var_equal = NA,
..hypothesis = NA,
..low_eqbound = NA,
..high_eqbound = NA,
..eqbound_type = NA,
..alpha = NA,
..desc = NA,
..plots = NA,
..descplots = NA,
..low_eqbound_d = NA,
..high_eqbound_d = NA,
..smd_type = NA)
)
dataTOSTtwoResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"dataTOSTtwoResults",
inherit = jmvcore::Group,
active = list(
text = function() private$.items[["text"]],
tost = function() private$.items[["tost"]],
eqb = function() private$.items[["eqb"]],
effsize = function() private$.items[["effsize"]],
desc = function() private$.items[["desc"]],
plots = function() private$.items[["plots"]],
descplots = function() private$.items[["descplots"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="TOST Independent Samples T-Test")
self$add(jmvcore::Html$new(
options=options,
name="text",
refs=list(
"TOSTER")))
self$add(jmvcore::Table$new(
options=options,
name="tost",
title="TOST Results",
rows="(deps)",
clearWith=list(
"group",
"alpha",
"hypothesis",
"low_eqbound",
"high_eqbound",
"eqbound_type",
"var_equal"),
columns=list(
list(
`name`="var",
`title`="",
`type`="text",
`content`="($key)"),
list(
`name`="b[0]",
`title`="",
`type`="text",
`content`="t-test"),
list(
`name`="t[0]",
`title`="t",
`type`="number"),
list(
`name`="df[0]",
`title`="df",
`type`="number"),
list(
`name`="p[0]",
`title`="p",
`type`="number",
`format`="zto,pvalue"),
list(
`name`="b[1]",
`title`="",
`type`="text",
`content`="TOST Upper"),
list(
`name`="t[1]",
`title`="t",
`type`="number"),
list(
`name`="df[1]",
`title`="df",
`type`="number"),
list(
`name`="p[1]",
`title`="p",
`type`="number",
`format`="zto,pvalue"),
list(
`name`="b[2]",
`title`="",
`type`="text",
`content`="TOST Lower"),
list(
`name`="t[2]",
`title`="t",
`type`="number"),
list(
`name`="df[2]",
`title`="df",
`type`="number"),
list(
`name`="p[2]",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="eqb",
title="Equivalence Bounds",
rows="(deps)",
clearWith=list(
"group",
"alpha",
"low_eqbound",
"high_eqbound",
"eqbound_type",
"var_equal"),
columns=list(
list(
`name`="var",
`title`="",
`type`="text",
`content`="($key)"),
list(
`name`="stat[cohen]",
`title`="",
`type`="text"),
list(
`name`="low[cohen]",
`title`="Low",
`type`="number"),
list(
`name`="high[cohen]",
`title`="High",
`type`="number"),
list(
`name`="stat[raw]",
`title`="",
`type`="text"),
list(
`name`="low[raw]",
`title`="Low",
`type`="number"),
list(
`name`="high[raw]",
`title`="High",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="effsize",
title="Effect Sizes",
rows="(deps)",
clearWith=list(
"group",
"alpha",
"low_eqbound",
"high_eqbound",
"eqbound_type",
"var_equal"),
columns=list(
list(
`name`="var",
`title`="",
`type`="text",
`content`="($key)"),
list(
`name`="stat[cohen]",
`title`="",
`type`="text"),
list(
`name`="est[cohen]",
`title`="Estimate",
`type`="number"),
list(
`name`="cil[cohen]",
`title`="Lower",
`superTitle`="Confidence Interval"),
list(
`name`="ciu[cohen]",
`title`="Upper",
`superTitle`="Confidence Interval"),
list(
`name`="stat[raw]",
`title`="",
`type`="text",
`content`="Raw"),
list(
`name`="est[raw]",
`title`="Estimate",
`type`="number"),
list(
`name`="cil[raw]",
`title`="Lower",
`superTitle`="Confidence Interval"),
list(
`name`="ciu[raw]",
`title`="Upper",
`superTitle`="Confidence Interval"))))
self$add(jmvcore::Table$new(
options=options,
name="desc",
title="Descriptives",
visible="(desc)",
rows="(deps)",
clearWith=list(
"group"),
columns=list(
list(
`name`="name[1]",
`title`="",
`type`="text"),
list(
`name`="n[1]",
`title`="N",
`type`="integer"),
list(
`name`="m[1]",
`title`="Mean",
`type`="number"),
list(
`name`="med[1]",
`title`="Median",
`type`="number"),
list(
`name`="sd[1]",
`title`="SD",
`type`="number"),
list(
`name`="se[1]",
`title`="SE",
`type`="number"),
list(
`name`="name[2]",
`title`="",
`type`="text"),
list(
`name`="n[2]",
`title`="N",
`type`="integer"),
list(
`name`="m[2]",
`title`="Mean",
`type`="number"),
list(
`name`="med[2]",
`title`="Median",
`type`="number"),
list(
`name`="sd[2]",
`title`="SD",
`type`="number"),
list(
`name`="se[2]",
`title`="SE",
`type`="number"))))
self$add(jmvcore::Array$new(
options=options,
name="plots",
title="Effect Size Plot",
items="(deps)",
visible="(plots)",
template=jmvcore::Image$new(
options=options,
title="$key",
renderFun=".plot",
width=500,
height=500,
clearWith=list(
"group",
"alpha",
"hypothesis",
"smd_type",
"low_eqbound",
"high_eqbound",
"eqbound_type",
"var_equal"))))
self$add(jmvcore::Array$new(
options=options,
name="descplots",
title="Data Plot",
items="(deps)",
visible="(descplots)",
template=jmvcore::Image$new(
options=options,
title="$key",
renderFun=".descplot",
width=400,
height=375,
clearWith=list(
"group",
"alpha",
"hypothesis",
"smd_type",
"low_eqbound",
"high_eqbound",
"eqbound_type",
"var_equal"))))}))
dataTOSTtwoBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"dataTOSTtwoBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "TOSTER",
name = "dataTOSTtwo",
version = c(1,0,0),
options = options,
results = dataTOSTtwoResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE)
}))
#' TOST Independent Samples T-Test
#'
#' TOST Independent Samples T-Test for jamovi. This function is not meant to
#' be utilized in R. See t_TOST function.
#'
#' @examples
#' library(TOSTER)
#'
#' ## Load iris dataset, remove one of the three groups so two are left
#'
#' data<-iris[which(iris$Species!="versicolor"),]
#'
#' ## TOST procedure on the raw data
#'
#' dataTOSTtwo(data, deps="Sepal.Width", group="Species", var_equal = TRUE, low_eqbound = -0.5,
#' high_eqbound = 0.5, alpha = 0.05, desc = TRUE, plots = TRUE)
#'
#' @section References:
#' Berger, R. L., & Hsu, J. C. (1996). Bioequivalence Trials, Intersection-Union Tests and Equivalence Confidence Sets. Statistical Science, 11(4), 283-302.
#'
#' Gruman, J. A., Cribbie, R. A., & Arpin-Cribbie, C. A. (2007). The effects of heteroscedasticity on tests of equivalence. Journal of Modern Applied Statistical Methods, 6(1), 133-140, formula for Welch's t-test on page 135
#'
#' @param data the data as a data frame
#' @param deps a vector of strings naming dependent variables in \code{data}
#' @param group a string naming the grouping variable in \code{data}; must
#' have two levels
#' @param var_equal \code{TRUE} or \code{FALSE} (default), assume equal
#' variances
#' @param hypothesis \code{'EQU'} for equivalence (default), or \code{'MET'}
#' for minimal effects test, the alternative hypothesis.
#' @param low_eqbound a number (default: -0.5) the lower equivalence/MET
#' bounds
#' @param high_eqbound a number (default: 0.5) the upper equivalence/MET
#' bounds
#' @param eqbound_type \code{'SMD'} (default) or \code{'raw'}; whether the
#' bounds are specified in Cohen's d or raw units respectively
#' @param alpha alpha level (default = 0.05)
#' @param desc \code{TRUE} or \code{FALSE} (default), provide descriptive
#' statistics
#' @param plots \code{TRUE} or \code{FALSE} (default), provide effect size
#' plots
#' @param descplots \code{TRUE} or \code{FALSE} (default), provide plots
#' @param low_eqbound_d deprecated
#' @param high_eqbound_d deprecated
#' @param smd_type \code{'d'} (default) or \code{'g'}; whether the calculated
#' effect size is biased (d) or bias-corrected (g).
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$text} \tab \tab \tab \tab \tab a html \cr
#' \code{results$tost} \tab \tab \tab \tab \tab a table \cr
#' \code{results$eqb} \tab \tab \tab \tab \tab a table \cr
#' \code{results$effsize} \tab \tab \tab \tab \tab a table \cr
#' \code{results$desc} \tab \tab \tab \tab \tab a table \cr
#' \code{results$plots} \tab \tab \tab \tab \tab an array of images \cr
#' \code{results$descplots} \tab \tab \tab \tab \tab an array of images \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$tost$asDF}
#'
#' \code{as.data.frame(results$tost)}
#'
#' @export
dataTOSTtwo <- function(
data,
deps,
group,
var_equal = FALSE,
hypothesis = "EQU",
low_eqbound = -0.5,
high_eqbound = 0.5,
eqbound_type = "raw",
alpha = 0.05,
desc = FALSE,
plots = FALSE,
descplots = FALSE,
low_eqbound_d = -999999999,
high_eqbound_d = -999999999,
smd_type = "g") {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("dataTOSTtwo requires jmvcore to be installed (restart may be required)")
if ( ! missing(deps)) deps <- jmvcore::resolveQuo(jmvcore::enquo(deps))
if ( ! missing(group)) group <- jmvcore::resolveQuo(jmvcore::enquo(group))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(deps), deps, NULL),
`if`( ! missing(group), group, NULL))
options <- dataTOSTtwoOptions$new(
deps = deps,
group = group,
var_equal = var_equal,
hypothesis = hypothesis,
low_eqbound = low_eqbound,
high_eqbound = high_eqbound,
eqbound_type = eqbound_type,
alpha = alpha,
desc = desc,
plots = plots,
descplots = descplots,
low_eqbound_d = low_eqbound_d,
high_eqbound_d = high_eqbound_d,
smd_type = smd_type)
analysis <- dataTOSTtwoClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
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