R/ttestps.h.R
In jamovi/Rjamovi: The 'jamovi' Analyses
Defines functions
ttestPS
# This file is automatically generated, you probably don't want to edit this
ttestPSOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"ttestPSOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
pairs = NULL,
students = TRUE,
bf = FALSE,
bfPrior = 0.707,
wilcoxon = FALSE,
hypothesis = "different",
norm = FALSE,
qq = FALSE,
meanDiff = FALSE,
ci = FALSE,
ciWidth = 95,
effectSize = FALSE,
ciES = FALSE,
ciWidthES = 95,
desc = FALSE,
plots = FALSE,
miss = "perAnalysis", ...) {
super$initialize(
package="jmv",
name="ttestPS",
requiresData=TRUE,
...)
private$..pairs <- jmvcore::OptionPairs$new(
"pairs",
pairs,
suggested=list(
"continuous"),
permitted=list(
"numeric"))
private$..students <- jmvcore::OptionBool$new(
"students",
students,
default=TRUE)
private$..bf <- jmvcore::OptionBool$new(
"bf",
bf,
default=FALSE)
private$..bfPrior <- jmvcore::OptionNumber$new(
"bfPrior",
bfPrior,
default=0.707,
min=0.5,
max=2)
private$..wilcoxon <- jmvcore::OptionBool$new(
"wilcoxon",
wilcoxon,
default=FALSE)
private$..hypothesis <- jmvcore::OptionList$new(
"hypothesis",
hypothesis,
options=list(
"different",
"oneGreater",
"twoGreater"),
default="different")
private$..norm <- jmvcore::OptionBool$new(
"norm",
norm,
default=FALSE)
private$..qq <- jmvcore::OptionBool$new(
"qq",
qq,
default=FALSE)
private$..meanDiff <- jmvcore::OptionBool$new(
"meanDiff",
meanDiff,
default=FALSE)
private$..ci <- jmvcore::OptionBool$new(
"ci",
ci,
default=FALSE)
private$..ciWidth <- jmvcore::OptionNumber$new(
"ciWidth",
ciWidth,
min=50,
max=99.9,
default=95)
private$..effectSize <- jmvcore::OptionBool$new(
"effectSize",
effectSize,
default=FALSE)
private$..ciES <- jmvcore::OptionBool$new(
"ciES",
ciES,
default=FALSE)
private$..ciWidthES <- jmvcore::OptionNumber$new(
"ciWidthES",
ciWidthES,
min=50,
max=99.9,
default=95)
private$..desc <- jmvcore::OptionBool$new(
"desc",
desc,
default=FALSE)
private$..plots <- jmvcore::OptionBool$new(
"plots",
plots,
default=FALSE)
private$..miss <- jmvcore::OptionList$new(
"miss",
miss,
options=list(
"perAnalysis",
"listwise"),
default="perAnalysis")
self$.addOption(private$..pairs)
self$.addOption(private$..students)
self$.addOption(private$..bf)
self$.addOption(private$..bfPrior)
self$.addOption(private$..wilcoxon)
self$.addOption(private$..hypothesis)
self$.addOption(private$..norm)
self$.addOption(private$..qq)
self$.addOption(private$..meanDiff)
self$.addOption(private$..ci)
self$.addOption(private$..ciWidth)
self$.addOption(private$..effectSize)
self$.addOption(private$..ciES)
self$.addOption(private$..ciWidthES)
self$.addOption(private$..desc)
self$.addOption(private$..plots)
self$.addOption(private$..miss)
}),
active = list(
pairs = function() private$..pairs$value,
students = function() private$..students$value,
bf = function() private$..bf$value,
bfPrior = function() private$..bfPrior$value,
wilcoxon = function() private$..wilcoxon$value,
hypothesis = function() private$..hypothesis$value,
norm = function() private$..norm$value,
qq = function() private$..qq$value,
meanDiff = function() private$..meanDiff$value,
ci = function() private$..ci$value,
ciWidth = function() private$..ciWidth$value,
effectSize = function() private$..effectSize$value,
ciES = function() private$..ciES$value,
ciWidthES = function() private$..ciWidthES$value,
desc = function() private$..desc$value,
plots = function() private$..plots$value,
miss = function() private$..miss$value),
private = list(
..pairs = NA,
..students = NA,
..bf = NA,
..bfPrior = NA,
..wilcoxon = NA,
..hypothesis = NA,
..norm = NA,
..qq = NA,
..meanDiff = NA,
..ci = NA,
..ciWidth = NA,
..effectSize = NA,
..ciES = NA,
..ciWidthES = NA,
..desc = NA,
..plots = NA,
..miss = NA)
)
ttestPSResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"ttestPSResults",
inherit = jmvcore::Group,
active = list(
ttest = function() private$.items[["ttest"]],
norm = function() private$.items[["norm"]],
desc = function() private$.items[["desc"]],
plots = function() private$.items[["plots"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Paired Samples T-Test")
self$add(jmvcore::Table$new(
options=options,
name="ttest",
title="Paired Samples T-Test",
rows="(pairs)",
clearWith=list(
"miss",
"hypothesis",
"ciWidth",
"bfPrior",
"ciWidthES"),
columns=list(
list(
`name`="var1[stud]",
`title`="",
`type`="text",
`combineBelow`=TRUE,
`visible`="(students)"),
list(
`name`="var2[stud]",
`title`="",
`type`="text",
`combineBelow`=TRUE,
`visible`="(students)"),
list(
`name`="test[stud]",
`title`="",
`type`="text",
`content`="Student's t",
`visible`="(students)"),
list(
`name`="stat[stud]",
`title`="statistic",
`type`="number",
`visible`="(students)"),
list(
`name`="err[stud]",
`title`="error %",
`type`="number",
`visible`="(students && bf)",
`content`=""),
list(
`name`="df[stud]",
`title`="df",
`type`="number",
`visible`="(students)"),
list(
`name`="p[stud]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(students)"),
list(
`name`="md[stud]",
`title`="Mean difference",
`type`="number",
`visible`="(meanDiff && students)"),
list(
`name`="sed[stud]",
`title`="SE difference",
`type`="number",
`visible`="(meanDiff && students)"),
list(
`name`="cil[stud]",
`title`="Lower",
`type`="number",
`visible`="(ci && meanDiff && students)"),
list(
`name`="ciu[stud]",
`title`="Upper",
`type`="number",
`visible`="(ci && meanDiff && students)"),
list(
`name`="esType[stud]",
`title`="",
`content`="Cohen's d",
`type`="text",
`visible`="(effectSize && students)"),
list(
`name`="es[stud]",
`title`="Effect Size",
`type`="number",
`visible`="(effectSize && students)"),
list(
`name`="ciles[stud]",
`title`="Lower",
`type`="number",
`visible`="(ciES && effectSize && students)"),
list(
`name`="ciues[stud]",
`title`="Upper",
`type`="number",
`visible`="(ciES && effectSize && students)"),
list(
`name`="var1[bf]",
`title`="",
`type`="text",
`combineBelow`=TRUE,
`visible`="(bf)"),
list(
`name`="var2[bf]",
`title`="",
`type`="text",
`combineBelow`=TRUE,
`visible`="(bf)"),
list(
`name`="test[bf]",
`title`="",
`type`="text",
`content`="Bayes factor\u2081\u2080",
`visible`="(bf)"),
list(
`name`="stat[bf]",
`title`="Statistic",
`type`="number",
`visible`="(bf)",
`refs`=list(
"BF",
"btt")),
list(
`name`="err[bf]",
`title`="\u00B1%",
`type`="number",
`visible`="(bf)"),
list(
`name`="df[bf]",
`title`="df",
`type`="number",
`visible`="(bf)",
`content`=""),
list(
`name`="p[bf]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(bf)",
`content`=""),
list(
`name`="md[bf]",
`title`="Mean difference",
`type`="number",
`visible`="(meanDiff && bf)",
`content`=""),
list(
`name`="sed[bf]",
`title`="SE difference",
`type`="number",
`visible`="(meanDiff && bf)",
`content`=""),
list(
`name`="cil[bf]",
`title`="Lower",
`type`="number",
`visible`="(ci && meanDiff && bf)",
`content`=""),
list(
`name`="ciu[bf]",
`title`="Upper",
`type`="number",
`visible`="(ci && meanDiff && bf)",
`content`=""),
list(
`name`="esType[bf]",
`title`="",
`content`="",
`type`="text",
`visible`="(effectSize && bf)"),
list(
`name`="es[bf]",
`title`="Effect Size",
`type`="number",
`visible`="(effectSize && bf)",
`content`=""),
list(
`name`="ciles[bf]",
`title`="Lower",
`type`="number",
`visible`="(ciES && effectSize && bf)",
`content`=""),
list(
`name`="ciues[bf]",
`title`="Upper",
`type`="number",
`visible`="(ciES && effectSize && bf)",
`content`=""),
list(
`name`="var1[wilc]",
`title`="",
`type`="text",
`combineBelow`=TRUE,
`visible`="(wilcoxon)"),
list(
`name`="var2[wilc]",
`title`="",
`type`="text",
`combineBelow`=TRUE,
`visible`="(wilcoxon)"),
list(
`name`="test[wilc]",
`type`="text",
`title`="",
`content`="Wilcoxon W",
`visible`="(wilcoxon)"),
list(
`name`="stat[wilc]",
`title`="Statistic",
`type`="number",
`visible`="(wilcoxon)"),
list(
`name`="err[wilc]",
`title`="\u00B1%",
`type`="number",
`visible`="(wilcoxon && bf)",
`content`=""),
list(
`name`="p[wilc]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(wilcoxon)"),
list(
`name`="md[wilc]",
`title`="Mean difference",
`type`="number",
`visible`="(meanDiff && wilcoxon)"),
list(
`name`="sed[wilc]",
`title`="SE difference",
`type`="number",
`visible`="(meanDiff && wilcoxon)"),
list(
`name`="cil[wilc]",
`title`="Lower",
`type`="number",
`visible`="(ci && meanDiff && wilcoxon)"),
list(
`name`="ciu[wilc]",
`title`="Upper",
`type`="number",
`visible`="(ci && meanDiff && wilcoxon)"),
list(
`name`="esType[wilc]",
`title`="",
`content`="Rank biserial correlation",
`type`="text",
`visible`="(effectSize && wilcoxon)",
`refs`="Kerby2014"),
list(
`name`="es[wilc]",
`title`="Effect Size",
`type`="number",
`visible`="(effectSize && wilcoxon)"),
list(
`name`="ciles[wilc]",
`title`="Lower",
`type`="number",
`visible`="(ciES && effectSize && wilcoxon)"),
list(
`name`="ciues[wilc]",
`title`="Upper",
`type`="number",
`visible`="(ciES && effectSize && wilcoxon)"))))
self$add(jmvcore::Table$new(
options=options,
name="norm",
title="Normality Test (Shapiro-Wilk)",
visible="(norm)",
rows="(pairs)",
notes=list(
`p`="A low p-value suggests a violation of the assumption of normality"),
clearWith=list(
"miss"),
columns=list(
list(
`name`="var1",
`title`="",
`type`="text"),
list(
`name`="sep",
`title`="",
`type`="text",
`content`="-",
`format`="narrow"),
list(
`name`="var2",
`title`="",
`type`="text"),
list(
`name`="w",
`title`="W",
`type`="number"),
list(
`name`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="desc",
title="Descriptives",
visible="(desc)",
clearWith=list(
"miss"),
columns=list(
list(
`name`="name",
`title`="",
`content`=".",
`type`="text"),
list(
`name`="num",
`title`="N",
`type`="integer"),
list(
`name`="m",
`title`="Mean",
`type`="number"),
list(
`name`="med",
`title`="Median",
`type`="number"),
list(
`name`="sd",
`title`="SD",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"))))
self$add(jmvcore::Array$new(
options=options,
name="plots",
title="Plots",
items="(pairs)",
clearWith=list(
"miss"),
template=R6::R6Class(
inherit = jmvcore::Group,
active = list(
desc = function() private$.items[["desc"]],
qq = function() private$.items[["qq"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="undefined",
title="no title")
self$add(jmvcore::Image$new(
options=options,
name="desc",
visible="(plots)",
renderFun=".desc",
clearWith=list()))
self$add(jmvcore::Image$new(
options=options,
name="qq",
visible="(qq)",
width=350,
height=300,
requiresData=TRUE,
renderFun=".qq",
clearWith=list()))}))$new(options=options)))}))
ttestPSBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"ttestPSBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "jmv",
name = "ttestPS",
version = c(1,0,0),
options = options,
results = ttestPSResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = TRUE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
#' Paired Samples T-Test
#'
#' The Student's paired samples t-test (sometimes called a
#' dependent-samples t-test) is used to test the null hypothesis that the
#' difference between pairs of measurements is equal to zero. A low p-value
#' suggests that the null hypothesis is not true, and that the
#' difference between the measurement pairs is not zero.
#'
#' The Student's paired samples t-test assumes that pair differences follow
#' a normal distribution -- in the case that one is unwilling to assume
#' this, the non-parametric Wilcoxon signed-rank can be used in it's place
#' (However, note that the Wilcoxon signed-rank has a slightly different
#' null hypothesis; that the two groups of measurements follow the same
#' distribution).
#'
#'
#' @examples
#' \donttest{
#' data('bugs', package = 'jmv')
#'
#' ttestPS(bugs, pairs = list(
#' list(i1 = 'LDLF', i2 = 'LDHF')))
#'
#' #
#' # PAIRED SAMPLES T-TEST
#' #
#' # Paired Samples T-Test
#' # --------------------------------------------------------------
#' # statistic df p
#' # --------------------------------------------------------------
#' # LDLF LDHF Student's t -6.65 90.0 < .001
#' # --------------------------------------------------------------
#' #
#'}
#' @param data the data as a data frame
#' @param pairs a list of lists specifying the pairs of measurement in
#' \code{data}
#' @param students \code{TRUE} (default) or \code{FALSE}, perform Student's
#' t-tests
#' @param bf \code{TRUE} or \code{FALSE} (default), provide Bayes factors
#' @param bfPrior a number between 0.5 and 2 (default 0.707), the prior width
#' to use in calculating Bayes factors
#' @param wilcoxon \code{TRUE} or \code{FALSE} (default), perform Wilcoxon
#' signed rank tests
#' @param hypothesis \code{'different'} (default), \code{'oneGreater'} or
#' \code{'twoGreater'}, the alternative hypothesis; measure 1 different to
#' measure 2, measure 1 greater than measure 2, and measure 2 greater than
#' measure 1 respectively
#' @param norm \code{TRUE} or \code{FALSE} (default), perform Shapiro-wilk
#' normality tests
#' @param qq \code{TRUE} or \code{FALSE} (default), provide a Q-Q plot of
#' residuals
#' @param meanDiff \code{TRUE} or \code{FALSE} (default), provide means and
#' standard errors
#' @param ci \code{TRUE} or \code{FALSE} (default), provide confidence
#' intervals
#' @param ciWidth a number between 50 and 99.9 (default: 95), the width of
#' confidence intervals
#' @param effectSize \code{TRUE} or \code{FALSE} (default), provide effect
#' sizes
#' @param ciES \code{TRUE} or \code{FALSE} (default), provide confidence
#' intervals for the effect-sizes
#' @param ciWidthES a number between 50 and 99.9 (default: 95), the width of
#' confidence intervals for the effect sizes
#' @param desc \code{TRUE} or \code{FALSE} (default), provide descriptive
#' statistics
#' @param plots \code{TRUE} or \code{FALSE} (default), provide descriptive
#' plots
#' @param miss \code{'perAnalysis'} or \code{'listwise'}, how to handle
#' missing values; \code{'perAnalysis'} excludes missing values for individual
#' dependent variables, \code{'listwise'} excludes a row from all analyses if
#' one of its entries is missing
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$ttest} \tab \tab \tab \tab \tab a table containing the t-test results \cr
#' \code{results$norm} \tab \tab \tab \tab \tab a table containing the normality test results \cr
#' \code{results$desc} \tab \tab \tab \tab \tab a table containing the descriptives \cr
#' \code{results$plots} \tab \tab \tab \tab \tab an array of the descriptive plots \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$ttest$asDF}
#'
#' \code{as.data.frame(results$ttest)}
#'
#' @export
ttestPS <- function(
data,
pairs,
students = TRUE,
bf = FALSE,
bfPrior = 0.707,
wilcoxon = FALSE,
hypothesis = "different",
norm = FALSE,
qq = FALSE,
meanDiff = FALSE,
ci = FALSE,
ciWidth = 95,
effectSize = FALSE,
ciES = FALSE,
ciWidthES = 95,
desc = FALSE,
plots = FALSE,
miss = "perAnalysis") {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("ttestPS requires jmvcore to be installed (restart may be required)")
if (missing(data))
data <- jmvcore::marshalData(
parent.frame())
options <- ttestPSOptions$new(
pairs = pairs,
students = students,
bf = bf,
bfPrior = bfPrior,
wilcoxon = wilcoxon,
hypothesis = hypothesis,
norm = norm,
qq = qq,
meanDiff = meanDiff,
ci = ci,
ciWidth = ciWidth,
effectSize = effectSize,
ciES = ciES,
ciWidthES = ciWidthES,
desc = desc,
plots = plots,
miss = miss)
analysis <- ttestPSClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
jamovi/Rjamovi documentation built on Jan. 17, 2025, 10:29 p.m.
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Defines functions ttestPS
# This file is automatically generated, you probably don't want to edit this
ttestPSOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"ttestPSOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
pairs = NULL,
students = TRUE,
bf = FALSE,
bfPrior = 0.707,
wilcoxon = FALSE,
hypothesis = "different",
norm = FALSE,
qq = FALSE,
meanDiff = FALSE,
ci = FALSE,
ciWidth = 95,
effectSize = FALSE,
ciES = FALSE,
ciWidthES = 95,
desc = FALSE,
plots = FALSE,
miss = "perAnalysis", ...) {
super$initialize(
package="jmv",
name="ttestPS",
requiresData=TRUE,
...)
private$..pairs <- jmvcore::OptionPairs$new(
"pairs",
pairs,
suggested=list(
"continuous"),
permitted=list(
"numeric"))
private$..students <- jmvcore::OptionBool$new(
"students",
students,
default=TRUE)
private$..bf <- jmvcore::OptionBool$new(
"bf",
bf,
default=FALSE)
private$..bfPrior <- jmvcore::OptionNumber$new(
"bfPrior",
bfPrior,
default=0.707,
min=0.5,
max=2)
private$..wilcoxon <- jmvcore::OptionBool$new(
"wilcoxon",
wilcoxon,
default=FALSE)
private$..hypothesis <- jmvcore::OptionList$new(
"hypothesis",
hypothesis,
options=list(
"different",
"oneGreater",
"twoGreater"),
default="different")
private$..norm <- jmvcore::OptionBool$new(
"norm",
norm,
default=FALSE)
private$..qq <- jmvcore::OptionBool$new(
"qq",
qq,
default=FALSE)
private$..meanDiff <- jmvcore::OptionBool$new(
"meanDiff",
meanDiff,
default=FALSE)
private$..ci <- jmvcore::OptionBool$new(
"ci",
ci,
default=FALSE)
private$..ciWidth <- jmvcore::OptionNumber$new(
"ciWidth",
ciWidth,
min=50,
max=99.9,
default=95)
private$..effectSize <- jmvcore::OptionBool$new(
"effectSize",
effectSize,
default=FALSE)
private$..ciES <- jmvcore::OptionBool$new(
"ciES",
ciES,
default=FALSE)
private$..ciWidthES <- jmvcore::OptionNumber$new(
"ciWidthES",
ciWidthES,
min=50,
max=99.9,
default=95)
private$..desc <- jmvcore::OptionBool$new(
"desc",
desc,
default=FALSE)
private$..plots <- jmvcore::OptionBool$new(
"plots",
plots,
default=FALSE)
private$..miss <- jmvcore::OptionList$new(
"miss",
miss,
options=list(
"perAnalysis",
"listwise"),
default="perAnalysis")
self$.addOption(private$..pairs)
self$.addOption(private$..students)
self$.addOption(private$..bf)
self$.addOption(private$..bfPrior)
self$.addOption(private$..wilcoxon)
self$.addOption(private$..hypothesis)
self$.addOption(private$..norm)
self$.addOption(private$..qq)
self$.addOption(private$..meanDiff)
self$.addOption(private$..ci)
self$.addOption(private$..ciWidth)
self$.addOption(private$..effectSize)
self$.addOption(private$..ciES)
self$.addOption(private$..ciWidthES)
self$.addOption(private$..desc)
self$.addOption(private$..plots)
self$.addOption(private$..miss)
}),
active = list(
pairs = function() private$..pairs$value,
students = function() private$..students$value,
bf = function() private$..bf$value,
bfPrior = function() private$..bfPrior$value,
wilcoxon = function() private$..wilcoxon$value,
hypothesis = function() private$..hypothesis$value,
norm = function() private$..norm$value,
qq = function() private$..qq$value,
meanDiff = function() private$..meanDiff$value,
ci = function() private$..ci$value,
ciWidth = function() private$..ciWidth$value,
effectSize = function() private$..effectSize$value,
ciES = function() private$..ciES$value,
ciWidthES = function() private$..ciWidthES$value,
desc = function() private$..desc$value,
plots = function() private$..plots$value,
miss = function() private$..miss$value),
private = list(
..pairs = NA,
..students = NA,
..bf = NA,
..bfPrior = NA,
..wilcoxon = NA,
..hypothesis = NA,
..norm = NA,
..qq = NA,
..meanDiff = NA,
..ci = NA,
..ciWidth = NA,
..effectSize = NA,
..ciES = NA,
..ciWidthES = NA,
..desc = NA,
..plots = NA,
..miss = NA)
)
ttestPSResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"ttestPSResults",
inherit = jmvcore::Group,
active = list(
ttest = function() private$.items[["ttest"]],
norm = function() private$.items[["norm"]],
desc = function() private$.items[["desc"]],
plots = function() private$.items[["plots"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Paired Samples T-Test")
self$add(jmvcore::Table$new(
options=options,
name="ttest",
title="Paired Samples T-Test",
rows="(pairs)",
clearWith=list(
"miss",
"hypothesis",
"ciWidth",
"bfPrior",
"ciWidthES"),
columns=list(
list(
`name`="var1[stud]",
`title`="",
`type`="text",
`combineBelow`=TRUE,
`visible`="(students)"),
list(
`name`="var2[stud]",
`title`="",
`type`="text",
`combineBelow`=TRUE,
`visible`="(students)"),
list(
`name`="test[stud]",
`title`="",
`type`="text",
`content`="Student's t",
`visible`="(students)"),
list(
`name`="stat[stud]",
`title`="statistic",
`type`="number",
`visible`="(students)"),
list(
`name`="err[stud]",
`title`="error %",
`type`="number",
`visible`="(students && bf)",
`content`=""),
list(
`name`="df[stud]",
`title`="df",
`type`="number",
`visible`="(students)"),
list(
`name`="p[stud]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(students)"),
list(
`name`="md[stud]",
`title`="Mean difference",
`type`="number",
`visible`="(meanDiff && students)"),
list(
`name`="sed[stud]",
`title`="SE difference",
`type`="number",
`visible`="(meanDiff && students)"),
list(
`name`="cil[stud]",
`title`="Lower",
`type`="number",
`visible`="(ci && meanDiff && students)"),
list(
`name`="ciu[stud]",
`title`="Upper",
`type`="number",
`visible`="(ci && meanDiff && students)"),
list(
`name`="esType[stud]",
`title`="",
`content`="Cohen's d",
`type`="text",
`visible`="(effectSize && students)"),
list(
`name`="es[stud]",
`title`="Effect Size",
`type`="number",
`visible`="(effectSize && students)"),
list(
`name`="ciles[stud]",
`title`="Lower",
`type`="number",
`visible`="(ciES && effectSize && students)"),
list(
`name`="ciues[stud]",
`title`="Upper",
`type`="number",
`visible`="(ciES && effectSize && students)"),
list(
`name`="var1[bf]",
`title`="",
`type`="text",
`combineBelow`=TRUE,
`visible`="(bf)"),
list(
`name`="var2[bf]",
`title`="",
`type`="text",
`combineBelow`=TRUE,
`visible`="(bf)"),
list(
`name`="test[bf]",
`title`="",
`type`="text",
`content`="Bayes factor\u2081\u2080",
`visible`="(bf)"),
list(
`name`="stat[bf]",
`title`="Statistic",
`type`="number",
`visible`="(bf)",
`refs`=list(
"BF",
"btt")),
list(
`name`="err[bf]",
`title`="\u00B1%",
`type`="number",
`visible`="(bf)"),
list(
`name`="df[bf]",
`title`="df",
`type`="number",
`visible`="(bf)",
`content`=""),
list(
`name`="p[bf]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(bf)",
`content`=""),
list(
`name`="md[bf]",
`title`="Mean difference",
`type`="number",
`visible`="(meanDiff && bf)",
`content`=""),
list(
`name`="sed[bf]",
`title`="SE difference",
`type`="number",
`visible`="(meanDiff && bf)",
`content`=""),
list(
`name`="cil[bf]",
`title`="Lower",
`type`="number",
`visible`="(ci && meanDiff && bf)",
`content`=""),
list(
`name`="ciu[bf]",
`title`="Upper",
`type`="number",
`visible`="(ci && meanDiff && bf)",
`content`=""),
list(
`name`="esType[bf]",
`title`="",
`content`="",
`type`="text",
`visible`="(effectSize && bf)"),
list(
`name`="es[bf]",
`title`="Effect Size",
`type`="number",
`visible`="(effectSize && bf)",
`content`=""),
list(
`name`="ciles[bf]",
`title`="Lower",
`type`="number",
`visible`="(ciES && effectSize && bf)",
`content`=""),
list(
`name`="ciues[bf]",
`title`="Upper",
`type`="number",
`visible`="(ciES && effectSize && bf)",
`content`=""),
list(
`name`="var1[wilc]",
`title`="",
`type`="text",
`combineBelow`=TRUE,
`visible`="(wilcoxon)"),
list(
`name`="var2[wilc]",
`title`="",
`type`="text",
`combineBelow`=TRUE,
`visible`="(wilcoxon)"),
list(
`name`="test[wilc]",
`type`="text",
`title`="",
`content`="Wilcoxon W",
`visible`="(wilcoxon)"),
list(
`name`="stat[wilc]",
`title`="Statistic",
`type`="number",
`visible`="(wilcoxon)"),
list(
`name`="err[wilc]",
`title`="\u00B1%",
`type`="number",
`visible`="(wilcoxon && bf)",
`content`=""),
list(
`name`="p[wilc]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(wilcoxon)"),
list(
`name`="md[wilc]",
`title`="Mean difference",
`type`="number",
`visible`="(meanDiff && wilcoxon)"),
list(
`name`="sed[wilc]",
`title`="SE difference",
`type`="number",
`visible`="(meanDiff && wilcoxon)"),
list(
`name`="cil[wilc]",
`title`="Lower",
`type`="number",
`visible`="(ci && meanDiff && wilcoxon)"),
list(
`name`="ciu[wilc]",
`title`="Upper",
`type`="number",
`visible`="(ci && meanDiff && wilcoxon)"),
list(
`name`="esType[wilc]",
`title`="",
`content`="Rank biserial correlation",
`type`="text",
`visible`="(effectSize && wilcoxon)",
`refs`="Kerby2014"),
list(
`name`="es[wilc]",
`title`="Effect Size",
`type`="number",
`visible`="(effectSize && wilcoxon)"),
list(
`name`="ciles[wilc]",
`title`="Lower",
`type`="number",
`visible`="(ciES && effectSize && wilcoxon)"),
list(
`name`="ciues[wilc]",
`title`="Upper",
`type`="number",
`visible`="(ciES && effectSize && wilcoxon)"))))
self$add(jmvcore::Table$new(
options=options,
name="norm",
title="Normality Test (Shapiro-Wilk)",
visible="(norm)",
rows="(pairs)",
notes=list(
`p`="A low p-value suggests a violation of the assumption of normality"),
clearWith=list(
"miss"),
columns=list(
list(
`name`="var1",
`title`="",
`type`="text"),
list(
`name`="sep",
`title`="",
`type`="text",
`content`="-",
`format`="narrow"),
list(
`name`="var2",
`title`="",
`type`="text"),
list(
`name`="w",
`title`="W",
`type`="number"),
list(
`name`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="desc",
title="Descriptives",
visible="(desc)",
clearWith=list(
"miss"),
columns=list(
list(
`name`="name",
`title`="",
`content`=".",
`type`="text"),
list(
`name`="num",
`title`="N",
`type`="integer"),
list(
`name`="m",
`title`="Mean",
`type`="number"),
list(
`name`="med",
`title`="Median",
`type`="number"),
list(
`name`="sd",
`title`="SD",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"))))
self$add(jmvcore::Array$new(
options=options,
name="plots",
title="Plots",
items="(pairs)",
clearWith=list(
"miss"),
template=R6::R6Class(
inherit = jmvcore::Group,
active = list(
desc = function() private$.items[["desc"]],
qq = function() private$.items[["qq"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="undefined",
title="no title")
self$add(jmvcore::Image$new(
options=options,
name="desc",
visible="(plots)",
renderFun=".desc",
clearWith=list()))
self$add(jmvcore::Image$new(
options=options,
name="qq",
visible="(qq)",
width=350,
height=300,
requiresData=TRUE,
renderFun=".qq",
clearWith=list()))}))$new(options=options)))}))
ttestPSBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"ttestPSBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "jmv",
name = "ttestPS",
version = c(1,0,0),
options = options,
results = ttestPSResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = TRUE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
#' Paired Samples T-Test
#'
#' The Student's paired samples t-test (sometimes called a
#' dependent-samples t-test) is used to test the null hypothesis that the
#' difference between pairs of measurements is equal to zero. A low p-value
#' suggests that the null hypothesis is not true, and that the
#' difference between the measurement pairs is not zero.
#'
#' The Student's paired samples t-test assumes that pair differences follow
#' a normal distribution -- in the case that one is unwilling to assume
#' this, the non-parametric Wilcoxon signed-rank can be used in it's place
#' (However, note that the Wilcoxon signed-rank has a slightly different
#' null hypothesis; that the two groups of measurements follow the same
#' distribution).
#'
#'
#' @examples
#' \donttest{
#' data('bugs', package = 'jmv')
#'
#' ttestPS(bugs, pairs = list(
#' list(i1 = 'LDLF', i2 = 'LDHF')))
#'
#' #
#' # PAIRED SAMPLES T-TEST
#' #
#' # Paired Samples T-Test
#' # --------------------------------------------------------------
#' # statistic df p
#' # --------------------------------------------------------------
#' # LDLF LDHF Student's t -6.65 90.0 < .001
#' # --------------------------------------------------------------
#' #
#'}
#' @param data the data as a data frame
#' @param pairs a list of lists specifying the pairs of measurement in
#' \code{data}
#' @param students \code{TRUE} (default) or \code{FALSE}, perform Student's
#' t-tests
#' @param bf \code{TRUE} or \code{FALSE} (default), provide Bayes factors
#' @param bfPrior a number between 0.5 and 2 (default 0.707), the prior width
#' to use in calculating Bayes factors
#' @param wilcoxon \code{TRUE} or \code{FALSE} (default), perform Wilcoxon
#' signed rank tests
#' @param hypothesis \code{'different'} (default), \code{'oneGreater'} or
#' \code{'twoGreater'}, the alternative hypothesis; measure 1 different to
#' measure 2, measure 1 greater than measure 2, and measure 2 greater than
#' measure 1 respectively
#' @param norm \code{TRUE} or \code{FALSE} (default), perform Shapiro-wilk
#' normality tests
#' @param qq \code{TRUE} or \code{FALSE} (default), provide a Q-Q plot of
#' residuals
#' @param meanDiff \code{TRUE} or \code{FALSE} (default), provide means and
#' standard errors
#' @param ci \code{TRUE} or \code{FALSE} (default), provide confidence
#' intervals
#' @param ciWidth a number between 50 and 99.9 (default: 95), the width of
#' confidence intervals
#' @param effectSize \code{TRUE} or \code{FALSE} (default), provide effect
#' sizes
#' @param ciES \code{TRUE} or \code{FALSE} (default), provide confidence
#' intervals for the effect-sizes
#' @param ciWidthES a number between 50 and 99.9 (default: 95), the width of
#' confidence intervals for the effect sizes
#' @param desc \code{TRUE} or \code{FALSE} (default), provide descriptive
#' statistics
#' @param plots \code{TRUE} or \code{FALSE} (default), provide descriptive
#' plots
#' @param miss \code{'perAnalysis'} or \code{'listwise'}, how to handle
#' missing values; \code{'perAnalysis'} excludes missing values for individual
#' dependent variables, \code{'listwise'} excludes a row from all analyses if
#' one of its entries is missing
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$ttest} \tab \tab \tab \tab \tab a table containing the t-test results \cr
#' \code{results$norm} \tab \tab \tab \tab \tab a table containing the normality test results \cr
#' \code{results$desc} \tab \tab \tab \tab \tab a table containing the descriptives \cr
#' \code{results$plots} \tab \tab \tab \tab \tab an array of the descriptive plots \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$ttest$asDF}
#'
#' \code{as.data.frame(results$ttest)}
#'
#' @export
ttestPS <- function(
data,
pairs,
students = TRUE,
bf = FALSE,
bfPrior = 0.707,
wilcoxon = FALSE,
hypothesis = "different",
norm = FALSE,
qq = FALSE,
meanDiff = FALSE,
ci = FALSE,
ciWidth = 95,
effectSize = FALSE,
ciES = FALSE,
ciWidthES = 95,
desc = FALSE,
plots = FALSE,
miss = "perAnalysis") {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("ttestPS requires jmvcore to be installed (restart may be required)")
if (missing(data))
data <- jmvcore::marshalData(
parent.frame())
options <- ttestPSOptions$new(
pairs = pairs,
students = students,
bf = bf,
bfPrior = bfPrior,
wilcoxon = wilcoxon,
hypothesis = hypothesis,
norm = norm,
qq = qq,
meanDiff = meanDiff,
ci = ci,
ciWidth = ciWidth,
effectSize = effectSize,
ciES = ciES,
ciWidthES = ciWidthES,
desc = desc,
plots = plots,
miss = miss)
analysis <- ttestPSClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
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