R/jamoviproportion.h.R
In rcalinjageman/esci: Estimation Statistics with Confidence Intervals
Defines functions
jamoviproportion
Documented in
jamoviproportion
# This file is automatically generated, you probably don't want to edit this
jamoviproportionOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamoviproportionOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
switch = "from_raw",
outcome_variable = NULL,
cases = " ",
not_cases = " ",
case_label = "Affected",
not_case_label = "Not Affected",
outcome_variable_name = "My outcome variable",
count_NA = FALSE,
conf_level = 95,
show_details = FALSE,
plot_possible = FALSE,
evaluate_hypotheses = FALSE,
null_value = "0",
null_boundary = "0",
alpha = 0.05,
null_color = "#A40122",
es_plot_width = "300",
es_plot_height = "400",
ymin = "0",
ymax = "1",
breaks = "auto",
ylab = "auto",
xlab = "auto",
axis.text.y = "14",
axis.title.y = "15",
axis.text.x = "14",
axis.title.x = "15",
error_layout = "none",
shape_summary = "circle filled",
color_summary = "#008DF9",
fill_summary = "#008DF9",
size_summary = "4",
alpha_summary = "1",
linetype_summary = "solid", ...) {
super$initialize(
package="esci",
name="jamoviproportion",
requiresData=TRUE,
...)
private$..switch <- jmvcore::OptionList$new(
"switch",
switch,
default="from_raw",
options=list(
"from_raw",
"from_summary"))
private$..outcome_variable <- jmvcore::OptionVariables$new(
"outcome_variable",
outcome_variable,
suggested=list(
"nominal",
"ordinal"),
permitted=list(
"factor"))
private$..cases <- jmvcore::OptionString$new(
"cases",
cases,
default=" ")
private$..not_cases <- jmvcore::OptionString$new(
"not_cases",
not_cases,
default=" ")
private$..case_label <- jmvcore::OptionString$new(
"case_label",
case_label,
default="Affected")
private$..not_case_label <- jmvcore::OptionString$new(
"not_case_label",
not_case_label,
default="Not Affected")
private$..outcome_variable_name <- jmvcore::OptionString$new(
"outcome_variable_name",
outcome_variable_name,
default="My outcome variable")
private$..count_NA <- jmvcore::OptionBool$new(
"count_NA",
count_NA,
default=FALSE)
private$..conf_level <- jmvcore::OptionNumber$new(
"conf_level",
conf_level,
default=95)
private$..show_details <- jmvcore::OptionBool$new(
"show_details",
show_details,
default=FALSE)
private$..plot_possible <- jmvcore::OptionBool$new(
"plot_possible",
plot_possible,
default=FALSE)
private$..evaluate_hypotheses <- jmvcore::OptionBool$new(
"evaluate_hypotheses",
evaluate_hypotheses,
default=FALSE)
private$..null_value <- jmvcore::OptionString$new(
"null_value",
null_value,
default="0")
private$..null_boundary <- jmvcore::OptionString$new(
"null_boundary",
null_boundary,
default="0")
private$..alpha <- jmvcore::OptionNumber$new(
"alpha",
alpha,
default=0.05)
private$..null_color <- jmvcore::OptionList$new(
"null_color",
null_color,
default="#A40122",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..es_plot_width <- jmvcore::OptionString$new(
"es_plot_width",
es_plot_width,
default="300")
private$..es_plot_height <- jmvcore::OptionString$new(
"es_plot_height",
es_plot_height,
default="400")
private$..ymin <- jmvcore::OptionString$new(
"ymin",
ymin,
default="0")
private$..ymax <- jmvcore::OptionString$new(
"ymax",
ymax,
default="1")
private$..breaks <- jmvcore::OptionString$new(
"breaks",
breaks,
default="auto")
private$..ylab <- jmvcore::OptionString$new(
"ylab",
ylab,
default="auto")
private$..xlab <- jmvcore::OptionString$new(
"xlab",
xlab,
default="auto")
private$..axis.text.y <- jmvcore::OptionString$new(
"axis.text.y",
axis.text.y,
default="14")
private$..axis.title.y <- jmvcore::OptionString$new(
"axis.title.y",
axis.title.y,
default="15")
private$..axis.text.x <- jmvcore::OptionString$new(
"axis.text.x",
axis.text.x,
default="14")
private$..axis.title.x <- jmvcore::OptionString$new(
"axis.title.x",
axis.title.x,
default="15")
private$..error_layout <- jmvcore::OptionList$new(
"error_layout",
error_layout,
default="none",
options=list(
"none"))
private$..shape_summary <- jmvcore::OptionList$new(
"shape_summary",
shape_summary,
default="circle filled",
options=list(
"circle filled",
"square filled",
"triangle filled",
"diamond filled"))
private$..color_summary <- jmvcore::OptionList$new(
"color_summary",
color_summary,
default="#008DF9",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..fill_summary <- jmvcore::OptionList$new(
"fill_summary",
fill_summary,
default="#008DF9",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..size_summary <- jmvcore::OptionList$new(
"size_summary",
size_summary,
default="4",
options=list(
"1",
"2",
"3",
"4",
"5",
"6"))
private$..alpha_summary <- jmvcore::OptionList$new(
"alpha_summary",
alpha_summary,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..linetype_summary <- jmvcore::OptionList$new(
"linetype_summary",
linetype_summary,
default="solid",
options=list(
"solid",
"dotted",
"dotdash",
"dashed",
"blank"))
self$.addOption(private$..switch)
self$.addOption(private$..outcome_variable)
self$.addOption(private$..cases)
self$.addOption(private$..not_cases)
self$.addOption(private$..case_label)
self$.addOption(private$..not_case_label)
self$.addOption(private$..outcome_variable_name)
self$.addOption(private$..count_NA)
self$.addOption(private$..conf_level)
self$.addOption(private$..show_details)
self$.addOption(private$..plot_possible)
self$.addOption(private$..evaluate_hypotheses)
self$.addOption(private$..null_value)
self$.addOption(private$..null_boundary)
self$.addOption(private$..alpha)
self$.addOption(private$..null_color)
self$.addOption(private$..es_plot_width)
self$.addOption(private$..es_plot_height)
self$.addOption(private$..ymin)
self$.addOption(private$..ymax)
self$.addOption(private$..breaks)
self$.addOption(private$..ylab)
self$.addOption(private$..xlab)
self$.addOption(private$..axis.text.y)
self$.addOption(private$..axis.title.y)
self$.addOption(private$..axis.text.x)
self$.addOption(private$..axis.title.x)
self$.addOption(private$..error_layout)
self$.addOption(private$..shape_summary)
self$.addOption(private$..color_summary)
self$.addOption(private$..fill_summary)
self$.addOption(private$..size_summary)
self$.addOption(private$..alpha_summary)
self$.addOption(private$..linetype_summary)
}),
active = list(
switch = function() private$..switch$value,
outcome_variable = function() private$..outcome_variable$value,
cases = function() private$..cases$value,
not_cases = function() private$..not_cases$value,
case_label = function() private$..case_label$value,
not_case_label = function() private$..not_case_label$value,
outcome_variable_name = function() private$..outcome_variable_name$value,
count_NA = function() private$..count_NA$value,
conf_level = function() private$..conf_level$value,
show_details = function() private$..show_details$value,
plot_possible = function() private$..plot_possible$value,
evaluate_hypotheses = function() private$..evaluate_hypotheses$value,
null_value = function() private$..null_value$value,
null_boundary = function() private$..null_boundary$value,
alpha = function() private$..alpha$value,
null_color = function() private$..null_color$value,
es_plot_width = function() private$..es_plot_width$value,
es_plot_height = function() private$..es_plot_height$value,
ymin = function() private$..ymin$value,
ymax = function() private$..ymax$value,
breaks = function() private$..breaks$value,
ylab = function() private$..ylab$value,
xlab = function() private$..xlab$value,
axis.text.y = function() private$..axis.text.y$value,
axis.title.y = function() private$..axis.title.y$value,
axis.text.x = function() private$..axis.text.x$value,
axis.title.x = function() private$..axis.title.x$value,
error_layout = function() private$..error_layout$value,
shape_summary = function() private$..shape_summary$value,
color_summary = function() private$..color_summary$value,
fill_summary = function() private$..fill_summary$value,
size_summary = function() private$..size_summary$value,
alpha_summary = function() private$..alpha_summary$value,
linetype_summary = function() private$..linetype_summary$value),
private = list(
..switch = NA,
..outcome_variable = NA,
..cases = NA,
..not_cases = NA,
..case_label = NA,
..not_case_label = NA,
..outcome_variable_name = NA,
..count_NA = NA,
..conf_level = NA,
..show_details = NA,
..plot_possible = NA,
..evaluate_hypotheses = NA,
..null_value = NA,
..null_boundary = NA,
..alpha = NA,
..null_color = NA,
..es_plot_width = NA,
..es_plot_height = NA,
..ymin = NA,
..ymax = NA,
..breaks = NA,
..ylab = NA,
..xlab = NA,
..axis.text.y = NA,
..axis.title.y = NA,
..axis.text.x = NA,
..axis.title.x = NA,
..error_layout = NA,
..shape_summary = NA,
..color_summary = NA,
..fill_summary = NA,
..size_summary = NA,
..alpha_summary = NA,
..linetype_summary = NA)
)
jamoviproportionResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamoviproportionResults",
inherit = jmvcore::Group,
active = list(
debug = function() private$.items[["debug"]],
help = function() private$.items[["help"]],
overview = function() private$.items[["overview"]],
point_null = function() private$.items[["point_null"]],
interval_null = function() private$.items[["interval_null"]],
magnitude_plot_warnings = function() private$.items[["magnitude_plot_warnings"]],
estimation_plots = function() private$.items[["estimation_plots"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Proportions: Single Group")
self$add(jmvcore::Preformatted$new(
options=options,
name="debug",
visible=TRUE))
self$add(jmvcore::Html$new(
options=options,
name="help",
visible=FALSE))
self$add(jmvcore::Table$new(
options=options,
name="overview",
title="Overview",
rows=1,
refs="prop1",
clearWith=list(
"outcome_variable",
"cases",
"not_cases",
"case_label",
"not_case_label",
"outcome_variable_name",
"count_NA",
"conf_level",
"show_details"),
columns=list(
list(
`name`="outcome_variable_name",
`title`="Outcome variable",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="outcome_variable_level",
`type`="text",
`title`="Level"),
list(
`name`="cases",
`title`="Cases",
`type`="integer"),
list(
`name`="n",
`title`="<i>N</i>",
`type`="integer"),
list(
`name`="P",
`title`="<i>P</i>",
`type`="number"),
list(
`name`="P_LL",
`title`="LL",
`type`="number"),
list(
`name`="P_UL",
`title`="UL",
`type`="number"),
list(
`name`="P_SE",
`type`="number",
`title`="<i>SE</i><sub>Proportion</sub>",
`visible`="(show_details)"),
list(
`name`="P_adjusted",
`type`="number",
`title`="<i>P</i><sub>adjusted</sub>",
`visible`="(show_details)"))))
self$add(jmvcore::Table$new(
options=options,
name="point_null",
title="Hypothesis Evaluation",
rows=1,
visible="(evaluate_hypotheses & null_boundary == 0)",
clearWith=list(
"outcome_variable",
"cases",
"not_cases",
"case_label",
"not_case_label",
"outcome_variable_name",
"count_NA",
"conf_level",
"show_details",
"null_value",
"null_boundary"),
columns=list(
list(
`name`="effect_plus",
`title`="Effect",
`type`="text",
`combineBelow`=FALSE),
list(
`name`="null_words",
`title`="<i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="CI",
`title`="CI",
`type`="text"),
list(
`name`="CI_compare",
`title`="Compare CI with <i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="t",
`title`="<i>z</i>"),
list(
`name`="p",
`title`="<i>p</i>, two tailed",
`type`="number",
`format`="zto,pvalue"),
list(
`name`="null_decision",
`title`="<i>H</i><sub>0</sub> decision"),
list(
`name`="conclusion",
`title`="Conclusion",
`type`="text"))))
self$add(jmvcore::Table$new(
options=options,
name="interval_null",
title="Hypothesis Evaluation",
rows=1,
visible="(evaluate_hypotheses & null_boundary != 0)",
clearWith=list(
"outcome_variable",
"cases",
"not_cases",
"case_label",
"not_case_label",
"outcome_variable_name",
"count_NA",
"conf_level",
"show_details",
"null_value",
"null_boundary"),
columns=list(
list(
`name`="effect_plus",
`title`="Effect",
`type`="text",
`combineBelow`=FALSE),
list(
`name`="rope",
`title`="<i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="CI",
`title`="CI",
`type`="text"),
list(
`name`="rope_compare",
`title`="Compare CI with <i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="p_result",
`title`="<i>p</i>, two tailed",
`type`="text"),
list(
`name`="conclusion",
`title`="Conclusion",
`type`="text"))))
self$add(jmvcore::Html$new(
options=options,
name="magnitude_plot_warnings",
title="Figure Warnings",
visible=TRUE))
self$add(jmvcore::Array$new(
options=options,
name="estimation_plots",
title="Estimation Figure",
refs="ggdist",
template=jmvcore::Image$new(
options=options,
title="$key",
width=300,
height=450,
requiresData=TRUE,
renderFun=".estimation_plots")))}))
jamoviproportionBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamoviproportionBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "esci",
name = "jamoviproportion",
version = c(1,0,0),
options = options,
results = jamoviproportionResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
#' Proportions: Single Group
#'
#'
#' @param switch .
#' @param data .
#' @param outcome_variable .
#' @param cases .
#' @param not_cases .
#' @param case_label .
#' @param not_case_label .
#' @param outcome_variable_name .
#' @param count_NA .
#' @param conf_level .
#' @param show_details .
#' @param plot_possible .
#' @param evaluate_hypotheses .
#' @param null_value .
#' @param null_boundary .
#' @param alpha .
#' @param null_color .
#' @param es_plot_width .
#' @param es_plot_height .
#' @param ymin .
#' @param ymax .
#' @param breaks .
#' @param ylab .
#' @param xlab .
#' @param axis.text.y .
#' @param axis.title.y .
#' @param axis.text.x .
#' @param axis.title.x .
#' @param error_layout .
#' @param shape_summary .
#' @param color_summary .
#' @param fill_summary .
#' @param size_summary .
#' @param alpha_summary .
#' @param linetype_summary .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$debug} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$help} \tab \tab \tab \tab \tab a html \cr
#' \code{results$overview} \tab \tab \tab \tab \tab a table \cr
#' \code{results$point_null} \tab \tab \tab \tab \tab a table \cr
#' \code{results$interval_null} \tab \tab \tab \tab \tab a table \cr
#' \code{results$magnitude_plot_warnings} \tab \tab \tab \tab \tab a html \cr
#' \code{results$estimation_plots} \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$overview$asDF}
#'
#' \code{as.data.frame(results$overview)}
#'
#' @export
jamoviproportion <- function(
switch = "from_raw",
data,
outcome_variable,
cases = " ",
not_cases = " ",
case_label = "Affected",
not_case_label = "Not Affected",
outcome_variable_name = "My outcome variable",
count_NA = FALSE,
conf_level = 95,
show_details = FALSE,
plot_possible = FALSE,
evaluate_hypotheses = FALSE,
null_value = "0",
null_boundary = "0",
alpha = 0.05,
null_color = "#A40122",
es_plot_width = "300",
es_plot_height = "400",
ymin = "0",
ymax = "1",
breaks = "auto",
ylab = "auto",
xlab = "auto",
axis.text.y = "14",
axis.title.y = "15",
axis.text.x = "14",
axis.title.x = "15",
error_layout = "none",
shape_summary = "circle filled",
color_summary = "#008DF9",
fill_summary = "#008DF9",
size_summary = "4",
alpha_summary = "1",
linetype_summary = "solid") {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("jamoviproportion requires jmvcore to be installed (restart may be required)")
if ( ! missing(outcome_variable)) outcome_variable <- jmvcore::resolveQuo(jmvcore::enquo(outcome_variable))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(outcome_variable), outcome_variable, NULL))
for (v in outcome_variable) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
options <- jamoviproportionOptions$new(
switch = switch,
outcome_variable = outcome_variable,
cases = cases,
not_cases = not_cases,
case_label = case_label,
not_case_label = not_case_label,
outcome_variable_name = outcome_variable_name,
count_NA = count_NA,
conf_level = conf_level,
show_details = show_details,
plot_possible = plot_possible,
evaluate_hypotheses = evaluate_hypotheses,
null_value = null_value,
null_boundary = null_boundary,
alpha = alpha,
null_color = null_color,
es_plot_width = es_plot_width,
es_plot_height = es_plot_height,
ymin = ymin,
ymax = ymax,
breaks = breaks,
ylab = ylab,
xlab = xlab,
axis.text.y = axis.text.y,
axis.title.y = axis.title.y,
axis.text.x = axis.text.x,
axis.title.x = axis.title.x,
error_layout = error_layout,
shape_summary = shape_summary,
color_summary = color_summary,
fill_summary = fill_summary,
size_summary = size_summary,
alpha_summary = alpha_summary,
linetype_summary = linetype_summary)
analysis <- jamoviproportionClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
rcalinjageman/esci documentation built on March 29, 2024, 7:30 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions jamoviproportion
Documented in jamoviproportion
# This file is automatically generated, you probably don't want to edit this
jamoviproportionOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamoviproportionOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
switch = "from_raw",
outcome_variable = NULL,
cases = " ",
not_cases = " ",
case_label = "Affected",
not_case_label = "Not Affected",
outcome_variable_name = "My outcome variable",
count_NA = FALSE,
conf_level = 95,
show_details = FALSE,
plot_possible = FALSE,
evaluate_hypotheses = FALSE,
null_value = "0",
null_boundary = "0",
alpha = 0.05,
null_color = "#A40122",
es_plot_width = "300",
es_plot_height = "400",
ymin = "0",
ymax = "1",
breaks = "auto",
ylab = "auto",
xlab = "auto",
axis.text.y = "14",
axis.title.y = "15",
axis.text.x = "14",
axis.title.x = "15",
error_layout = "none",
shape_summary = "circle filled",
color_summary = "#008DF9",
fill_summary = "#008DF9",
size_summary = "4",
alpha_summary = "1",
linetype_summary = "solid", ...) {
super$initialize(
package="esci",
name="jamoviproportion",
requiresData=TRUE,
...)
private$..switch <- jmvcore::OptionList$new(
"switch",
switch,
default="from_raw",
options=list(
"from_raw",
"from_summary"))
private$..outcome_variable <- jmvcore::OptionVariables$new(
"outcome_variable",
outcome_variable,
suggested=list(
"nominal",
"ordinal"),
permitted=list(
"factor"))
private$..cases <- jmvcore::OptionString$new(
"cases",
cases,
default=" ")
private$..not_cases <- jmvcore::OptionString$new(
"not_cases",
not_cases,
default=" ")
private$..case_label <- jmvcore::OptionString$new(
"case_label",
case_label,
default="Affected")
private$..not_case_label <- jmvcore::OptionString$new(
"not_case_label",
not_case_label,
default="Not Affected")
private$..outcome_variable_name <- jmvcore::OptionString$new(
"outcome_variable_name",
outcome_variable_name,
default="My outcome variable")
private$..count_NA <- jmvcore::OptionBool$new(
"count_NA",
count_NA,
default=FALSE)
private$..conf_level <- jmvcore::OptionNumber$new(
"conf_level",
conf_level,
default=95)
private$..show_details <- jmvcore::OptionBool$new(
"show_details",
show_details,
default=FALSE)
private$..plot_possible <- jmvcore::OptionBool$new(
"plot_possible",
plot_possible,
default=FALSE)
private$..evaluate_hypotheses <- jmvcore::OptionBool$new(
"evaluate_hypotheses",
evaluate_hypotheses,
default=FALSE)
private$..null_value <- jmvcore::OptionString$new(
"null_value",
null_value,
default="0")
private$..null_boundary <- jmvcore::OptionString$new(
"null_boundary",
null_boundary,
default="0")
private$..alpha <- jmvcore::OptionNumber$new(
"alpha",
alpha,
default=0.05)
private$..null_color <- jmvcore::OptionList$new(
"null_color",
null_color,
default="#A40122",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..es_plot_width <- jmvcore::OptionString$new(
"es_plot_width",
es_plot_width,
default="300")
private$..es_plot_height <- jmvcore::OptionString$new(
"es_plot_height",
es_plot_height,
default="400")
private$..ymin <- jmvcore::OptionString$new(
"ymin",
ymin,
default="0")
private$..ymax <- jmvcore::OptionString$new(
"ymax",
ymax,
default="1")
private$..breaks <- jmvcore::OptionString$new(
"breaks",
breaks,
default="auto")
private$..ylab <- jmvcore::OptionString$new(
"ylab",
ylab,
default="auto")
private$..xlab <- jmvcore::OptionString$new(
"xlab",
xlab,
default="auto")
private$..axis.text.y <- jmvcore::OptionString$new(
"axis.text.y",
axis.text.y,
default="14")
private$..axis.title.y <- jmvcore::OptionString$new(
"axis.title.y",
axis.title.y,
default="15")
private$..axis.text.x <- jmvcore::OptionString$new(
"axis.text.x",
axis.text.x,
default="14")
private$..axis.title.x <- jmvcore::OptionString$new(
"axis.title.x",
axis.title.x,
default="15")
private$..error_layout <- jmvcore::OptionList$new(
"error_layout",
error_layout,
default="none",
options=list(
"none"))
private$..shape_summary <- jmvcore::OptionList$new(
"shape_summary",
shape_summary,
default="circle filled",
options=list(
"circle filled",
"square filled",
"triangle filled",
"diamond filled"))
private$..color_summary <- jmvcore::OptionList$new(
"color_summary",
color_summary,
default="#008DF9",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..fill_summary <- jmvcore::OptionList$new(
"fill_summary",
fill_summary,
default="#008DF9",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..size_summary <- jmvcore::OptionList$new(
"size_summary",
size_summary,
default="4",
options=list(
"1",
"2",
"3",
"4",
"5",
"6"))
private$..alpha_summary <- jmvcore::OptionList$new(
"alpha_summary",
alpha_summary,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..linetype_summary <- jmvcore::OptionList$new(
"linetype_summary",
linetype_summary,
default="solid",
options=list(
"solid",
"dotted",
"dotdash",
"dashed",
"blank"))
self$.addOption(private$..switch)
self$.addOption(private$..outcome_variable)
self$.addOption(private$..cases)
self$.addOption(private$..not_cases)
self$.addOption(private$..case_label)
self$.addOption(private$..not_case_label)
self$.addOption(private$..outcome_variable_name)
self$.addOption(private$..count_NA)
self$.addOption(private$..conf_level)
self$.addOption(private$..show_details)
self$.addOption(private$..plot_possible)
self$.addOption(private$..evaluate_hypotheses)
self$.addOption(private$..null_value)
self$.addOption(private$..null_boundary)
self$.addOption(private$..alpha)
self$.addOption(private$..null_color)
self$.addOption(private$..es_plot_width)
self$.addOption(private$..es_plot_height)
self$.addOption(private$..ymin)
self$.addOption(private$..ymax)
self$.addOption(private$..breaks)
self$.addOption(private$..ylab)
self$.addOption(private$..xlab)
self$.addOption(private$..axis.text.y)
self$.addOption(private$..axis.title.y)
self$.addOption(private$..axis.text.x)
self$.addOption(private$..axis.title.x)
self$.addOption(private$..error_layout)
self$.addOption(private$..shape_summary)
self$.addOption(private$..color_summary)
self$.addOption(private$..fill_summary)
self$.addOption(private$..size_summary)
self$.addOption(private$..alpha_summary)
self$.addOption(private$..linetype_summary)
}),
active = list(
switch = function() private$..switch$value,
outcome_variable = function() private$..outcome_variable$value,
cases = function() private$..cases$value,
not_cases = function() private$..not_cases$value,
case_label = function() private$..case_label$value,
not_case_label = function() private$..not_case_label$value,
outcome_variable_name = function() private$..outcome_variable_name$value,
count_NA = function() private$..count_NA$value,
conf_level = function() private$..conf_level$value,
show_details = function() private$..show_details$value,
plot_possible = function() private$..plot_possible$value,
evaluate_hypotheses = function() private$..evaluate_hypotheses$value,
null_value = function() private$..null_value$value,
null_boundary = function() private$..null_boundary$value,
alpha = function() private$..alpha$value,
null_color = function() private$..null_color$value,
es_plot_width = function() private$..es_plot_width$value,
es_plot_height = function() private$..es_plot_height$value,
ymin = function() private$..ymin$value,
ymax = function() private$..ymax$value,
breaks = function() private$..breaks$value,
ylab = function() private$..ylab$value,
xlab = function() private$..xlab$value,
axis.text.y = function() private$..axis.text.y$value,
axis.title.y = function() private$..axis.title.y$value,
axis.text.x = function() private$..axis.text.x$value,
axis.title.x = function() private$..axis.title.x$value,
error_layout = function() private$..error_layout$value,
shape_summary = function() private$..shape_summary$value,
color_summary = function() private$..color_summary$value,
fill_summary = function() private$..fill_summary$value,
size_summary = function() private$..size_summary$value,
alpha_summary = function() private$..alpha_summary$value,
linetype_summary = function() private$..linetype_summary$value),
private = list(
..switch = NA,
..outcome_variable = NA,
..cases = NA,
..not_cases = NA,
..case_label = NA,
..not_case_label = NA,
..outcome_variable_name = NA,
..count_NA = NA,
..conf_level = NA,
..show_details = NA,
..plot_possible = NA,
..evaluate_hypotheses = NA,
..null_value = NA,
..null_boundary = NA,
..alpha = NA,
..null_color = NA,
..es_plot_width = NA,
..es_plot_height = NA,
..ymin = NA,
..ymax = NA,
..breaks = NA,
..ylab = NA,
..xlab = NA,
..axis.text.y = NA,
..axis.title.y = NA,
..axis.text.x = NA,
..axis.title.x = NA,
..error_layout = NA,
..shape_summary = NA,
..color_summary = NA,
..fill_summary = NA,
..size_summary = NA,
..alpha_summary = NA,
..linetype_summary = NA)
)
jamoviproportionResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamoviproportionResults",
inherit = jmvcore::Group,
active = list(
debug = function() private$.items[["debug"]],
help = function() private$.items[["help"]],
overview = function() private$.items[["overview"]],
point_null = function() private$.items[["point_null"]],
interval_null = function() private$.items[["interval_null"]],
magnitude_plot_warnings = function() private$.items[["magnitude_plot_warnings"]],
estimation_plots = function() private$.items[["estimation_plots"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Proportions: Single Group")
self$add(jmvcore::Preformatted$new(
options=options,
name="debug",
visible=TRUE))
self$add(jmvcore::Html$new(
options=options,
name="help",
visible=FALSE))
self$add(jmvcore::Table$new(
options=options,
name="overview",
title="Overview",
rows=1,
refs="prop1",
clearWith=list(
"outcome_variable",
"cases",
"not_cases",
"case_label",
"not_case_label",
"outcome_variable_name",
"count_NA",
"conf_level",
"show_details"),
columns=list(
list(
`name`="outcome_variable_name",
`title`="Outcome variable",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="outcome_variable_level",
`type`="text",
`title`="Level"),
list(
`name`="cases",
`title`="Cases",
`type`="integer"),
list(
`name`="n",
`title`="<i>N</i>",
`type`="integer"),
list(
`name`="P",
`title`="<i>P</i>",
`type`="number"),
list(
`name`="P_LL",
`title`="LL",
`type`="number"),
list(
`name`="P_UL",
`title`="UL",
`type`="number"),
list(
`name`="P_SE",
`type`="number",
`title`="<i>SE</i><sub>Proportion</sub>",
`visible`="(show_details)"),
list(
`name`="P_adjusted",
`type`="number",
`title`="<i>P</i><sub>adjusted</sub>",
`visible`="(show_details)"))))
self$add(jmvcore::Table$new(
options=options,
name="point_null",
title="Hypothesis Evaluation",
rows=1,
visible="(evaluate_hypotheses & null_boundary == 0)",
clearWith=list(
"outcome_variable",
"cases",
"not_cases",
"case_label",
"not_case_label",
"outcome_variable_name",
"count_NA",
"conf_level",
"show_details",
"null_value",
"null_boundary"),
columns=list(
list(
`name`="effect_plus",
`title`="Effect",
`type`="text",
`combineBelow`=FALSE),
list(
`name`="null_words",
`title`="<i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="CI",
`title`="CI",
`type`="text"),
list(
`name`="CI_compare",
`title`="Compare CI with <i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="t",
`title`="<i>z</i>"),
list(
`name`="p",
`title`="<i>p</i>, two tailed",
`type`="number",
`format`="zto,pvalue"),
list(
`name`="null_decision",
`title`="<i>H</i><sub>0</sub> decision"),
list(
`name`="conclusion",
`title`="Conclusion",
`type`="text"))))
self$add(jmvcore::Table$new(
options=options,
name="interval_null",
title="Hypothesis Evaluation",
rows=1,
visible="(evaluate_hypotheses & null_boundary != 0)",
clearWith=list(
"outcome_variable",
"cases",
"not_cases",
"case_label",
"not_case_label",
"outcome_variable_name",
"count_NA",
"conf_level",
"show_details",
"null_value",
"null_boundary"),
columns=list(
list(
`name`="effect_plus",
`title`="Effect",
`type`="text",
`combineBelow`=FALSE),
list(
`name`="rope",
`title`="<i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="CI",
`title`="CI",
`type`="text"),
list(
`name`="rope_compare",
`title`="Compare CI with <i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="p_result",
`title`="<i>p</i>, two tailed",
`type`="text"),
list(
`name`="conclusion",
`title`="Conclusion",
`type`="text"))))
self$add(jmvcore::Html$new(
options=options,
name="magnitude_plot_warnings",
title="Figure Warnings",
visible=TRUE))
self$add(jmvcore::Array$new(
options=options,
name="estimation_plots",
title="Estimation Figure",
refs="ggdist",
template=jmvcore::Image$new(
options=options,
title="$key",
width=300,
height=450,
requiresData=TRUE,
renderFun=".estimation_plots")))}))
jamoviproportionBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamoviproportionBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "esci",
name = "jamoviproportion",
version = c(1,0,0),
options = options,
results = jamoviproportionResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
#' Proportions: Single Group
#'
#'
#' @param switch .
#' @param data .
#' @param outcome_variable .
#' @param cases .
#' @param not_cases .
#' @param case_label .
#' @param not_case_label .
#' @param outcome_variable_name .
#' @param count_NA .
#' @param conf_level .
#' @param show_details .
#' @param plot_possible .
#' @param evaluate_hypotheses .
#' @param null_value .
#' @param null_boundary .
#' @param alpha .
#' @param null_color .
#' @param es_plot_width .
#' @param es_plot_height .
#' @param ymin .
#' @param ymax .
#' @param breaks .
#' @param ylab .
#' @param xlab .
#' @param axis.text.y .
#' @param axis.title.y .
#' @param axis.text.x .
#' @param axis.title.x .
#' @param error_layout .
#' @param shape_summary .
#' @param color_summary .
#' @param fill_summary .
#' @param size_summary .
#' @param alpha_summary .
#' @param linetype_summary .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$debug} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$help} \tab \tab \tab \tab \tab a html \cr
#' \code{results$overview} \tab \tab \tab \tab \tab a table \cr
#' \code{results$point_null} \tab \tab \tab \tab \tab a table \cr
#' \code{results$interval_null} \tab \tab \tab \tab \tab a table \cr
#' \code{results$magnitude_plot_warnings} \tab \tab \tab \tab \tab a html \cr
#' \code{results$estimation_plots} \tab \tab \tab \tab \tab an array of images \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$overview$asDF}
#'
#' \code{as.data.frame(results$overview)}
#'
#' @export
jamoviproportion <- function(
switch = "from_raw",
data,
outcome_variable,
cases = " ",
not_cases = " ",
case_label = "Affected",
not_case_label = "Not Affected",
outcome_variable_name = "My outcome variable",
count_NA = FALSE,
conf_level = 95,
show_details = FALSE,
plot_possible = FALSE,
evaluate_hypotheses = FALSE,
null_value = "0",
null_boundary = "0",
alpha = 0.05,
null_color = "#A40122",
es_plot_width = "300",
es_plot_height = "400",
ymin = "0",
ymax = "1",
breaks = "auto",
ylab = "auto",
xlab = "auto",
axis.text.y = "14",
axis.title.y = "15",
axis.text.x = "14",
axis.title.x = "15",
error_layout = "none",
shape_summary = "circle filled",
color_summary = "#008DF9",
fill_summary = "#008DF9",
size_summary = "4",
alpha_summary = "1",
linetype_summary = "solid") {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("jamoviproportion requires jmvcore to be installed (restart may be required)")
if ( ! missing(outcome_variable)) outcome_variable <- jmvcore::resolveQuo(jmvcore::enquo(outcome_variable))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(outcome_variable), outcome_variable, NULL))
for (v in outcome_variable) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
options <- jamoviproportionOptions$new(
switch = switch,
outcome_variable = outcome_variable,
cases = cases,
not_cases = not_cases,
case_label = case_label,
not_case_label = not_case_label,
outcome_variable_name = outcome_variable_name,
count_NA = count_NA,
conf_level = conf_level,
show_details = show_details,
plot_possible = plot_possible,
evaluate_hypotheses = evaluate_hypotheses,
null_value = null_value,
null_boundary = null_boundary,
alpha = alpha,
null_color = null_color,
es_plot_width = es_plot_width,
es_plot_height = es_plot_height,
ymin = ymin,
ymax = ymax,
breaks = breaks,
ylab = ylab,
xlab = xlab,
axis.text.y = axis.text.y,
axis.title.y = axis.title.y,
axis.text.x = axis.text.x,
axis.title.x = axis.title.x,
error_layout = error_layout,
shape_summary = shape_summary,
color_summary = color_summary,
fill_summary = fill_summary,
size_summary = size_summary,
alpha_summary = alpha_summary,
linetype_summary = linetype_summary)
analysis <- jamoviproportionClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.