R/jamovipdifftwo.h.R
In rcalinjageman/esci: Estimation Statistics with Confidence Intervals
Defines functions
jamovipdifftwo
Documented in
jamovipdifftwo
# This file is automatically generated, you probably don't want to edit this
jamovipdifftwoOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamovipdifftwoOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
switch = "from_raw",
outcome_variable = NULL,
grouping_variable = NULL,
comparison_cases = " ",
comparison_not_cases = " ",
reference_cases = " ",
reference_not_cases = " ",
case_label = "Sick",
not_case_label = "Well",
grouping_variable_level1 = "Treated",
grouping_variable_level2 = "Control",
outcome_variable_name = "Outcome variable",
grouping_variable_name = "Grouping variable",
count_NA = FALSE,
show_ratio = FALSE,
show_chi_square = FALSE,
chi_table_option = "both",
show_phi = FALSE,
conf_level = 95,
show_details = FALSE,
evaluate_hypotheses = FALSE,
null_value = "0",
null_boundary = "0",
alpha = 0.05,
null_color = "#A40122",
es_plot_width = "400",
es_plot_height = "450",
ymin = "auto",
ymax = "auto",
ybreaks = "auto",
ylab = "auto",
xlab = "auto",
axis.text.y = "14",
axis.title.y = "15",
axis.text.x = "14",
axis.title.x = "15",
simple_contrast_labels = TRUE,
error_layout = "none",
difference_axis_breaks = "auto",
shape_summary_reference = "circle filled",
shape_summary_comparison = "circle filled",
shape_summary_difference = "triangle filled",
color_summary_reference = "#008DF9",
color_summary_comparison = "#009F81",
color_summary_difference = "black",
fill_summary_reference = "#008DF9",
fill_summary_comparison = "#009F81",
fill_summary_difference = "black",
size_summary_reference = "4",
size_summary_comparison = "4",
size_summary_difference = "4",
alpha_summary_reference = "1",
alpha_summary_comparison = "1",
alpha_summary_difference = "1",
linetype_summary_reference = "solid",
linetype_summary_comparison = "solid",
linetype_summary_difference = "solid", ...) {
super$initialize(
package="esci",
name="jamovipdifftwo",
requiresData=TRUE,
...)
private$..switch <- jmvcore::OptionList$new(
"switch",
switch,
default="from_raw",
options=list(
"from_raw",
"from_summary"))
private$..outcome_variable <- jmvcore::OptionVariables$new(
"outcome_variable",
outcome_variable,
suggested=list(
"nominal",
"ordinal"),
permitted=list(
"factor"))
private$..grouping_variable <- jmvcore::OptionVariable$new(
"grouping_variable",
grouping_variable,
suggested=list(
"nominal",
"ordinal"),
permitted=list(
"factor"))
private$..comparison_cases <- jmvcore::OptionString$new(
"comparison_cases",
comparison_cases,
default=" ")
private$..comparison_not_cases <- jmvcore::OptionString$new(
"comparison_not_cases",
comparison_not_cases,
default=" ")
private$..reference_cases <- jmvcore::OptionString$new(
"reference_cases",
reference_cases,
default=" ")
private$..reference_not_cases <- jmvcore::OptionString$new(
"reference_not_cases",
reference_not_cases,
default=" ")
private$..case_label <- jmvcore::OptionString$new(
"case_label",
case_label,
default="Sick")
private$..not_case_label <- jmvcore::OptionString$new(
"not_case_label",
not_case_label,
default="Well")
private$..grouping_variable_level1 <- jmvcore::OptionString$new(
"grouping_variable_level1",
grouping_variable_level1,
default="Treated")
private$..grouping_variable_level2 <- jmvcore::OptionString$new(
"grouping_variable_level2",
grouping_variable_level2,
default="Control")
private$..outcome_variable_name <- jmvcore::OptionString$new(
"outcome_variable_name",
outcome_variable_name,
default="Outcome variable")
private$..grouping_variable_name <- jmvcore::OptionString$new(
"grouping_variable_name",
grouping_variable_name,
default="Grouping variable")
private$..count_NA <- jmvcore::OptionBool$new(
"count_NA",
count_NA,
default=FALSE)
private$..show_ratio <- jmvcore::OptionBool$new(
"show_ratio",
show_ratio,
default=FALSE)
private$..show_chi_square <- jmvcore::OptionBool$new(
"show_chi_square",
show_chi_square,
default=FALSE)
private$..chi_table_option <- jmvcore::OptionList$new(
"chi_table_option",
chi_table_option,
options=list(
"observed",
"expected",
"both"),
default="both")
private$..show_phi <- jmvcore::OptionBool$new(
"show_phi",
show_phi,
default=FALSE)
private$..conf_level <- jmvcore::OptionNumber$new(
"conf_level",
conf_level,
default=95)
private$..show_details <- jmvcore::OptionBool$new(
"show_details",
show_details,
default=FALSE)
private$..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$new(
"es_plot_width",
es_plot_width,
default="400")
private$..es_plot_height <- jmvcore::OptionString$new(
"es_plot_height",
es_plot_height,
default="450")
private$..ymin <- jmvcore::OptionString$new(
"ymin",
ymin,
default="auto")
private$..ymax <- jmvcore::OptionString$new(
"ymax",
ymax,
default="auto")
private$..ybreaks <- jmvcore::OptionString$new(
"ybreaks",
ybreaks,
default="auto")
private$..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$new(
"axis.title.x",
axis.title.x,
default="15")
private$..simple_contrast_labels <- jmvcore::OptionBool$new(
"simple_contrast_labels",
simple_contrast_labels,
default=TRUE)
private$..error_layout <- jmvcore::OptionList$new(
"error_layout",
error_layout,
default="none",
options=list(
"none"))
private$..difference_axis_breaks <- jmvcore::OptionString$new(
"difference_axis_breaks",
difference_axis_breaks,
default="auto")
private$..shape_summary_reference <- jmvcore::OptionList$new(
"shape_summary_reference",
shape_summary_reference,
default="circle filled",
options=list(
"circle filled",
"square filled",
"triangle filled",
"diamond filled"))
private$..shape_summary_comparison <- jmvcore::OptionList$new(
"shape_summary_comparison",
shape_summary_comparison,
default="circle filled",
options=list(
"circle filled",
"square filled",
"triangle filled",
"diamond filled"))
private$..shape_summary_difference <- jmvcore::OptionList$new(
"shape_summary_difference",
shape_summary_difference,
default="triangle filled",
options=list(
"circle filled",
"square filled",
"triangle filled",
"diamond filled"))
private$..color_summary_reference <- jmvcore::OptionList$new(
"color_summary_reference",
color_summary_reference,
default="#008DF9",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..color_summary_comparison <- jmvcore::OptionList$new(
"color_summary_comparison",
color_summary_comparison,
default="#009F81",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..color_summary_difference <- jmvcore::OptionList$new(
"color_summary_difference",
color_summary_difference,
default="black",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..fill_summary_reference <- jmvcore::OptionList$new(
"fill_summary_reference",
fill_summary_reference,
default="#008DF9",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..fill_summary_comparison <- jmvcore::OptionList$new(
"fill_summary_comparison",
fill_summary_comparison,
default="#009F81",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..fill_summary_difference <- jmvcore::OptionList$new(
"fill_summary_difference",
fill_summary_difference,
default="black",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..size_summary_reference <- jmvcore::OptionList$new(
"size_summary_reference",
size_summary_reference,
default="4",
options=list(
"1",
"2",
"3",
"4",
"5",
"6"))
private$..size_summary_comparison <- jmvcore::OptionList$new(
"size_summary_comparison",
size_summary_comparison,
default="4",
options=list(
"1",
"2",
"3",
"4",
"5",
"6"))
private$..size_summary_difference <- jmvcore::OptionList$new(
"size_summary_difference",
size_summary_difference,
default="4",
options=list(
"1",
"2",
"3",
"4",
"5",
"6"))
private$..alpha_summary_reference <- jmvcore::OptionList$new(
"alpha_summary_reference",
alpha_summary_reference,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_summary_comparison <- jmvcore::OptionList$new(
"alpha_summary_comparison",
alpha_summary_comparison,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_summary_difference <- jmvcore::OptionList$new(
"alpha_summary_difference",
alpha_summary_difference,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..linetype_summary_reference <- jmvcore::OptionList$new(
"linetype_summary_reference",
linetype_summary_reference,
default="solid",
options=list(
"solid",
"dotted",
"dotdash",
"dashed",
"blank"))
private$..linetype_summary_comparison <- jmvcore::OptionList$new(
"linetype_summary_comparison",
linetype_summary_comparison,
default="solid",
options=list(
"solid",
"dotted",
"dotdash",
"dashed",
"blank"))
private$..linetype_summary_difference <- jmvcore::OptionList$new(
"linetype_summary_difference",
linetype_summary_difference,
default="solid",
options=list(
"solid",
"dotted",
"dotdash",
"dashed",
"blank"))
self$.addOption(private$..switch)
self$.addOption(private$..outcome_variable)
self$.addOption(private$..grouping_variable)
self$.addOption(private$..comparison_cases)
self$.addOption(private$..comparison_not_cases)
self$.addOption(private$..reference_cases)
self$.addOption(private$..reference_not_cases)
self$.addOption(private$..case_label)
self$.addOption(private$..not_case_label)
self$.addOption(private$..grouping_variable_level1)
self$.addOption(private$..grouping_variable_level2)
self$.addOption(private$..outcome_variable_name)
self$.addOption(private$..grouping_variable_name)
self$.addOption(private$..count_NA)
self$.addOption(private$..show_ratio)
self$.addOption(private$..show_chi_square)
self$.addOption(private$..chi_table_option)
self$.addOption(private$..show_phi)
self$.addOption(private$..conf_level)
self$.addOption(private$..show_details)
self$.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$..ybreaks)
self$.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$..simple_contrast_labels)
self$.addOption(private$..error_layout)
self$.addOption(private$..difference_axis_breaks)
self$.addOption(private$..shape_summary_reference)
self$.addOption(private$..shape_summary_comparison)
self$.addOption(private$..shape_summary_difference)
self$.addOption(private$..color_summary_reference)
self$.addOption(private$..color_summary_comparison)
self$.addOption(private$..color_summary_difference)
self$.addOption(private$..fill_summary_reference)
self$.addOption(private$..fill_summary_comparison)
self$.addOption(private$..fill_summary_difference)
self$.addOption(private$..size_summary_reference)
self$.addOption(private$..size_summary_comparison)
self$.addOption(private$..size_summary_difference)
self$.addOption(private$..alpha_summary_reference)
self$.addOption(private$..alpha_summary_comparison)
self$.addOption(private$..alpha_summary_difference)
self$.addOption(private$..linetype_summary_reference)
self$.addOption(private$..linetype_summary_comparison)
self$.addOption(private$..linetype_summary_difference)
}),
active = list(
switch = function() private$..switch$value,
outcome_variable = function() private$..outcome_variable$value,
grouping_variable = function() private$..grouping_variable$value,
comparison_cases = function() private$..comparison_cases$value,
comparison_not_cases = function() private$..comparison_not_cases$value,
reference_cases = function() private$..reference_cases$value,
reference_not_cases = function() private$..reference_not_cases$value,
case_label = function() private$..case_label$value,
not_case_label = function() private$..not_case_label$value,
grouping_variable_level1 = function() private$..grouping_variable_level1$value,
grouping_variable_level2 = function() private$..grouping_variable_level2$value,
outcome_variable_name = function() private$..outcome_variable_name$value,
grouping_variable_name = function() private$..grouping_variable_name$value,
count_NA = function() private$..count_NA$value,
show_ratio = function() private$..show_ratio$value,
show_chi_square = function() private$..show_chi_square$value,
chi_table_option = function() private$..chi_table_option$value,
show_phi = function() private$..show_phi$value,
conf_level = function() private$..conf_level$value,
show_details = function() private$..show_details$value,
evaluate_hypotheses = function() private$..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$value,
ybreaks = function() private$..ybreaks$value,
ylab = function() private$..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$value,
simple_contrast_labels = function() private$..simple_contrast_labels$value,
error_layout = function() private$..error_layout$value,
difference_axis_breaks = function() private$..difference_axis_breaks$value,
shape_summary_reference = function() private$..shape_summary_reference$value,
shape_summary_comparison = function() private$..shape_summary_comparison$value,
shape_summary_difference = function() private$..shape_summary_difference$value,
color_summary_reference = function() private$..color_summary_reference$value,
color_summary_comparison = function() private$..color_summary_comparison$value,
color_summary_difference = function() private$..color_summary_difference$value,
fill_summary_reference = function() private$..fill_summary_reference$value,
fill_summary_comparison = function() private$..fill_summary_comparison$value,
fill_summary_difference = function() private$..fill_summary_difference$value,
size_summary_reference = function() private$..size_summary_reference$value,
size_summary_comparison = function() private$..size_summary_comparison$value,
size_summary_difference = function() private$..size_summary_difference$value,
alpha_summary_reference = function() private$..alpha_summary_reference$value,
alpha_summary_comparison = function() private$..alpha_summary_comparison$value,
alpha_summary_difference = function() private$..alpha_summary_difference$value,
linetype_summary_reference = function() private$..linetype_summary_reference$value,
linetype_summary_comparison = function() private$..linetype_summary_comparison$value,
linetype_summary_difference = function() private$..linetype_summary_difference$value),
private = list(
..switch = NA,
..outcome_variable = NA,
..grouping_variable = NA,
..comparison_cases = NA,
..comparison_not_cases = NA,
..reference_cases = NA,
..reference_not_cases = NA,
..case_label = NA,
..not_case_label = NA,
..grouping_variable_level1 = NA,
..grouping_variable_level2 = NA,
..outcome_variable_name = NA,
..grouping_variable_name = NA,
..count_NA = NA,
..show_ratio = NA,
..show_chi_square = NA,
..chi_table_option = NA,
..show_phi = NA,
..conf_level = NA,
..show_details = NA,
..evaluate_hypotheses = NA,
..null_value = NA,
..null_boundary = NA,
..alpha = NA,
..null_color = NA,
..es_plot_width = NA,
..es_plot_height = NA,
..ymin = NA,
..ymax = NA,
..ybreaks = NA,
..ylab = NA,
..xlab = NA,
..axis.text.y = NA,
..axis.title.y = NA,
..axis.text.x = NA,
..axis.title.x = NA,
..simple_contrast_labels = NA,
..error_layout = NA,
..difference_axis_breaks = NA,
..shape_summary_reference = NA,
..shape_summary_comparison = NA,
..shape_summary_difference = NA,
..color_summary_reference = NA,
..color_summary_comparison = NA,
..color_summary_difference = NA,
..fill_summary_reference = NA,
..fill_summary_comparison = NA,
..fill_summary_difference = NA,
..size_summary_reference = NA,
..size_summary_comparison = NA,
..size_summary_difference = NA,
..alpha_summary_reference = NA,
..alpha_summary_comparison = NA,
..alpha_summary_difference = NA,
..linetype_summary_reference = NA,
..linetype_summary_comparison = NA,
..linetype_summary_difference = NA)
)
jamovipdifftwoResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamovipdifftwoResults",
inherit = jmvcore::Group,
active = list(
debug = function() private$.items[["debug"]],
help = function() private$.items[["help"]],
overview = function() private$.items[["overview"]],
es_proportion_difference = function() private$.items[["es_proportion_difference"]],
contingency_table = function() private$.items[["contingency_table"]],
es_phi = function() private$.items[["es_phi"]],
es_odds_ratio = function() private$.items[["es_odds_ratio"]],
point_null = function() private$.items[["point_null"]],
interval_null = function() private$.items[["interval_null"]],
estimation_plot_warnings = function() private$.items[["estimation_plot_warnings"]],
estimation_plots = function() private$.items[["estimation_plots"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Proportions: Two Groups")
self$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$new(
options=options,
name="overview",
title="Overview",
rows=1,
clearWith=list(
"outcome_variable",
"grouping_variable",
"comparison_cases",
"comparison_not_cases",
"reference_cases",
"reference_not_cases",
"case_label",
"not_case_label",
"grouping_variable_level1",
"grouping_variable_level2",
"outcome_variable_name",
"grouping_variable_name",
"count_NA",
"conf_level",
"show_details"),
columns=list(
list(
`name`="grouping_variable_name",
`title`="Grouping variable",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="grouping_variable_level",
`title`="Grouping variable level",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="outcome_variable_name",
`title`="Outcome variable",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="outcome_variable_level",
`title`="Outcome variable level",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="cases",
`title`="Cases",
`type`="integer"),
list(
`name`="n",
`title`="<i>n</i>",
`type`="integer"),
list(
`name`="P",
`title`="<i>P</i>",
`type`="number"),
list(
`name`="P_LL",
`title`="LL",
`type`="number"),
list(
`name`="P_UL",
`title`="UL",
`type`="number"),
list(
`name`="P_SE",
`type`="number",
`title`="<i>SE</i><sub>Proportion</sub>",
`visible`="(show_details)"),
list(
`name`="P_adjusted",
`type`="number",
`title`="<i>P</i><sub>adjusted</sub>",
`visible`="(show_details)"))))
self$add(jmvcore::Table$new(
options=options,
name="es_proportion_difference",
title="Proportion Difference",
rows=3,
refs="prop1",
clearWith=list(
"outcome_variable",
"grouping_variable",
"comparison_cases",
"comparison_not_cases",
"reference_cases",
"reference_not_cases",
"case_label",
"not_case_label",
"grouping_variable_level1",
"grouping_variable_level2",
"outcome_variable_name",
"grouping_variable_name",
"count_NA",
"conf_level",
"show_details"),
columns=list(
list(
`name`="grouping_variable_name",
`title`="Grouping variable",
`type`="text",
`combineBelow`=TRUE,
`visible`=FALSE),
list(
`name`="outcome_variable_name",
`title`="Outcome variable",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="effect",
`title`="Effect",
`type`="text",
`visible`=FALSE),
list(
`name`="effect_plus",
`title`="Effect",
`type`="text"),
list(
`name`="effect_size",
`type`="number",
`title`="<i>P</i>"),
list(
`name`="LL",
`title`="LL",
`type`="number"),
list(
`name`="UL",
`title`="UL",
`type`="number"),
list(
`name`="SE",
`title`="<i>SE</i>",
`type`="number",
`visible`="(show_details)"),
list(
`name`="effect_size_adjusted",
`title`="<i>P</i><sub>adjusted</sub>",
`type`="number",
`visible`="(show_details)"))))
self$add(jmvcore::Table$new(
options=options,
name="contingency_table",
title="Chi-Square Analysis",
rows=0,
visible="(show_chi_square)",
clearWith=list(
"outcome_variable",
"grouping_variable",
"comparison_cases",
"comparison_not_cases",
"reference_cases",
"reference_not_cases",
"case_label",
"not_case_label",
"grouping_variable_level1",
"grouping_variable_level2",
"outcome_variable_name",
"grouping_variable_name",
"count_NA",
"conf_level",
"show_details"),
columns=list(
list(
`name`="outcome_variable_level",
`title`="Outcome variable level",
`type`="text"))))
self$add(jmvcore::Table$new(
options=options,
name="es_phi",
title="Correlation",
rows=1,
visible="(show_phi)",
clearWith=list(
"outcome_variable",
"grouping_variable",
"comparison_cases",
"comparison_not_cases",
"reference_cases",
"reference_not_cases",
"case_label",
"not_case_label",
"grouping_variable_level1",
"grouping_variable_level2",
"outcome_variable_name",
"grouping_variable_name",
"count_NA",
"conf_level",
"show_details"),
columns=list(
list(
`name`="grouping_variable_name",
`title`="Grouping variable",
`type`="text",
`combineBelow`=TRUE,
`visible`=FALSE),
list(
`name`="outcome_variable_name",
`title`="Outcome variable",
`type`="text",
`combineBelow`=TRUE,
`visible`=FALSE),
list(
`name`="effect",
`title`="Effect",
`type`="text"),
list(
`name`="effect_size",
`type`="number",
`title`="ϕ"),
list(
`name`="LL",
`title`="LL",
`type`="number"),
list(
`name`="UL",
`title`="UL",
`type`="number"),
list(
`name`="SE",
`title`="<i>SE</i>",
`type`="number",
`visible`="(show_details)"))))
self$add(jmvcore::Table$new(
options=options,
name="es_odds_ratio",
title="Odds Ratio",
rows=1,
visible=TRUE,
clearWith=list(
"outcome_variable",
"grouping_variable",
"comparison_cases",
"comparison_not_cases",
"reference_cases",
"reference_not_cases",
"case_label",
"not_case_label",
"grouping_variable_level1",
"grouping_variable_level2",
"outcome_variable_name",
"grouping_variable_name",
"count_NA",
"conf_level",
"show_details"),
columns=list(
list(
`name`="grouping_variable_name",
`title`="Grouping variable",
`type`="text",
`combineBelow`=TRUE,
`visible`=FALSE),
list(
`name`="outcome_variable_name",
`title`="Outcome variable",
`type`="text"),
list(
`name`="effect",
`title`="Effect",
`type`="text",
`visible`=FALSE),
list(
`name`="effect_plus",
`title`="Effect",
`type`="text"),
list(
`name`="effect_size",
`type`="number",
`title`="<i>OR</i>"),
list(
`name`="LL",
`title`="LL",
`type`="number"),
list(
`name`="UL",
`title`="UL",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="point_null",
title="Hypothesis Evaluation",
rows=1,
visible="(evaluate_hypotheses & null_boundary == 0)",
clearWith=list(
"outcome_variable",
"grouping_variable",
"comparison_cases",
"comparison_not_cases",
"reference_cases",
"reference_not_cases",
"case_label",
"not_case_label",
"grouping_variable_level1",
"grouping_variable_level2",
"outcome_variable_name",
"grouping_variable_name",
"count_NA",
"conf_level",
"show_details",
"null_value",
"null_boundary"),
columns=list(
list(
`name`="outcome_variable_name",
`title`="Outcome variable",
`visible`=TRUE,
`type`="text",
`combineBelow`=TRUE),
list(
`name`="effect",
`title`="Effect",
`type`="text",
`visible`=FALSE,
`combineBelow`=FALSE),
list(
`name`="effect_plus",
`title`="Effect",
`type`="text",
`combineBelow`=FALSE),
list(
`name`="null_words",
`title`="<i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="CI",
`title`="CI",
`type`="text"),
list(
`name`="CI_compare",
`title`="Compare CI with <i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="t",
`title`="<i>z</i>",
`type`="number"),
list(
`name`="p",
`title`="<i>p</i>, two-tailed",
`type`="number",
`format`="zto,pvalue"),
list(
`name`="null_decision",
`title`="<i>H</i><sub>0</sub> decision"),
list(
`name`="conclusion",
`title`="Conclusion",
`type`="text"))))
self$add(jmvcore::Table$new(
options=options,
name="interval_null",
title="Hypothesis Evaluation",
rows=1,
visible="(evaluate_hypotheses & null_boundary != 0)",
columns=list(
list(
`name`="outcome_variable_name",
`title`="Outcome variable",
`visible`=TRUE,
`type`="text",
`combineBelow`=TRUE),
list(
`name`="effect_plus",
`title`="Effect",
`type`="text",
`combineBelow`=FALSE),
list(
`name`="rope",
`title`="<i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="CI",
`title`="CI",
`type`="text"),
list(
`name`="rope_compare",
`title`="Compare CI with <i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="p_result",
`title`="<i>p</i>, two tailed",
`type`="text"),
list(
`name`="conclusion",
`title`="Conclusion",
`type`="text"))))
self$add(jmvcore::Html$new(
options=options,
name="estimation_plot_warnings",
title="Estimation Figure Warnings",
visible=TRUE))
self$add(jmvcore::Array$new(
options=options,
name="estimation_plots",
title="Estimation Figure",
refs="ggdist",
template=jmvcore::Image$new(
options=options,
title="$key",
width=300,
height=450,
requiresData=TRUE,
renderFun=".estimation_plots")))}))
jamovipdifftwoBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamovipdifftwoBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "esci",
name = "jamovipdifftwo",
version = c(1,0,0),
options = options,
results = jamovipdifftwoResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
#' Proportions: Two Groups
#'
#'
#' @param switch .
#' @param data .
#' @param outcome_variable .
#' @param grouping_variable .
#' @param comparison_cases .
#' @param comparison_not_cases .
#' @param reference_cases .
#' @param reference_not_cases .
#' @param case_label .
#' @param not_case_label .
#' @param grouping_variable_level1 .
#' @param grouping_variable_level2 .
#' @param outcome_variable_name .
#' @param grouping_variable_name .
#' @param count_NA .
#' @param show_ratio .
#' @param show_chi_square .
#' @param chi_table_option .
#' @param show_phi .
#' @param conf_level .
#' @param show_details .
#' @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 ybreaks .
#' @param ylab .
#' @param xlab .
#' @param axis.text.y .
#' @param axis.title.y .
#' @param axis.text.x .
#' @param axis.title.x .
#' @param simple_contrast_labels .
#' @param error_layout .
#' @param difference_axis_breaks .
#' @param shape_summary_reference .
#' @param shape_summary_comparison .
#' @param shape_summary_difference .
#' @param color_summary_reference .
#' @param color_summary_comparison .
#' @param color_summary_difference .
#' @param fill_summary_reference .
#' @param fill_summary_comparison .
#' @param fill_summary_difference .
#' @param size_summary_reference .
#' @param size_summary_comparison .
#' @param size_summary_difference .
#' @param alpha_summary_reference .
#' @param alpha_summary_comparison .
#' @param alpha_summary_difference .
#' @param linetype_summary_reference .
#' @param linetype_summary_comparison .
#' @param linetype_summary_difference .
#' @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$es_proportion_difference} \tab \tab \tab \tab \tab a table \cr
#' \code{results$contingency_table} \tab \tab \tab \tab \tab a table \cr
#' \code{results$es_phi} \tab \tab \tab \tab \tab a table \cr
#' \code{results$es_odds_ratio} \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$estimation_plot_warnings} \tab \tab \tab \tab \tab a html \cr
#' \code{results$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
jamovipdifftwo <- function(
switch = "from_raw",
data,
outcome_variable,
grouping_variable,
comparison_cases = " ",
comparison_not_cases = " ",
reference_cases = " ",
reference_not_cases = " ",
case_label = "Sick",
not_case_label = "Well",
grouping_variable_level1 = "Treated",
grouping_variable_level2 = "Control",
outcome_variable_name = "Outcome variable",
grouping_variable_name = "Grouping variable",
count_NA = FALSE,
show_ratio = FALSE,
show_chi_square = FALSE,
chi_table_option = "both",
show_phi = FALSE,
conf_level = 95,
show_details = FALSE,
evaluate_hypotheses = FALSE,
null_value = "0",
null_boundary = "0",
alpha = 0.05,
null_color = "#A40122",
es_plot_width = "400",
es_plot_height = "450",
ymin = "auto",
ymax = "auto",
ybreaks = "auto",
ylab = "auto",
xlab = "auto",
axis.text.y = "14",
axis.title.y = "15",
axis.text.x = "14",
axis.title.x = "15",
simple_contrast_labels = TRUE,
error_layout = "none",
difference_axis_breaks = "auto",
shape_summary_reference = "circle filled",
shape_summary_comparison = "circle filled",
shape_summary_difference = "triangle filled",
color_summary_reference = "#008DF9",
color_summary_comparison = "#009F81",
color_summary_difference = "black",
fill_summary_reference = "#008DF9",
fill_summary_comparison = "#009F81",
fill_summary_difference = "black",
size_summary_reference = "4",
size_summary_comparison = "4",
size_summary_difference = "4",
alpha_summary_reference = "1",
alpha_summary_comparison = "1",
alpha_summary_difference = "1",
linetype_summary_reference = "solid",
linetype_summary_comparison = "solid",
linetype_summary_difference = "solid") {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("jamovipdifftwo requires jmvcore to be installed (restart may be required)")
if ( ! missing(outcome_variable)) outcome_variable <- jmvcore::resolveQuo(jmvcore::enquo(outcome_variable))
if ( ! missing(grouping_variable)) grouping_variable <- jmvcore::resolveQuo(jmvcore::enquo(grouping_variable))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(outcome_variable), outcome_variable, NULL),
`if`( ! missing(grouping_variable), grouping_variable, NULL))
for (v in outcome_variable) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
for (v in grouping_variable) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
options <- jamovipdifftwoOptions$new(
switch = switch,
outcome_variable = outcome_variable,
grouping_variable = grouping_variable,
comparison_cases = comparison_cases,
comparison_not_cases = comparison_not_cases,
reference_cases = reference_cases,
reference_not_cases = reference_not_cases,
case_label = case_label,
not_case_label = not_case_label,
grouping_variable_level1 = grouping_variable_level1,
grouping_variable_level2 = grouping_variable_level2,
outcome_variable_name = outcome_variable_name,
grouping_variable_name = grouping_variable_name,
count_NA = count_NA,
show_ratio = show_ratio,
show_chi_square = show_chi_square,
chi_table_option = chi_table_option,
show_phi = show_phi,
conf_level = conf_level,
show_details = show_details,
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,
ybreaks = ybreaks,
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,
simple_contrast_labels = simple_contrast_labels,
error_layout = error_layout,
difference_axis_breaks = difference_axis_breaks,
shape_summary_reference = shape_summary_reference,
shape_summary_comparison = shape_summary_comparison,
shape_summary_difference = shape_summary_difference,
color_summary_reference = color_summary_reference,
color_summary_comparison = color_summary_comparison,
color_summary_difference = color_summary_difference,
fill_summary_reference = fill_summary_reference,
fill_summary_comparison = fill_summary_comparison,
fill_summary_difference = fill_summary_difference,
size_summary_reference = size_summary_reference,
size_summary_comparison = size_summary_comparison,
size_summary_difference = size_summary_difference,
alpha_summary_reference = alpha_summary_reference,
alpha_summary_comparison = alpha_summary_comparison,
alpha_summary_difference = alpha_summary_difference,
linetype_summary_reference = linetype_summary_reference,
linetype_summary_comparison = linetype_summary_comparison,
linetype_summary_difference = linetype_summary_difference)
analysis <- jamovipdifftwoClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
rcalinjageman/esci documentation built on March 29, 2024, 7:30 p.m.
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Defines functions jamovipdifftwo
Documented in jamovipdifftwo
# This file is automatically generated, you probably don't want to edit this
jamovipdifftwoOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamovipdifftwoOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
switch = "from_raw",
outcome_variable = NULL,
grouping_variable = NULL,
comparison_cases = " ",
comparison_not_cases = " ",
reference_cases = " ",
reference_not_cases = " ",
case_label = "Sick",
not_case_label = "Well",
grouping_variable_level1 = "Treated",
grouping_variable_level2 = "Control",
outcome_variable_name = "Outcome variable",
grouping_variable_name = "Grouping variable",
count_NA = FALSE,
show_ratio = FALSE,
show_chi_square = FALSE,
chi_table_option = "both",
show_phi = FALSE,
conf_level = 95,
show_details = FALSE,
evaluate_hypotheses = FALSE,
null_value = "0",
null_boundary = "0",
alpha = 0.05,
null_color = "#A40122",
es_plot_width = "400",
es_plot_height = "450",
ymin = "auto",
ymax = "auto",
ybreaks = "auto",
ylab = "auto",
xlab = "auto",
axis.text.y = "14",
axis.title.y = "15",
axis.text.x = "14",
axis.title.x = "15",
simple_contrast_labels = TRUE,
error_layout = "none",
difference_axis_breaks = "auto",
shape_summary_reference = "circle filled",
shape_summary_comparison = "circle filled",
shape_summary_difference = "triangle filled",
color_summary_reference = "#008DF9",
color_summary_comparison = "#009F81",
color_summary_difference = "black",
fill_summary_reference = "#008DF9",
fill_summary_comparison = "#009F81",
fill_summary_difference = "black",
size_summary_reference = "4",
size_summary_comparison = "4",
size_summary_difference = "4",
alpha_summary_reference = "1",
alpha_summary_comparison = "1",
alpha_summary_difference = "1",
linetype_summary_reference = "solid",
linetype_summary_comparison = "solid",
linetype_summary_difference = "solid", ...) {
super$initialize(
package="esci",
name="jamovipdifftwo",
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$..grouping_variable <- jmvcore::OptionVariable$new(
"grouping_variable",
grouping_variable,
suggested=list(
"nominal",
"ordinal"),
permitted=list(
"factor"))
private$..comparison_cases <- jmvcore::OptionString$new(
"comparison_cases",
comparison_cases,
default=" ")
private$..comparison_not_cases <- jmvcore::OptionString$new(
"comparison_not_cases",
comparison_not_cases,
default=" ")
private$..reference_cases <- jmvcore::OptionString$new(
"reference_cases",
reference_cases,
default=" ")
private$..reference_not_cases <- jmvcore::OptionString$new(
"reference_not_cases",
reference_not_cases,
default=" ")
private$..case_label <- jmvcore::OptionString$new(
"case_label",
case_label,
default="Sick")
private$..not_case_label <- jmvcore::OptionString$new(
"not_case_label",
not_case_label,
default="Well")
private$..grouping_variable_level1 <- jmvcore::OptionString$new(
"grouping_variable_level1",
grouping_variable_level1,
default="Treated")
private$..grouping_variable_level2 <- jmvcore::OptionString$new(
"grouping_variable_level2",
grouping_variable_level2,
default="Control")
private$..outcome_variable_name <- jmvcore::OptionString$new(
"outcome_variable_name",
outcome_variable_name,
default="Outcome variable")
private$..grouping_variable_name <- jmvcore::OptionString$new(
"grouping_variable_name",
grouping_variable_name,
default="Grouping variable")
private$..count_NA <- jmvcore::OptionBool$new(
"count_NA",
count_NA,
default=FALSE)
private$..show_ratio <- jmvcore::OptionBool$new(
"show_ratio",
show_ratio,
default=FALSE)
private$..show_chi_square <- jmvcore::OptionBool$new(
"show_chi_square",
show_chi_square,
default=FALSE)
private$..chi_table_option <- jmvcore::OptionList$new(
"chi_table_option",
chi_table_option,
options=list(
"observed",
"expected",
"both"),
default="both")
private$..show_phi <- jmvcore::OptionBool$new(
"show_phi",
show_phi,
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$..evaluate_hypotheses <- jmvcore::OptionBool$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="400")
private$..es_plot_height <- jmvcore::OptionString$new(
"es_plot_height",
es_plot_height,
default="450")
private$..ymin <- jmvcore::OptionString$new(
"ymin",
ymin,
default="auto")
private$..ymax <- jmvcore::OptionString$new(
"ymax",
ymax,
default="auto")
private$..ybreaks <- jmvcore::OptionString$new(
"ybreaks",
ybreaks,
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$..simple_contrast_labels <- jmvcore::OptionBool$new(
"simple_contrast_labels",
simple_contrast_labels,
default=TRUE)
private$..error_layout <- jmvcore::OptionList$new(
"error_layout",
error_layout,
default="none",
options=list(
"none"))
private$..difference_axis_breaks <- jmvcore::OptionString$new(
"difference_axis_breaks",
difference_axis_breaks,
default="auto")
private$..shape_summary_reference <- jmvcore::OptionList$new(
"shape_summary_reference",
shape_summary_reference,
default="circle filled",
options=list(
"circle filled",
"square filled",
"triangle filled",
"diamond filled"))
private$..shape_summary_comparison <- jmvcore::OptionList$new(
"shape_summary_comparison",
shape_summary_comparison,
default="circle filled",
options=list(
"circle filled",
"square filled",
"triangle filled",
"diamond filled"))
private$..shape_summary_difference <- jmvcore::OptionList$new(
"shape_summary_difference",
shape_summary_difference,
default="triangle filled",
options=list(
"circle filled",
"square filled",
"triangle filled",
"diamond filled"))
private$..color_summary_reference <- jmvcore::OptionList$new(
"color_summary_reference",
color_summary_reference,
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$..color_summary_comparison <- jmvcore::OptionList$new(
"color_summary_comparison",
color_summary_comparison,
default="#009F81",
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$..color_summary_difference <- jmvcore::OptionList$new(
"color_summary_difference",
color_summary_difference,
default="black",
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$..fill_summary_reference <- jmvcore::OptionList$new(
"fill_summary_reference",
fill_summary_reference,
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$..fill_summary_comparison <- jmvcore::OptionList$new(
"fill_summary_comparison",
fill_summary_comparison,
default="#009F81",
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$..fill_summary_difference <- jmvcore::OptionList$new(
"fill_summary_difference",
fill_summary_difference,
default="black",
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$..size_summary_reference <- jmvcore::OptionList$new(
"size_summary_reference",
size_summary_reference,
default="4",
options=list(
"1",
"2",
"3",
"4",
"5",
"6"))
private$..size_summary_comparison <- jmvcore::OptionList$new(
"size_summary_comparison",
size_summary_comparison,
default="4",
options=list(
"1",
"2",
"3",
"4",
"5",
"6"))
private$..size_summary_difference <- jmvcore::OptionList$new(
"size_summary_difference",
size_summary_difference,
default="4",
options=list(
"1",
"2",
"3",
"4",
"5",
"6"))
private$..alpha_summary_reference <- jmvcore::OptionList$new(
"alpha_summary_reference",
alpha_summary_reference,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_summary_comparison <- jmvcore::OptionList$new(
"alpha_summary_comparison",
alpha_summary_comparison,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_summary_difference <- jmvcore::OptionList$new(
"alpha_summary_difference",
alpha_summary_difference,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..linetype_summary_reference <- jmvcore::OptionList$new(
"linetype_summary_reference",
linetype_summary_reference,
default="solid",
options=list(
"solid",
"dotted",
"dotdash",
"dashed",
"blank"))
private$..linetype_summary_comparison <- jmvcore::OptionList$new(
"linetype_summary_comparison",
linetype_summary_comparison,
default="solid",
options=list(
"solid",
"dotted",
"dotdash",
"dashed",
"blank"))
private$..linetype_summary_difference <- jmvcore::OptionList$new(
"linetype_summary_difference",
linetype_summary_difference,
default="solid",
options=list(
"solid",
"dotted",
"dotdash",
"dashed",
"blank"))
self$.addOption(private$..switch)
self$.addOption(private$..outcome_variable)
self$.addOption(private$..grouping_variable)
self$.addOption(private$..comparison_cases)
self$.addOption(private$..comparison_not_cases)
self$.addOption(private$..reference_cases)
self$.addOption(private$..reference_not_cases)
self$.addOption(private$..case_label)
self$.addOption(private$..not_case_label)
self$.addOption(private$..grouping_variable_level1)
self$.addOption(private$..grouping_variable_level2)
self$.addOption(private$..outcome_variable_name)
self$.addOption(private$..grouping_variable_name)
self$.addOption(private$..count_NA)
self$.addOption(private$..show_ratio)
self$.addOption(private$..show_chi_square)
self$.addOption(private$..chi_table_option)
self$.addOption(private$..show_phi)
self$.addOption(private$..conf_level)
self$.addOption(private$..show_details)
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$.addOption(private$..ybreaks)
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$.addOption(private$..simple_contrast_labels)
self$.addOption(private$..error_layout)
self$.addOption(private$..difference_axis_breaks)
self$.addOption(private$..shape_summary_reference)
self$.addOption(private$..shape_summary_comparison)
self$.addOption(private$..shape_summary_difference)
self$.addOption(private$..color_summary_reference)
self$.addOption(private$..color_summary_comparison)
self$.addOption(private$..color_summary_difference)
self$.addOption(private$..fill_summary_reference)
self$.addOption(private$..fill_summary_comparison)
self$.addOption(private$..fill_summary_difference)
self$.addOption(private$..size_summary_reference)
self$.addOption(private$..size_summary_comparison)
self$.addOption(private$..size_summary_difference)
self$.addOption(private$..alpha_summary_reference)
self$.addOption(private$..alpha_summary_comparison)
self$.addOption(private$..alpha_summary_difference)
self$.addOption(private$..linetype_summary_reference)
self$.addOption(private$..linetype_summary_comparison)
self$.addOption(private$..linetype_summary_difference)
}),
active = list(
switch = function() private$..switch$value,
outcome_variable = function() private$..outcome_variable$value,
grouping_variable = function() private$..grouping_variable$value,
comparison_cases = function() private$..comparison_cases$value,
comparison_not_cases = function() private$..comparison_not_cases$value,
reference_cases = function() private$..reference_cases$value,
reference_not_cases = function() private$..reference_not_cases$value,
case_label = function() private$..case_label$value,
not_case_label = function() private$..not_case_label$value,
grouping_variable_level1 = function() private$..grouping_variable_level1$value,
grouping_variable_level2 = function() private$..grouping_variable_level2$value,
outcome_variable_name = function() private$..outcome_variable_name$value,
grouping_variable_name = function() private$..grouping_variable_name$value,
count_NA = function() private$..count_NA$value,
show_ratio = function() private$..show_ratio$value,
show_chi_square = function() private$..show_chi_square$value,
chi_table_option = function() private$..chi_table_option$value,
show_phi = function() private$..show_phi$value,
conf_level = function() private$..conf_level$value,
show_details = function() private$..show_details$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,
ybreaks = function() private$..ybreaks$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,
simple_contrast_labels = function() private$..simple_contrast_labels$value,
error_layout = function() private$..error_layout$value,
difference_axis_breaks = function() private$..difference_axis_breaks$value,
shape_summary_reference = function() private$..shape_summary_reference$value,
shape_summary_comparison = function() private$..shape_summary_comparison$value,
shape_summary_difference = function() private$..shape_summary_difference$value,
color_summary_reference = function() private$..color_summary_reference$value,
color_summary_comparison = function() private$..color_summary_comparison$value,
color_summary_difference = function() private$..color_summary_difference$value,
fill_summary_reference = function() private$..fill_summary_reference$value,
fill_summary_comparison = function() private$..fill_summary_comparison$value,
fill_summary_difference = function() private$..fill_summary_difference$value,
size_summary_reference = function() private$..size_summary_reference$value,
size_summary_comparison = function() private$..size_summary_comparison$value,
size_summary_difference = function() private$..size_summary_difference$value,
alpha_summary_reference = function() private$..alpha_summary_reference$value,
alpha_summary_comparison = function() private$..alpha_summary_comparison$value,
alpha_summary_difference = function() private$..alpha_summary_difference$value,
linetype_summary_reference = function() private$..linetype_summary_reference$value,
linetype_summary_comparison = function() private$..linetype_summary_comparison$value,
linetype_summary_difference = function() private$..linetype_summary_difference$value),
private = list(
..switch = NA,
..outcome_variable = NA,
..grouping_variable = NA,
..comparison_cases = NA,
..comparison_not_cases = NA,
..reference_cases = NA,
..reference_not_cases = NA,
..case_label = NA,
..not_case_label = NA,
..grouping_variable_level1 = NA,
..grouping_variable_level2 = NA,
..outcome_variable_name = NA,
..grouping_variable_name = NA,
..count_NA = NA,
..show_ratio = NA,
..show_chi_square = NA,
..chi_table_option = NA,
..show_phi = NA,
..conf_level = NA,
..show_details = 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,
..ybreaks = NA,
..ylab = NA,
..xlab = NA,
..axis.text.y = NA,
..axis.title.y = NA,
..axis.text.x = NA,
..axis.title.x = NA,
..simple_contrast_labels = NA,
..error_layout = NA,
..difference_axis_breaks = NA,
..shape_summary_reference = NA,
..shape_summary_comparison = NA,
..shape_summary_difference = NA,
..color_summary_reference = NA,
..color_summary_comparison = NA,
..color_summary_difference = NA,
..fill_summary_reference = NA,
..fill_summary_comparison = NA,
..fill_summary_difference = NA,
..size_summary_reference = NA,
..size_summary_comparison = NA,
..size_summary_difference = NA,
..alpha_summary_reference = NA,
..alpha_summary_comparison = NA,
..alpha_summary_difference = NA,
..linetype_summary_reference = NA,
..linetype_summary_comparison = NA,
..linetype_summary_difference = NA)
)
jamovipdifftwoResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamovipdifftwoResults",
inherit = jmvcore::Group,
active = list(
debug = function() private$.items[["debug"]],
help = function() private$.items[["help"]],
overview = function() private$.items[["overview"]],
es_proportion_difference = function() private$.items[["es_proportion_difference"]],
contingency_table = function() private$.items[["contingency_table"]],
es_phi = function() private$.items[["es_phi"]],
es_odds_ratio = function() private$.items[["es_odds_ratio"]],
point_null = function() private$.items[["point_null"]],
interval_null = function() private$.items[["interval_null"]],
estimation_plot_warnings = function() private$.items[["estimation_plot_warnings"]],
estimation_plots = function() private$.items[["estimation_plots"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Proportions: Two Groups")
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,
clearWith=list(
"outcome_variable",
"grouping_variable",
"comparison_cases",
"comparison_not_cases",
"reference_cases",
"reference_not_cases",
"case_label",
"not_case_label",
"grouping_variable_level1",
"grouping_variable_level2",
"outcome_variable_name",
"grouping_variable_name",
"count_NA",
"conf_level",
"show_details"),
columns=list(
list(
`name`="grouping_variable_name",
`title`="Grouping variable",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="grouping_variable_level",
`title`="Grouping variable level",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="outcome_variable_name",
`title`="Outcome variable",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="outcome_variable_level",
`title`="Outcome variable level",
`type`="text",
`combineBelow`=TRUE),
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="es_proportion_difference",
title="Proportion Difference",
rows=3,
refs="prop1",
clearWith=list(
"outcome_variable",
"grouping_variable",
"comparison_cases",
"comparison_not_cases",
"reference_cases",
"reference_not_cases",
"case_label",
"not_case_label",
"grouping_variable_level1",
"grouping_variable_level2",
"outcome_variable_name",
"grouping_variable_name",
"count_NA",
"conf_level",
"show_details"),
columns=list(
list(
`name`="grouping_variable_name",
`title`="Grouping variable",
`type`="text",
`combineBelow`=TRUE,
`visible`=FALSE),
list(
`name`="outcome_variable_name",
`title`="Outcome variable",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="effect",
`title`="Effect",
`type`="text",
`visible`=FALSE),
list(
`name`="effect_plus",
`title`="Effect",
`type`="text"),
list(
`name`="effect_size",
`type`="number",
`title`="<i>P</i>"),
list(
`name`="LL",
`title`="LL",
`type`="number"),
list(
`name`="UL",
`title`="UL",
`type`="number"),
list(
`name`="SE",
`title`="<i>SE</i>",
`type`="number",
`visible`="(show_details)"),
list(
`name`="effect_size_adjusted",
`title`="<i>P</i><sub>adjusted</sub>",
`type`="number",
`visible`="(show_details)"))))
self$add(jmvcore::Table$new(
options=options,
name="contingency_table",
title="Chi-Square Analysis",
rows=0,
visible="(show_chi_square)",
clearWith=list(
"outcome_variable",
"grouping_variable",
"comparison_cases",
"comparison_not_cases",
"reference_cases",
"reference_not_cases",
"case_label",
"not_case_label",
"grouping_variable_level1",
"grouping_variable_level2",
"outcome_variable_name",
"grouping_variable_name",
"count_NA",
"conf_level",
"show_details"),
columns=list(
list(
`name`="outcome_variable_level",
`title`="Outcome variable level",
`type`="text"))))
self$add(jmvcore::Table$new(
options=options,
name="es_phi",
title="Correlation",
rows=1,
visible="(show_phi)",
clearWith=list(
"outcome_variable",
"grouping_variable",
"comparison_cases",
"comparison_not_cases",
"reference_cases",
"reference_not_cases",
"case_label",
"not_case_label",
"grouping_variable_level1",
"grouping_variable_level2",
"outcome_variable_name",
"grouping_variable_name",
"count_NA",
"conf_level",
"show_details"),
columns=list(
list(
`name`="grouping_variable_name",
`title`="Grouping variable",
`type`="text",
`combineBelow`=TRUE,
`visible`=FALSE),
list(
`name`="outcome_variable_name",
`title`="Outcome variable",
`type`="text",
`combineBelow`=TRUE,
`visible`=FALSE),
list(
`name`="effect",
`title`="Effect",
`type`="text"),
list(
`name`="effect_size",
`type`="number",
`title`="ϕ"),
list(
`name`="LL",
`title`="LL",
`type`="number"),
list(
`name`="UL",
`title`="UL",
`type`="number"),
list(
`name`="SE",
`title`="<i>SE</i>",
`type`="number",
`visible`="(show_details)"))))
self$add(jmvcore::Table$new(
options=options,
name="es_odds_ratio",
title="Odds Ratio",
rows=1,
visible=TRUE,
clearWith=list(
"outcome_variable",
"grouping_variable",
"comparison_cases",
"comparison_not_cases",
"reference_cases",
"reference_not_cases",
"case_label",
"not_case_label",
"grouping_variable_level1",
"grouping_variable_level2",
"outcome_variable_name",
"grouping_variable_name",
"count_NA",
"conf_level",
"show_details"),
columns=list(
list(
`name`="grouping_variable_name",
`title`="Grouping variable",
`type`="text",
`combineBelow`=TRUE,
`visible`=FALSE),
list(
`name`="outcome_variable_name",
`title`="Outcome variable",
`type`="text"),
list(
`name`="effect",
`title`="Effect",
`type`="text",
`visible`=FALSE),
list(
`name`="effect_plus",
`title`="Effect",
`type`="text"),
list(
`name`="effect_size",
`type`="number",
`title`="<i>OR</i>"),
list(
`name`="LL",
`title`="LL",
`type`="number"),
list(
`name`="UL",
`title`="UL",
`type`="number"))))
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",
"grouping_variable",
"comparison_cases",
"comparison_not_cases",
"reference_cases",
"reference_not_cases",
"case_label",
"not_case_label",
"grouping_variable_level1",
"grouping_variable_level2",
"outcome_variable_name",
"grouping_variable_name",
"count_NA",
"conf_level",
"show_details",
"null_value",
"null_boundary"),
columns=list(
list(
`name`="outcome_variable_name",
`title`="Outcome variable",
`visible`=TRUE,
`type`="text",
`combineBelow`=TRUE),
list(
`name`="effect",
`title`="Effect",
`type`="text",
`visible`=FALSE,
`combineBelow`=FALSE),
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>",
`type`="number"),
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)",
columns=list(
list(
`name`="outcome_variable_name",
`title`="Outcome variable",
`visible`=TRUE,
`type`="text",
`combineBelow`=TRUE),
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="estimation_plot_warnings",
title="Estimation 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")))}))
jamovipdifftwoBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamovipdifftwoBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "esci",
name = "jamovipdifftwo",
version = c(1,0,0),
options = options,
results = jamovipdifftwoResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
#' Proportions: Two Groups
#'
#'
#' @param switch .
#' @param data .
#' @param outcome_variable .
#' @param grouping_variable .
#' @param comparison_cases .
#' @param comparison_not_cases .
#' @param reference_cases .
#' @param reference_not_cases .
#' @param case_label .
#' @param not_case_label .
#' @param grouping_variable_level1 .
#' @param grouping_variable_level2 .
#' @param outcome_variable_name .
#' @param grouping_variable_name .
#' @param count_NA .
#' @param show_ratio .
#' @param show_chi_square .
#' @param chi_table_option .
#' @param show_phi .
#' @param conf_level .
#' @param show_details .
#' @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 ybreaks .
#' @param ylab .
#' @param xlab .
#' @param axis.text.y .
#' @param axis.title.y .
#' @param axis.text.x .
#' @param axis.title.x .
#' @param simple_contrast_labels .
#' @param error_layout .
#' @param difference_axis_breaks .
#' @param shape_summary_reference .
#' @param shape_summary_comparison .
#' @param shape_summary_difference .
#' @param color_summary_reference .
#' @param color_summary_comparison .
#' @param color_summary_difference .
#' @param fill_summary_reference .
#' @param fill_summary_comparison .
#' @param fill_summary_difference .
#' @param size_summary_reference .
#' @param size_summary_comparison .
#' @param size_summary_difference .
#' @param alpha_summary_reference .
#' @param alpha_summary_comparison .
#' @param alpha_summary_difference .
#' @param linetype_summary_reference .
#' @param linetype_summary_comparison .
#' @param linetype_summary_difference .
#' @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$overview} \tab \tab \tab \tab \tab a table \cr
#' \code{results$es_proportion_difference} \tab \tab \tab \tab \tab a table \cr
#' \code{results$contingency_table} \tab \tab \tab \tab \tab a table \cr
#' \code{results$es_phi} \tab \tab \tab \tab \tab a table \cr
#' \code{results$es_odds_ratio} \tab \tab \tab \tab \tab a table \cr
#' \code{results$point_null} \tab \tab \tab \tab \tab a table \cr
#' \code{results$interval_null} \tab \tab \tab \tab \tab a table \cr
#' \code{results$estimation_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
jamovipdifftwo <- function(
switch = "from_raw",
data,
outcome_variable,
grouping_variable,
comparison_cases = " ",
comparison_not_cases = " ",
reference_cases = " ",
reference_not_cases = " ",
case_label = "Sick",
not_case_label = "Well",
grouping_variable_level1 = "Treated",
grouping_variable_level2 = "Control",
outcome_variable_name = "Outcome variable",
grouping_variable_name = "Grouping variable",
count_NA = FALSE,
show_ratio = FALSE,
show_chi_square = FALSE,
chi_table_option = "both",
show_phi = FALSE,
conf_level = 95,
show_details = FALSE,
evaluate_hypotheses = FALSE,
null_value = "0",
null_boundary = "0",
alpha = 0.05,
null_color = "#A40122",
es_plot_width = "400",
es_plot_height = "450",
ymin = "auto",
ymax = "auto",
ybreaks = "auto",
ylab = "auto",
xlab = "auto",
axis.text.y = "14",
axis.title.y = "15",
axis.text.x = "14",
axis.title.x = "15",
simple_contrast_labels = TRUE,
error_layout = "none",
difference_axis_breaks = "auto",
shape_summary_reference = "circle filled",
shape_summary_comparison = "circle filled",
shape_summary_difference = "triangle filled",
color_summary_reference = "#008DF9",
color_summary_comparison = "#009F81",
color_summary_difference = "black",
fill_summary_reference = "#008DF9",
fill_summary_comparison = "#009F81",
fill_summary_difference = "black",
size_summary_reference = "4",
size_summary_comparison = "4",
size_summary_difference = "4",
alpha_summary_reference = "1",
alpha_summary_comparison = "1",
alpha_summary_difference = "1",
linetype_summary_reference = "solid",
linetype_summary_comparison = "solid",
linetype_summary_difference = "solid") {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("jamovipdifftwo requires jmvcore to be installed (restart may be required)")
if ( ! missing(outcome_variable)) outcome_variable <- jmvcore::resolveQuo(jmvcore::enquo(outcome_variable))
if ( ! missing(grouping_variable)) grouping_variable <- jmvcore::resolveQuo(jmvcore::enquo(grouping_variable))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(outcome_variable), outcome_variable, NULL),
`if`( ! missing(grouping_variable), grouping_variable, NULL))
for (v in outcome_variable) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
for (v in grouping_variable) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
options <- jamovipdifftwoOptions$new(
switch = switch,
outcome_variable = outcome_variable,
grouping_variable = grouping_variable,
comparison_cases = comparison_cases,
comparison_not_cases = comparison_not_cases,
reference_cases = reference_cases,
reference_not_cases = reference_not_cases,
case_label = case_label,
not_case_label = not_case_label,
grouping_variable_level1 = grouping_variable_level1,
grouping_variable_level2 = grouping_variable_level2,
outcome_variable_name = outcome_variable_name,
grouping_variable_name = grouping_variable_name,
count_NA = count_NA,
show_ratio = show_ratio,
show_chi_square = show_chi_square,
chi_table_option = chi_table_option,
show_phi = show_phi,
conf_level = conf_level,
show_details = show_details,
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,
ybreaks = ybreaks,
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,
simple_contrast_labels = simple_contrast_labels,
error_layout = error_layout,
difference_axis_breaks = difference_axis_breaks,
shape_summary_reference = shape_summary_reference,
shape_summary_comparison = shape_summary_comparison,
shape_summary_difference = shape_summary_difference,
color_summary_reference = color_summary_reference,
color_summary_comparison = color_summary_comparison,
color_summary_difference = color_summary_difference,
fill_summary_reference = fill_summary_reference,
fill_summary_comparison = fill_summary_comparison,
fill_summary_difference = fill_summary_difference,
size_summary_reference = size_summary_reference,
size_summary_comparison = size_summary_comparison,
size_summary_difference = size_summary_difference,
alpha_summary_reference = alpha_summary_reference,
alpha_summary_comparison = alpha_summary_comparison,
alpha_summary_difference = alpha_summary_difference,
linetype_summary_reference = linetype_summary_reference,
linetype_summary_comparison = linetype_summary_comparison,
linetype_summary_difference = linetype_summary_difference)
analysis <- jamovipdifftwoClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
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