Nothing
R/jamovimetapdiff.h.R
In esci: Estimation Statistics with Confidence Intervals
Defines functions
jamovimetapdiff
Documented in
jamovimetapdiff
# This file is automatically generated, you probably don't want to edit this
jamovimetapdiffOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamovimetapdiffOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
reference_cases = NULL,
reference_ns = NULL,
comparison_cases = NULL,
comparison_ns = NULL,
labels = NULL,
moderator = NULL,
effect_label = "My effect",
reported_effect_size = "RD",
conf_level = 95,
random_effects = "random_effects",
include_PIs = FALSE,
show_details = FALSE,
es_plot_width = "600",
es_plot_height = "750",
size_base = "2",
size_multiplier = "3",
axis.text.y = "14",
report_CIs = FALSE,
meta_diamond_height = ".25",
xlab = "auto",
xmin = "auto",
xmax = "auto",
xbreaks = "auto",
mark_zero = FALSE,
axis.text.x = "14",
axis.title.x = "15",
dlab = "auto",
dmin = "auto",
dmax = "auto",
dbreaks = "auto",
shape_raw_reference = "square filled",
shape_raw_comparison = "square filled",
shape_summary_difference = "triangle filled",
shape_raw_unused = "square filled",
color_raw_reference = "#008DF9",
color_raw_comparison = "#009F81",
color_raw_unused = "gray65",
color_summary_reference = "#008DF9",
color_summary_comparison = "#009F81",
color_summary_unused = "gray75",
color_summary_difference = "black",
color_summary_overall = "black",
fill_raw_reference = "#008DF9",
fill_raw_comparison = "#009F81",
fill_raw_unused = "gray65",
fill_summary_reference = "#008DF9",
fill_summary_comparison = "#009F81",
fill_summary_unused = "gray75",
fill_summary_difference = "black",
fill_summary_overall = "black",
alpha_raw_reference = "1",
alpha_raw_comparison = "1",
alpha_raw_unused = "1",
alpha_summary_reference = "1",
alpha_summary_comparison = "1",
alpha_summary_unused = "1",
alpha_summary_difference = "1",
alpha_summary_overall = "1",
linetype_raw_reference = "solid",
linetype_raw_comparison = "solid",
linetype_summary_difference = "solid",
linetype_raw_unused = "solid",
color_interval_reference = "black",
color_interval_comparison = "black",
color_interval_difference = "black",
color_interval_unused = "black",
size_interval_reference = ".50",
size_interval_comparison = ".50",
size_interval_difference = ".50",
size_interval_unused = ".50",
alpha_interval_reference = "1",
alpha_interval_comparison = "1",
alpha_interval_difference = "1",
alpha_interval_unused = "1", ...) {
super$initialize(
package="esci",
name="jamovimetapdiff",
requiresData=TRUE,
...)
private$..reference_cases <- jmvcore::OptionVariable$new(
"reference_cases",
reference_cases,
suggested=list(
"continuous"),
permitted=list(
"numeric"))
private$..reference_ns <- jmvcore::OptionVariable$new(
"reference_ns",
reference_ns,
suggested=list(
"continuous"),
permitted=list(
"numeric"))
private$..comparison_cases <- jmvcore::OptionVariable$new(
"comparison_cases",
comparison_cases,
suggested=list(
"continuous"),
permitted=list(
"numeric"))
private$..comparison_ns <- jmvcore::OptionVariable$new(
"comparison_ns",
comparison_ns,
suggested=list(
"continuous"),
permitted=list(
"numeric"))
private$..labels <- jmvcore::OptionVariable$new(
"labels",
labels,
suggested=list(
"nominal",
"ordinal"),
permitted=list(
"factor"))
private$..moderator <- jmvcore::OptionVariable$new(
"moderator",
moderator,
suggested=list(
"nominal",
"ordinal"),
permitted=list(
"factor"))
private$..effect_label <- jmvcore::OptionString$new(
"effect_label",
effect_label,
default="My effect")
private$..reported_effect_size <- jmvcore::OptionList$new(
"reported_effect_size",
reported_effect_size,
default="RD",
options=list(
"RD",
"RR",
"OR",
"AS",
"PETO"))
private$..conf_level <- jmvcore::OptionNumber$new(
"conf_level",
conf_level,
default=95)
private$..random_effects <- jmvcore::OptionList$new(
"random_effects",
random_effects,
default="random_effects",
options=list(
"random_effects",
"fixed_effects"))
private$..include_PIs <- jmvcore::OptionBool$new(
"include_PIs",
include_PIs,
default=FALSE)
private$..show_details <- jmvcore::OptionBool$new(
"show_details",
show_details,
default=FALSE)
private$..es_plot_width <- jmvcore::OptionString$new(
"es_plot_width",
es_plot_width,
default="600")
private$..es_plot_height <- jmvcore::OptionString$new(
"es_plot_height",
es_plot_height,
default="750")
private$..size_base <- jmvcore::OptionList$new(
"size_base",
size_base,
default="2",
options=list(
".25",
".50",
".75",
"1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"))
private$..size_multiplier <- jmvcore::OptionList$new(
"size_multiplier",
size_multiplier,
default="3",
options=list(
"1",
"1.1",
"1.2",
"1.3",
"1.5",
"1.75",
"2",
"2.5",
"3",
"3.5",
"4",
"4.5",
"5"))
private$..axis.text.y <- jmvcore::OptionString$new(
"axis.text.y",
axis.text.y,
default="14")
private$..report_CIs <- jmvcore::OptionBool$new(
"report_CIs",
report_CIs,
default=FALSE)
private$..meta_diamond_height <- jmvcore::OptionString$new(
"meta_diamond_height",
meta_diamond_height,
default=".25")
private$..xlab <- jmvcore::OptionString$new(
"xlab",
xlab,
default="auto")
private$..xmin <- jmvcore::OptionString$new(
"xmin",
xmin,
default="auto")
private$..xmax <- jmvcore::OptionString$new(
"xmax",
xmax,
default="auto")
private$..xbreaks <- jmvcore::OptionString$new(
"xbreaks",
xbreaks,
default="auto")
private$..mark_zero <- jmvcore::OptionBool$new(
"mark_zero",
mark_zero,
default=FALSE)
private$..axis.text.x <- jmvcore::OptionString$new(
"axis.text.x",
axis.text.x,
default="14")
private$..axis.title.x <- jmvcore::OptionString$new(
"axis.title.x",
axis.title.x,
default="15")
private$..dlab <- jmvcore::OptionString$new(
"dlab",
dlab,
default="auto")
private$..dmin <- jmvcore::OptionString$new(
"dmin",
dmin,
default="auto")
private$..dmax <- jmvcore::OptionString$new(
"dmax",
dmax,
default="auto")
private$..dbreaks <- jmvcore::OptionString$new(
"dbreaks",
dbreaks,
default="auto")
private$..shape_raw_reference <- jmvcore::OptionList$new(
"shape_raw_reference",
shape_raw_reference,
default="square filled",
options=list(
"circle filled",
"square filled",
"triangle filled",
"diamond filled"))
private$..shape_raw_comparison <- jmvcore::OptionList$new(
"shape_raw_comparison",
shape_raw_comparison,
default="square filled",
options=list(
"circle filled",
"square filled",
"triangle filled",
"diamond filled"))
private$..shape_summary_difference <- jmvcore::OptionList$new(
"shape_summary_difference",
shape_summary_difference,
default="triangle filled",
options=list(
"circle filled",
"square filled",
"triangle filled",
"diamond filled"))
private$..shape_raw_unused <- jmvcore::OptionList$new(
"shape_raw_unused",
shape_raw_unused,
default="square filled",
options=list(
"circle filled",
"square filled",
"triangle filled",
"diamond filled"))
private$..color_raw_reference <- jmvcore::OptionList$new(
"color_raw_reference",
color_raw_reference,
default="#008DF9",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..color_raw_comparison <- jmvcore::OptionList$new(
"color_raw_comparison",
color_raw_comparison,
default="#009F81",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..color_raw_unused <- jmvcore::OptionList$new(
"color_raw_unused",
color_raw_unused,
default="gray65",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..color_summary_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_unused <- jmvcore::OptionList$new(
"color_summary_unused",
color_summary_unused,
default="gray75",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..color_summary_difference <- jmvcore::OptionList$new(
"color_summary_difference",
color_summary_difference,
default="black",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..color_summary_overall <- jmvcore::OptionList$new(
"color_summary_overall",
color_summary_overall,
default="black",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..fill_raw_reference <- jmvcore::OptionList$new(
"fill_raw_reference",
fill_raw_reference,
default="#008DF9",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..fill_raw_comparison <- jmvcore::OptionList$new(
"fill_raw_comparison",
fill_raw_comparison,
default="#009F81",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..fill_raw_unused <- jmvcore::OptionList$new(
"fill_raw_unused",
fill_raw_unused,
default="gray65",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..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_unused <- jmvcore::OptionList$new(
"fill_summary_unused",
fill_summary_unused,
default="gray75",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..fill_summary_difference <- jmvcore::OptionList$new(
"fill_summary_difference",
fill_summary_difference,
default="black",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..fill_summary_overall <- jmvcore::OptionList$new(
"fill_summary_overall",
fill_summary_overall,
default="black",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..alpha_raw_reference <- jmvcore::OptionList$new(
"alpha_raw_reference",
alpha_raw_reference,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_raw_comparison <- jmvcore::OptionList$new(
"alpha_raw_comparison",
alpha_raw_comparison,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_raw_unused <- jmvcore::OptionList$new(
"alpha_raw_unused",
alpha_raw_unused,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..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_unused <- jmvcore::OptionList$new(
"alpha_summary_unused",
alpha_summary_unused,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_summary_difference <- jmvcore::OptionList$new(
"alpha_summary_difference",
alpha_summary_difference,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_summary_overall <- jmvcore::OptionList$new(
"alpha_summary_overall",
alpha_summary_overall,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..linetype_raw_reference <- jmvcore::OptionList$new(
"linetype_raw_reference",
linetype_raw_reference,
default="solid",
options=list(
"solid",
"dotted",
"dotdash",
"dashed",
"blank"))
private$..linetype_raw_comparison <- jmvcore::OptionList$new(
"linetype_raw_comparison",
linetype_raw_comparison,
default="solid",
options=list(
"solid",
"dotted",
"dotdash",
"dashed",
"blank"))
private$..linetype_summary_difference <- jmvcore::OptionList$new(
"linetype_summary_difference",
linetype_summary_difference,
default="solid",
options=list(
"solid",
"dotted",
"dotdash",
"dashed",
"blank"))
private$..linetype_raw_unused <- jmvcore::OptionList$new(
"linetype_raw_unused",
linetype_raw_unused,
default="solid",
options=list(
"solid",
"dotted",
"dotdash",
"dashed",
"blank"))
private$..color_interval_reference <- jmvcore::OptionList$new(
"color_interval_reference",
color_interval_reference,
default="black",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..color_interval_comparison <- jmvcore::OptionList$new(
"color_interval_comparison",
color_interval_comparison,
default="black",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..color_interval_difference <- jmvcore::OptionList$new(
"color_interval_difference",
color_interval_difference,
default="black",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..color_interval_unused <- jmvcore::OptionList$new(
"color_interval_unused",
color_interval_unused,
default="black",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..size_interval_reference <- jmvcore::OptionList$new(
"size_interval_reference",
size_interval_reference,
default=".50",
options=list(
".25",
".50",
".75",
"1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"))
private$..size_interval_comparison <- jmvcore::OptionList$new(
"size_interval_comparison",
size_interval_comparison,
default=".50",
options=list(
".25",
".50",
".75",
"1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"))
private$..size_interval_difference <- jmvcore::OptionList$new(
"size_interval_difference",
size_interval_difference,
default=".50",
options=list(
".25",
".50",
".75",
"1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"))
private$..size_interval_unused <- jmvcore::OptionList$new(
"size_interval_unused",
size_interval_unused,
default=".50",
options=list(
".25",
".50",
".75",
"1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"))
private$..alpha_interval_reference <- jmvcore::OptionList$new(
"alpha_interval_reference",
alpha_interval_reference,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_interval_comparison <- jmvcore::OptionList$new(
"alpha_interval_comparison",
alpha_interval_comparison,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_interval_difference <- jmvcore::OptionList$new(
"alpha_interval_difference",
alpha_interval_difference,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_interval_unused <- jmvcore::OptionList$new(
"alpha_interval_unused",
alpha_interval_unused,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
self$.addOption(private$..reference_cases)
self$.addOption(private$..reference_ns)
self$.addOption(private$..comparison_cases)
self$.addOption(private$..comparison_ns)
self$.addOption(private$..labels)
self$.addOption(private$..moderator)
self$.addOption(private$..effect_label)
self$.addOption(private$..reported_effect_size)
self$.addOption(private$..conf_level)
self$.addOption(private$..random_effects)
self$.addOption(private$..include_PIs)
self$.addOption(private$..show_details)
self$.addOption(private$..es_plot_width)
self$.addOption(private$..es_plot_height)
self$.addOption(private$..size_base)
self$.addOption(private$..size_multiplier)
self$.addOption(private$..axis.text.y)
self$.addOption(private$..report_CIs)
self$.addOption(private$..meta_diamond_height)
self$.addOption(private$..xlab)
self$.addOption(private$..xmin)
self$.addOption(private$..xmax)
self$.addOption(private$..xbreaks)
self$.addOption(private$..mark_zero)
self$.addOption(private$..axis.text.x)
self$.addOption(private$..axis.title.x)
self$.addOption(private$..dlab)
self$.addOption(private$..dmin)
self$.addOption(private$..dmax)
self$.addOption(private$..dbreaks)
self$.addOption(private$..shape_raw_reference)
self$.addOption(private$..shape_raw_comparison)
self$.addOption(private$..shape_summary_difference)
self$.addOption(private$..shape_raw_unused)
self$.addOption(private$..color_raw_reference)
self$.addOption(private$..color_raw_comparison)
self$.addOption(private$..color_raw_unused)
self$.addOption(private$..color_summary_reference)
self$.addOption(private$..color_summary_comparison)
self$.addOption(private$..color_summary_unused)
self$.addOption(private$..color_summary_difference)
self$.addOption(private$..color_summary_overall)
self$.addOption(private$..fill_raw_reference)
self$.addOption(private$..fill_raw_comparison)
self$.addOption(private$..fill_raw_unused)
self$.addOption(private$..fill_summary_reference)
self$.addOption(private$..fill_summary_comparison)
self$.addOption(private$..fill_summary_unused)
self$.addOption(private$..fill_summary_difference)
self$.addOption(private$..fill_summary_overall)
self$.addOption(private$..alpha_raw_reference)
self$.addOption(private$..alpha_raw_comparison)
self$.addOption(private$..alpha_raw_unused)
self$.addOption(private$..alpha_summary_reference)
self$.addOption(private$..alpha_summary_comparison)
self$.addOption(private$..alpha_summary_unused)
self$.addOption(private$..alpha_summary_difference)
self$.addOption(private$..alpha_summary_overall)
self$.addOption(private$..linetype_raw_reference)
self$.addOption(private$..linetype_raw_comparison)
self$.addOption(private$..linetype_summary_difference)
self$.addOption(private$..linetype_raw_unused)
self$.addOption(private$..color_interval_reference)
self$.addOption(private$..color_interval_comparison)
self$.addOption(private$..color_interval_difference)
self$.addOption(private$..color_interval_unused)
self$.addOption(private$..size_interval_reference)
self$.addOption(private$..size_interval_comparison)
self$.addOption(private$..size_interval_difference)
self$.addOption(private$..size_interval_unused)
self$.addOption(private$..alpha_interval_reference)
self$.addOption(private$..alpha_interval_comparison)
self$.addOption(private$..alpha_interval_difference)
self$.addOption(private$..alpha_interval_unused)
}),
active = list(
reference_cases = function() private$..reference_cases$value,
reference_ns = function() private$..reference_ns$value,
comparison_cases = function() private$..comparison_cases$value,
comparison_ns = function() private$..comparison_ns$value,
labels = function() private$..labels$value,
moderator = function() private$..moderator$value,
effect_label = function() private$..effect_label$value,
reported_effect_size = function() private$..reported_effect_size$value,
conf_level = function() private$..conf_level$value,
random_effects = function() private$..random_effects$value,
include_PIs = function() private$..include_PIs$value,
show_details = function() private$..show_details$value,
es_plot_width = function() private$..es_plot_width$value,
es_plot_height = function() private$..es_plot_height$value,
size_base = function() private$..size_base$value,
size_multiplier = function() private$..size_multiplier$value,
axis.text.y = function() private$..axis.text.y$value,
report_CIs = function() private$..report_CIs$value,
meta_diamond_height = function() private$..meta_diamond_height$value,
xlab = function() private$..xlab$value,
xmin = function() private$..xmin$value,
xmax = function() private$..xmax$value,
xbreaks = function() private$..xbreaks$value,
mark_zero = function() private$..mark_zero$value,
axis.text.x = function() private$..axis.text.x$value,
axis.title.x = function() private$..axis.title.x$value,
dlab = function() private$..dlab$value,
dmin = function() private$..dmin$value,
dmax = function() private$..dmax$value,
dbreaks = function() private$..dbreaks$value,
shape_raw_reference = function() private$..shape_raw_reference$value,
shape_raw_comparison = function() private$..shape_raw_comparison$value,
shape_summary_difference = function() private$..shape_summary_difference$value,
shape_raw_unused = function() private$..shape_raw_unused$value,
color_raw_reference = function() private$..color_raw_reference$value,
color_raw_comparison = function() private$..color_raw_comparison$value,
color_raw_unused = function() private$..color_raw_unused$value,
color_summary_reference = function() private$..color_summary_reference$value,
color_summary_comparison = function() private$..color_summary_comparison$value,
color_summary_unused = function() private$..color_summary_unused$value,
color_summary_difference = function() private$..color_summary_difference$value,
color_summary_overall = function() private$..color_summary_overall$value,
fill_raw_reference = function() private$..fill_raw_reference$value,
fill_raw_comparison = function() private$..fill_raw_comparison$value,
fill_raw_unused = function() private$..fill_raw_unused$value,
fill_summary_reference = function() private$..fill_summary_reference$value,
fill_summary_comparison = function() private$..fill_summary_comparison$value,
fill_summary_unused = function() private$..fill_summary_unused$value,
fill_summary_difference = function() private$..fill_summary_difference$value,
fill_summary_overall = function() private$..fill_summary_overall$value,
alpha_raw_reference = function() private$..alpha_raw_reference$value,
alpha_raw_comparison = function() private$..alpha_raw_comparison$value,
alpha_raw_unused = function() private$..alpha_raw_unused$value,
alpha_summary_reference = function() private$..alpha_summary_reference$value,
alpha_summary_comparison = function() private$..alpha_summary_comparison$value,
alpha_summary_unused = function() private$..alpha_summary_unused$value,
alpha_summary_difference = function() private$..alpha_summary_difference$value,
alpha_summary_overall = function() private$..alpha_summary_overall$value,
linetype_raw_reference = function() private$..linetype_raw_reference$value,
linetype_raw_comparison = function() private$..linetype_raw_comparison$value,
linetype_summary_difference = function() private$..linetype_summary_difference$value,
linetype_raw_unused = function() private$..linetype_raw_unused$value,
color_interval_reference = function() private$..color_interval_reference$value,
color_interval_comparison = function() private$..color_interval_comparison$value,
color_interval_difference = function() private$..color_interval_difference$value,
color_interval_unused = function() private$..color_interval_unused$value,
size_interval_reference = function() private$..size_interval_reference$value,
size_interval_comparison = function() private$..size_interval_comparison$value,
size_interval_difference = function() private$..size_interval_difference$value,
size_interval_unused = function() private$..size_interval_unused$value,
alpha_interval_reference = function() private$..alpha_interval_reference$value,
alpha_interval_comparison = function() private$..alpha_interval_comparison$value,
alpha_interval_difference = function() private$..alpha_interval_difference$value,
alpha_interval_unused = function() private$..alpha_interval_unused$value),
private = list(
..reference_cases = NA,
..reference_ns = NA,
..comparison_cases = NA,
..comparison_ns = NA,
..labels = NA,
..moderator = NA,
..effect_label = NA,
..reported_effect_size = NA,
..conf_level = NA,
..random_effects = NA,
..include_PIs = NA,
..show_details = NA,
..es_plot_width = NA,
..es_plot_height = NA,
..size_base = NA,
..size_multiplier = NA,
..axis.text.y = NA,
..report_CIs = NA,
..meta_diamond_height = NA,
..xlab = NA,
..xmin = NA,
..xmax = NA,
..xbreaks = NA,
..mark_zero = NA,
..axis.text.x = NA,
..axis.title.x = NA,
..dlab = NA,
..dmin = NA,
..dmax = NA,
..dbreaks = NA,
..shape_raw_reference = NA,
..shape_raw_comparison = NA,
..shape_summary_difference = NA,
..shape_raw_unused = NA,
..color_raw_reference = NA,
..color_raw_comparison = NA,
..color_raw_unused = NA,
..color_summary_reference = NA,
..color_summary_comparison = NA,
..color_summary_unused = NA,
..color_summary_difference = NA,
..color_summary_overall = NA,
..fill_raw_reference = NA,
..fill_raw_comparison = NA,
..fill_raw_unused = NA,
..fill_summary_reference = NA,
..fill_summary_comparison = NA,
..fill_summary_unused = NA,
..fill_summary_difference = NA,
..fill_summary_overall = NA,
..alpha_raw_reference = NA,
..alpha_raw_comparison = NA,
..alpha_raw_unused = NA,
..alpha_summary_reference = NA,
..alpha_summary_comparison = NA,
..alpha_summary_unused = NA,
..alpha_summary_difference = NA,
..alpha_summary_overall = NA,
..linetype_raw_reference = NA,
..linetype_raw_comparison = NA,
..linetype_summary_difference = NA,
..linetype_raw_unused = NA,
..color_interval_reference = NA,
..color_interval_comparison = NA,
..color_interval_difference = NA,
..color_interval_unused = NA,
..size_interval_reference = NA,
..size_interval_comparison = NA,
..size_interval_difference = NA,
..size_interval_unused = NA,
..alpha_interval_reference = NA,
..alpha_interval_comparison = NA,
..alpha_interval_difference = NA,
..alpha_interval_unused = NA)
)
jamovimetapdiffResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamovimetapdiffResults",
inherit = jmvcore::Group,
active = list(
debug = function() private$.items[["debug"]],
help = function() private$.items[["help"]],
raw_data = function() private$.items[["raw_data"]],
es_meta = function() private$.items[["es_meta"]],
es_heterogeneity = function() private$.items[["es_heterogeneity"]],
es_meta_difference = function() private$.items[["es_meta_difference"]],
estimation_plot_warnings = function() private$.items[["estimation_plot_warnings"]],
estimation_plots = function() private$.items[["estimation_plots"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Meta-Analysis: Difference in Proportions")
self$add(jmvcore::Html$new(
options=options,
name="debug",
visible=FALSE))
self$add(jmvcore::Html$new(
options=options,
name="help",
visible=FALSE))
self$add(jmvcore::Table$new(
options=options,
name="raw_data",
title="Table of Studies",
rows=1,
clearWith=list(
"reference_cases",
"reference_ns",
"comparison_cases",
"comparison_ns",
"labels",
"moderator",
"effect_label",
"reported_effect_size",
"conf_level",
"random_effects",
"show_details"),
columns=list(
list(
`name`="label",
`title`="Study label",
`type`="text"),
list(
`name`="moderator",
`title`="Moderator level",
`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`="weight",
`title`="Weight",
`type`="number",
`visible`="(show_details)"),
list(
`name`="SE",
`title`="<i>SE</i><sub>proportion<sub>",
`type`="number",
`visible`="(show_details)"),
list(
`name`="sample_variance",
`title`="<i>SE</i><sup>2</sup><sub>proportion<sub>",
`type`="number",
`visible`="(show_details)"),
list(
`name`="reference_P",
`title`="<i>P</i><sub>reference</sub>",
`type`="number"),
list(
`name`="reference_cases",
`title`="Cases<sub>reference</sub>",
`type`="integer",
`visible`="(show_details)"),
list(
`name`="reference_N",
`title`="<i>N</i><sub>reference</sub>",
`type`="integer",
`visible`="(show_details)"),
list(
`name`="comparison_P",
`title`="<i>P</i><sub>comparison</sub>",
`type`="number"),
list(
`name`="comparison_cases",
`title`="Cases<sub>comparison</sub>",
`type`="integer",
`visible`="(show_details)"),
list(
`name`="comparison_N",
`title`="<i>N</i><sub>comparison</sub>",
`type`="integer",
`visible`="(show_details)"))))
self$add(jmvcore::Table$new(
options=options,
name="es_meta",
title="Meta-Analytic Effect Sizes",
refs="metafor",
rows=1,
clearWith=list(
"reference_cases",
"reference_ns",
"comparison_cases",
"comparison_ns",
"labels",
"moderator",
"effect_label",
"reported_effect_size",
"conf_level",
"random_effects",
"show_details"),
columns=list(
list(
`name`="effect_label",
`title`="Effect",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="moderator_variable_name",
`title`="Moderator",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="moderator_variable_level",
`title`="Level",
`type`="text",
`combineBelow`=TRUE),
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`="k",
`title`="<i>k</i>",
`type`="integer"),
list(
`name`="PI_LL",
`title`="LL",
`type`="number",
`visible`="(include_PIs & random_effects == 'random_effects')"),
list(
`name`="PI_UL",
`title`="UL",
`type`="number",
`visible`="(include_PIs & random_effects == 'random_effects')"),
list(
`name`="p",
`visible`="(show_details)",
`title`="<i>p</i>, two tailed",
`type`="number",
`format`="zto,pvalue"),
list(
`name`="FE_CI_width",
`type`="number",
`title`="FE CI length",
`visible`="(show_details)"),
list(
`name`="RE_CI_width",
`type`="number",
`title`="RE CI length",
`visible`="(show_details)"))))
self$add(jmvcore::Table$new(
options=options,
name="es_heterogeneity",
title="Effect Size Heterogeneity",
rows=1,
clearWith=list(
"reference_cases",
"reference_ns",
"comparison_cases",
"comparison_ns",
"labels",
"moderator",
"effect_label",
"reported_effect_size",
"conf_level",
"random_effects",
"show_details"),
columns=list(
list(
`name`="measure",
`title`="Measure",
`type`="text",
`combineBelow`=TRUE,
`visible`=FALSE),
list(
`name`="measure_html",
`title`="Measure",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="moderator_level",
`title`="Level",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="estimate",
`type`="number",
`title`="Estimate"),
list(
`name`="LL",
`title`="LL",
`type`="number"),
list(
`name`="UL",
`title`="UL",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="es_meta_difference",
title="Moderator Analysis",
rows=3,
clearWith=list(
"reference_cases",
"reference_ns",
"comparison_cases",
"comparison_ns",
"labels",
"moderator",
"effect_label",
"reported_effect_size",
"conf_level",
"random_effects",
"show_details"),
columns=list(
list(
`name`="effect_label",
`title`="Effect",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="moderator_variable_name",
`title`="Moderator",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="moderator_level",
`title`="Level",
`type`="text",
`combineBelow`=TRUE),
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`="p",
`visible`="(show_details)",
`title`="<i>p</i>, two tailed",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Html$new(
options=options,
name="estimation_plot_warnings",
title="Forest Plot Warnings",
visible=TRUE))
self$add(jmvcore::Image$new(
options=options,
name="estimation_plots",
title="Forest Plot",
requiresData=TRUE,
width=400,
height=300,
renderFun=".estimation_plots"))}))
jamovimetapdiffBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamovimetapdiffBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "esci",
name = "jamovimetapdiff",
version = c(1,0,0),
options = options,
results = jamovimetapdiffResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
#' Meta-Analysis: Difference in Proportions
#'
#'
#' @param data .
#' @param reference_cases .
#' @param reference_ns .
#' @param comparison_cases .
#' @param comparison_ns .
#' @param labels .
#' @param moderator .
#' @param effect_label .
#' @param reported_effect_size .
#' @param conf_level .
#' @param random_effects .
#' @param include_PIs .
#' @param show_details .
#' @param es_plot_width .
#' @param es_plot_height .
#' @param size_base .
#' @param size_multiplier .
#' @param axis.text.y .
#' @param report_CIs .
#' @param meta_diamond_height .
#' @param xlab .
#' @param xmin .
#' @param xmax .
#' @param xbreaks .
#' @param mark_zero .
#' @param axis.text.x .
#' @param axis.title.x .
#' @param dlab .
#' @param dmin .
#' @param dmax .
#' @param dbreaks .
#' @param shape_raw_reference .
#' @param shape_raw_comparison .
#' @param shape_summary_difference .
#' @param shape_raw_unused .
#' @param color_raw_reference .
#' @param color_raw_comparison .
#' @param color_raw_unused .
#' @param color_summary_reference .
#' @param color_summary_comparison .
#' @param color_summary_unused .
#' @param color_summary_difference .
#' @param color_summary_overall .
#' @param fill_raw_reference .
#' @param fill_raw_comparison .
#' @param fill_raw_unused .
#' @param fill_summary_reference .
#' @param fill_summary_comparison .
#' @param fill_summary_unused .
#' @param fill_summary_difference .
#' @param fill_summary_overall .
#' @param alpha_raw_reference .
#' @param alpha_raw_comparison .
#' @param alpha_raw_unused .
#' @param alpha_summary_reference .
#' @param alpha_summary_comparison .
#' @param alpha_summary_unused .
#' @param alpha_summary_difference .
#' @param alpha_summary_overall .
#' @param linetype_raw_reference .
#' @param linetype_raw_comparison .
#' @param linetype_summary_difference .
#' @param linetype_raw_unused .
#' @param color_interval_reference .
#' @param color_interval_comparison .
#' @param color_interval_difference .
#' @param color_interval_unused .
#' @param size_interval_reference .
#' @param size_interval_comparison .
#' @param size_interval_difference .
#' @param size_interval_unused .
#' @param alpha_interval_reference .
#' @param alpha_interval_comparison .
#' @param alpha_interval_difference .
#' @param alpha_interval_unused .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$debug} \tab \tab \tab \tab \tab a html \cr
#' \code{results$help} \tab \tab \tab \tab \tab a html \cr
#' \code{results$raw_data} \tab \tab \tab \tab \tab a table \cr
#' \code{results$es_meta} \tab \tab \tab \tab \tab a table \cr
#' \code{results$es_heterogeneity} \tab \tab \tab \tab \tab a table \cr
#' \code{results$es_meta_difference} \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 image \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$raw_data$asDF}
#'
#' \code{as.data.frame(results$raw_data)}
#'
#' @export
jamovimetapdiff <- function(
data,
reference_cases,
reference_ns,
comparison_cases,
comparison_ns,
labels,
moderator,
effect_label = "My effect",
reported_effect_size = "RD",
conf_level = 95,
random_effects = "random_effects",
include_PIs = FALSE,
show_details = FALSE,
es_plot_width = "600",
es_plot_height = "750",
size_base = "2",
size_multiplier = "3",
axis.text.y = "14",
report_CIs = FALSE,
meta_diamond_height = ".25",
xlab = "auto",
xmin = "auto",
xmax = "auto",
xbreaks = "auto",
mark_zero = FALSE,
axis.text.x = "14",
axis.title.x = "15",
dlab = "auto",
dmin = "auto",
dmax = "auto",
dbreaks = "auto",
shape_raw_reference = "square filled",
shape_raw_comparison = "square filled",
shape_summary_difference = "triangle filled",
shape_raw_unused = "square filled",
color_raw_reference = "#008DF9",
color_raw_comparison = "#009F81",
color_raw_unused = "gray65",
color_summary_reference = "#008DF9",
color_summary_comparison = "#009F81",
color_summary_unused = "gray75",
color_summary_difference = "black",
color_summary_overall = "black",
fill_raw_reference = "#008DF9",
fill_raw_comparison = "#009F81",
fill_raw_unused = "gray65",
fill_summary_reference = "#008DF9",
fill_summary_comparison = "#009F81",
fill_summary_unused = "gray75",
fill_summary_difference = "black",
fill_summary_overall = "black",
alpha_raw_reference = "1",
alpha_raw_comparison = "1",
alpha_raw_unused = "1",
alpha_summary_reference = "1",
alpha_summary_comparison = "1",
alpha_summary_unused = "1",
alpha_summary_difference = "1",
alpha_summary_overall = "1",
linetype_raw_reference = "solid",
linetype_raw_comparison = "solid",
linetype_summary_difference = "solid",
linetype_raw_unused = "solid",
color_interval_reference = "black",
color_interval_comparison = "black",
color_interval_difference = "black",
color_interval_unused = "black",
size_interval_reference = ".50",
size_interval_comparison = ".50",
size_interval_difference = ".50",
size_interval_unused = ".50",
alpha_interval_reference = "1",
alpha_interval_comparison = "1",
alpha_interval_difference = "1",
alpha_interval_unused = "1") {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("jamovimetapdiff requires jmvcore to be installed (restart may be required)")
if ( ! missing(reference_cases)) reference_cases <- jmvcore::resolveQuo(jmvcore::enquo(reference_cases))
if ( ! missing(reference_ns)) reference_ns <- jmvcore::resolveQuo(jmvcore::enquo(reference_ns))
if ( ! missing(comparison_cases)) comparison_cases <- jmvcore::resolveQuo(jmvcore::enquo(comparison_cases))
if ( ! missing(comparison_ns)) comparison_ns <- jmvcore::resolveQuo(jmvcore::enquo(comparison_ns))
if ( ! missing(labels)) labels <- jmvcore::resolveQuo(jmvcore::enquo(labels))
if ( ! missing(moderator)) moderator <- jmvcore::resolveQuo(jmvcore::enquo(moderator))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(reference_cases), reference_cases, NULL),
`if`( ! missing(reference_ns), reference_ns, NULL),
`if`( ! missing(comparison_cases), comparison_cases, NULL),
`if`( ! missing(comparison_ns), comparison_ns, NULL),
`if`( ! missing(labels), labels, NULL),
`if`( ! missing(moderator), moderator, NULL))
for (v in labels) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
for (v in moderator) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
options <- jamovimetapdiffOptions$new(
reference_cases = reference_cases,
reference_ns = reference_ns,
comparison_cases = comparison_cases,
comparison_ns = comparison_ns,
labels = labels,
moderator = moderator,
effect_label = effect_label,
reported_effect_size = reported_effect_size,
conf_level = conf_level,
random_effects = random_effects,
include_PIs = include_PIs,
show_details = show_details,
es_plot_width = es_plot_width,
es_plot_height = es_plot_height,
size_base = size_base,
size_multiplier = size_multiplier,
axis.text.y = axis.text.y,
report_CIs = report_CIs,
meta_diamond_height = meta_diamond_height,
xlab = xlab,
xmin = xmin,
xmax = xmax,
xbreaks = xbreaks,
mark_zero = mark_zero,
axis.text.x = axis.text.x,
axis.title.x = axis.title.x,
dlab = dlab,
dmin = dmin,
dmax = dmax,
dbreaks = dbreaks,
shape_raw_reference = shape_raw_reference,
shape_raw_comparison = shape_raw_comparison,
shape_summary_difference = shape_summary_difference,
shape_raw_unused = shape_raw_unused,
color_raw_reference = color_raw_reference,
color_raw_comparison = color_raw_comparison,
color_raw_unused = color_raw_unused,
color_summary_reference = color_summary_reference,
color_summary_comparison = color_summary_comparison,
color_summary_unused = color_summary_unused,
color_summary_difference = color_summary_difference,
color_summary_overall = color_summary_overall,
fill_raw_reference = fill_raw_reference,
fill_raw_comparison = fill_raw_comparison,
fill_raw_unused = fill_raw_unused,
fill_summary_reference = fill_summary_reference,
fill_summary_comparison = fill_summary_comparison,
fill_summary_unused = fill_summary_unused,
fill_summary_difference = fill_summary_difference,
fill_summary_overall = fill_summary_overall,
alpha_raw_reference = alpha_raw_reference,
alpha_raw_comparison = alpha_raw_comparison,
alpha_raw_unused = alpha_raw_unused,
alpha_summary_reference = alpha_summary_reference,
alpha_summary_comparison = alpha_summary_comparison,
alpha_summary_unused = alpha_summary_unused,
alpha_summary_difference = alpha_summary_difference,
alpha_summary_overall = alpha_summary_overall,
linetype_raw_reference = linetype_raw_reference,
linetype_raw_comparison = linetype_raw_comparison,
linetype_summary_difference = linetype_summary_difference,
linetype_raw_unused = linetype_raw_unused,
color_interval_reference = color_interval_reference,
color_interval_comparison = color_interval_comparison,
color_interval_difference = color_interval_difference,
color_interval_unused = color_interval_unused,
size_interval_reference = size_interval_reference,
size_interval_comparison = size_interval_comparison,
size_interval_difference = size_interval_difference,
size_interval_unused = size_interval_unused,
alpha_interval_reference = alpha_interval_reference,
alpha_interval_comparison = alpha_interval_comparison,
alpha_interval_difference = alpha_interval_difference,
alpha_interval_unused = alpha_interval_unused)
analysis <- jamovimetapdiffClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
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Defines functions jamovimetapdiff
Documented in jamovimetapdiff
# This file is automatically generated, you probably don't want to edit this
jamovimetapdiffOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamovimetapdiffOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
reference_cases = NULL,
reference_ns = NULL,
comparison_cases = NULL,
comparison_ns = NULL,
labels = NULL,
moderator = NULL,
effect_label = "My effect",
reported_effect_size = "RD",
conf_level = 95,
random_effects = "random_effects",
include_PIs = FALSE,
show_details = FALSE,
es_plot_width = "600",
es_plot_height = "750",
size_base = "2",
size_multiplier = "3",
axis.text.y = "14",
report_CIs = FALSE,
meta_diamond_height = ".25",
xlab = "auto",
xmin = "auto",
xmax = "auto",
xbreaks = "auto",
mark_zero = FALSE,
axis.text.x = "14",
axis.title.x = "15",
dlab = "auto",
dmin = "auto",
dmax = "auto",
dbreaks = "auto",
shape_raw_reference = "square filled",
shape_raw_comparison = "square filled",
shape_summary_difference = "triangle filled",
shape_raw_unused = "square filled",
color_raw_reference = "#008DF9",
color_raw_comparison = "#009F81",
color_raw_unused = "gray65",
color_summary_reference = "#008DF9",
color_summary_comparison = "#009F81",
color_summary_unused = "gray75",
color_summary_difference = "black",
color_summary_overall = "black",
fill_raw_reference = "#008DF9",
fill_raw_comparison = "#009F81",
fill_raw_unused = "gray65",
fill_summary_reference = "#008DF9",
fill_summary_comparison = "#009F81",
fill_summary_unused = "gray75",
fill_summary_difference = "black",
fill_summary_overall = "black",
alpha_raw_reference = "1",
alpha_raw_comparison = "1",
alpha_raw_unused = "1",
alpha_summary_reference = "1",
alpha_summary_comparison = "1",
alpha_summary_unused = "1",
alpha_summary_difference = "1",
alpha_summary_overall = "1",
linetype_raw_reference = "solid",
linetype_raw_comparison = "solid",
linetype_summary_difference = "solid",
linetype_raw_unused = "solid",
color_interval_reference = "black",
color_interval_comparison = "black",
color_interval_difference = "black",
color_interval_unused = "black",
size_interval_reference = ".50",
size_interval_comparison = ".50",
size_interval_difference = ".50",
size_interval_unused = ".50",
alpha_interval_reference = "1",
alpha_interval_comparison = "1",
alpha_interval_difference = "1",
alpha_interval_unused = "1", ...) {
super$initialize(
package="esci",
name="jamovimetapdiff",
requiresData=TRUE,
...)
private$..reference_cases <- jmvcore::OptionVariable$new(
"reference_cases",
reference_cases,
suggested=list(
"continuous"),
permitted=list(
"numeric"))
private$..reference_ns <- jmvcore::OptionVariable$new(
"reference_ns",
reference_ns,
suggested=list(
"continuous"),
permitted=list(
"numeric"))
private$..comparison_cases <- jmvcore::OptionVariable$new(
"comparison_cases",
comparison_cases,
suggested=list(
"continuous"),
permitted=list(
"numeric"))
private$..comparison_ns <- jmvcore::OptionVariable$new(
"comparison_ns",
comparison_ns,
suggested=list(
"continuous"),
permitted=list(
"numeric"))
private$..labels <- jmvcore::OptionVariable$new(
"labels",
labels,
suggested=list(
"nominal",
"ordinal"),
permitted=list(
"factor"))
private$..moderator <- jmvcore::OptionVariable$new(
"moderator",
moderator,
suggested=list(
"nominal",
"ordinal"),
permitted=list(
"factor"))
private$..effect_label <- jmvcore::OptionString$new(
"effect_label",
effect_label,
default="My effect")
private$..reported_effect_size <- jmvcore::OptionList$new(
"reported_effect_size",
reported_effect_size,
default="RD",
options=list(
"RD",
"RR",
"OR",
"AS",
"PETO"))
private$..conf_level <- jmvcore::OptionNumber$new(
"conf_level",
conf_level,
default=95)
private$..random_effects <- jmvcore::OptionList$new(
"random_effects",
random_effects,
default="random_effects",
options=list(
"random_effects",
"fixed_effects"))
private$..include_PIs <- jmvcore::OptionBool$new(
"include_PIs",
include_PIs,
default=FALSE)
private$..show_details <- jmvcore::OptionBool$new(
"show_details",
show_details,
default=FALSE)
private$..es_plot_width <- jmvcore::OptionString$new(
"es_plot_width",
es_plot_width,
default="600")
private$..es_plot_height <- jmvcore::OptionString$new(
"es_plot_height",
es_plot_height,
default="750")
private$..size_base <- jmvcore::OptionList$new(
"size_base",
size_base,
default="2",
options=list(
".25",
".50",
".75",
"1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"))
private$..size_multiplier <- jmvcore::OptionList$new(
"size_multiplier",
size_multiplier,
default="3",
options=list(
"1",
"1.1",
"1.2",
"1.3",
"1.5",
"1.75",
"2",
"2.5",
"3",
"3.5",
"4",
"4.5",
"5"))
private$..axis.text.y <- jmvcore::OptionString$new(
"axis.text.y",
axis.text.y,
default="14")
private$..report_CIs <- jmvcore::OptionBool$new(
"report_CIs",
report_CIs,
default=FALSE)
private$..meta_diamond_height <- jmvcore::OptionString$new(
"meta_diamond_height",
meta_diamond_height,
default=".25")
private$..xlab <- jmvcore::OptionString$new(
"xlab",
xlab,
default="auto")
private$..xmin <- jmvcore::OptionString$new(
"xmin",
xmin,
default="auto")
private$..xmax <- jmvcore::OptionString$new(
"xmax",
xmax,
default="auto")
private$..xbreaks <- jmvcore::OptionString$new(
"xbreaks",
xbreaks,
default="auto")
private$..mark_zero <- jmvcore::OptionBool$new(
"mark_zero",
mark_zero,
default=FALSE)
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$..dlab <- jmvcore::OptionString$new(
"dlab",
dlab,
default="auto")
private$..dmin <- jmvcore::OptionString$new(
"dmin",
dmin,
default="auto")
private$..dmax <- jmvcore::OptionString$new(
"dmax",
dmax,
default="auto")
private$..dbreaks <- jmvcore::OptionString$new(
"dbreaks",
dbreaks,
default="auto")
private$..shape_raw_reference <- jmvcore::OptionList$new(
"shape_raw_reference",
shape_raw_reference,
default="square filled",
options=list(
"circle filled",
"square filled",
"triangle filled",
"diamond filled"))
private$..shape_raw_comparison <- jmvcore::OptionList$new(
"shape_raw_comparison",
shape_raw_comparison,
default="square 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$..shape_raw_unused <- jmvcore::OptionList$new(
"shape_raw_unused",
shape_raw_unused,
default="square filled",
options=list(
"circle filled",
"square filled",
"triangle filled",
"diamond filled"))
private$..color_raw_reference <- jmvcore::OptionList$new(
"color_raw_reference",
color_raw_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$..color_raw_comparison <- jmvcore::OptionList$new(
"color_raw_comparison",
color_raw_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$..color_raw_unused <- jmvcore::OptionList$new(
"color_raw_unused",
color_raw_unused,
default="gray65",
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$..color_summary_reference <- jmvcore::OptionList$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$..color_summary_unused <- jmvcore::OptionList$new(
"color_summary_unused",
color_summary_unused,
default="gray75",
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$..color_summary_overall <- jmvcore::OptionList$new(
"color_summary_overall",
color_summary_overall,
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$..fill_raw_reference <- jmvcore::OptionList$new(
"fill_raw_reference",
fill_raw_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$..fill_raw_comparison <- jmvcore::OptionList$new(
"fill_raw_comparison",
fill_raw_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$..fill_raw_unused <- jmvcore::OptionList$new(
"fill_raw_unused",
fill_raw_unused,
default="gray65",
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$..fill_summary_unused <- jmvcore::OptionList$new(
"fill_summary_unused",
fill_summary_unused,
default="gray75",
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$..fill_summary_overall <- jmvcore::OptionList$new(
"fill_summary_overall",
fill_summary_overall,
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$..alpha_raw_reference <- jmvcore::OptionList$new(
"alpha_raw_reference",
alpha_raw_reference,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_raw_comparison <- jmvcore::OptionList$new(
"alpha_raw_comparison",
alpha_raw_comparison,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_raw_unused <- jmvcore::OptionList$new(
"alpha_raw_unused",
alpha_raw_unused,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
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$..alpha_summary_unused <- jmvcore::OptionList$new(
"alpha_summary_unused",
alpha_summary_unused,
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$..alpha_summary_overall <- jmvcore::OptionList$new(
"alpha_summary_overall",
alpha_summary_overall,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..linetype_raw_reference <- jmvcore::OptionList$new(
"linetype_raw_reference",
linetype_raw_reference,
default="solid",
options=list(
"solid",
"dotted",
"dotdash",
"dashed",
"blank"))
private$..linetype_raw_comparison <- jmvcore::OptionList$new(
"linetype_raw_comparison",
linetype_raw_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"))
private$..linetype_raw_unused <- jmvcore::OptionList$new(
"linetype_raw_unused",
linetype_raw_unused,
default="solid",
options=list(
"solid",
"dotted",
"dotdash",
"dashed",
"blank"))
private$..color_interval_reference <- jmvcore::OptionList$new(
"color_interval_reference",
color_interval_reference,
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$..color_interval_comparison <- jmvcore::OptionList$new(
"color_interval_comparison",
color_interval_comparison,
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$..color_interval_difference <- jmvcore::OptionList$new(
"color_interval_difference",
color_interval_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$..color_interval_unused <- jmvcore::OptionList$new(
"color_interval_unused",
color_interval_unused,
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$..size_interval_reference <- jmvcore::OptionList$new(
"size_interval_reference",
size_interval_reference,
default=".50",
options=list(
".25",
".50",
".75",
"1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"))
private$..size_interval_comparison <- jmvcore::OptionList$new(
"size_interval_comparison",
size_interval_comparison,
default=".50",
options=list(
".25",
".50",
".75",
"1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"))
private$..size_interval_difference <- jmvcore::OptionList$new(
"size_interval_difference",
size_interval_difference,
default=".50",
options=list(
".25",
".50",
".75",
"1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"))
private$..size_interval_unused <- jmvcore::OptionList$new(
"size_interval_unused",
size_interval_unused,
default=".50",
options=list(
".25",
".50",
".75",
"1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"))
private$..alpha_interval_reference <- jmvcore::OptionList$new(
"alpha_interval_reference",
alpha_interval_reference,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_interval_comparison <- jmvcore::OptionList$new(
"alpha_interval_comparison",
alpha_interval_comparison,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_interval_difference <- jmvcore::OptionList$new(
"alpha_interval_difference",
alpha_interval_difference,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_interval_unused <- jmvcore::OptionList$new(
"alpha_interval_unused",
alpha_interval_unused,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
self$.addOption(private$..reference_cases)
self$.addOption(private$..reference_ns)
self$.addOption(private$..comparison_cases)
self$.addOption(private$..comparison_ns)
self$.addOption(private$..labels)
self$.addOption(private$..moderator)
self$.addOption(private$..effect_label)
self$.addOption(private$..reported_effect_size)
self$.addOption(private$..conf_level)
self$.addOption(private$..random_effects)
self$.addOption(private$..include_PIs)
self$.addOption(private$..show_details)
self$.addOption(private$..es_plot_width)
self$.addOption(private$..es_plot_height)
self$.addOption(private$..size_base)
self$.addOption(private$..size_multiplier)
self$.addOption(private$..axis.text.y)
self$.addOption(private$..report_CIs)
self$.addOption(private$..meta_diamond_height)
self$.addOption(private$..xlab)
self$.addOption(private$..xmin)
self$.addOption(private$..xmax)
self$.addOption(private$..xbreaks)
self$.addOption(private$..mark_zero)
self$.addOption(private$..axis.text.x)
self$.addOption(private$..axis.title.x)
self$.addOption(private$..dlab)
self$.addOption(private$..dmin)
self$.addOption(private$..dmax)
self$.addOption(private$..dbreaks)
self$.addOption(private$..shape_raw_reference)
self$.addOption(private$..shape_raw_comparison)
self$.addOption(private$..shape_summary_difference)
self$.addOption(private$..shape_raw_unused)
self$.addOption(private$..color_raw_reference)
self$.addOption(private$..color_raw_comparison)
self$.addOption(private$..color_raw_unused)
self$.addOption(private$..color_summary_reference)
self$.addOption(private$..color_summary_comparison)
self$.addOption(private$..color_summary_unused)
self$.addOption(private$..color_summary_difference)
self$.addOption(private$..color_summary_overall)
self$.addOption(private$..fill_raw_reference)
self$.addOption(private$..fill_raw_comparison)
self$.addOption(private$..fill_raw_unused)
self$.addOption(private$..fill_summary_reference)
self$.addOption(private$..fill_summary_comparison)
self$.addOption(private$..fill_summary_unused)
self$.addOption(private$..fill_summary_difference)
self$.addOption(private$..fill_summary_overall)
self$.addOption(private$..alpha_raw_reference)
self$.addOption(private$..alpha_raw_comparison)
self$.addOption(private$..alpha_raw_unused)
self$.addOption(private$..alpha_summary_reference)
self$.addOption(private$..alpha_summary_comparison)
self$.addOption(private$..alpha_summary_unused)
self$.addOption(private$..alpha_summary_difference)
self$.addOption(private$..alpha_summary_overall)
self$.addOption(private$..linetype_raw_reference)
self$.addOption(private$..linetype_raw_comparison)
self$.addOption(private$..linetype_summary_difference)
self$.addOption(private$..linetype_raw_unused)
self$.addOption(private$..color_interval_reference)
self$.addOption(private$..color_interval_comparison)
self$.addOption(private$..color_interval_difference)
self$.addOption(private$..color_interval_unused)
self$.addOption(private$..size_interval_reference)
self$.addOption(private$..size_interval_comparison)
self$.addOption(private$..size_interval_difference)
self$.addOption(private$..size_interval_unused)
self$.addOption(private$..alpha_interval_reference)
self$.addOption(private$..alpha_interval_comparison)
self$.addOption(private$..alpha_interval_difference)
self$.addOption(private$..alpha_interval_unused)
}),
active = list(
reference_cases = function() private$..reference_cases$value,
reference_ns = function() private$..reference_ns$value,
comparison_cases = function() private$..comparison_cases$value,
comparison_ns = function() private$..comparison_ns$value,
labels = function() private$..labels$value,
moderator = function() private$..moderator$value,
effect_label = function() private$..effect_label$value,
reported_effect_size = function() private$..reported_effect_size$value,
conf_level = function() private$..conf_level$value,
random_effects = function() private$..random_effects$value,
include_PIs = function() private$..include_PIs$value,
show_details = function() private$..show_details$value,
es_plot_width = function() private$..es_plot_width$value,
es_plot_height = function() private$..es_plot_height$value,
size_base = function() private$..size_base$value,
size_multiplier = function() private$..size_multiplier$value,
axis.text.y = function() private$..axis.text.y$value,
report_CIs = function() private$..report_CIs$value,
meta_diamond_height = function() private$..meta_diamond_height$value,
xlab = function() private$..xlab$value,
xmin = function() private$..xmin$value,
xmax = function() private$..xmax$value,
xbreaks = function() private$..xbreaks$value,
mark_zero = function() private$..mark_zero$value,
axis.text.x = function() private$..axis.text.x$value,
axis.title.x = function() private$..axis.title.x$value,
dlab = function() private$..dlab$value,
dmin = function() private$..dmin$value,
dmax = function() private$..dmax$value,
dbreaks = function() private$..dbreaks$value,
shape_raw_reference = function() private$..shape_raw_reference$value,
shape_raw_comparison = function() private$..shape_raw_comparison$value,
shape_summary_difference = function() private$..shape_summary_difference$value,
shape_raw_unused = function() private$..shape_raw_unused$value,
color_raw_reference = function() private$..color_raw_reference$value,
color_raw_comparison = function() private$..color_raw_comparison$value,
color_raw_unused = function() private$..color_raw_unused$value,
color_summary_reference = function() private$..color_summary_reference$value,
color_summary_comparison = function() private$..color_summary_comparison$value,
color_summary_unused = function() private$..color_summary_unused$value,
color_summary_difference = function() private$..color_summary_difference$value,
color_summary_overall = function() private$..color_summary_overall$value,
fill_raw_reference = function() private$..fill_raw_reference$value,
fill_raw_comparison = function() private$..fill_raw_comparison$value,
fill_raw_unused = function() private$..fill_raw_unused$value,
fill_summary_reference = function() private$..fill_summary_reference$value,
fill_summary_comparison = function() private$..fill_summary_comparison$value,
fill_summary_unused = function() private$..fill_summary_unused$value,
fill_summary_difference = function() private$..fill_summary_difference$value,
fill_summary_overall = function() private$..fill_summary_overall$value,
alpha_raw_reference = function() private$..alpha_raw_reference$value,
alpha_raw_comparison = function() private$..alpha_raw_comparison$value,
alpha_raw_unused = function() private$..alpha_raw_unused$value,
alpha_summary_reference = function() private$..alpha_summary_reference$value,
alpha_summary_comparison = function() private$..alpha_summary_comparison$value,
alpha_summary_unused = function() private$..alpha_summary_unused$value,
alpha_summary_difference = function() private$..alpha_summary_difference$value,
alpha_summary_overall = function() private$..alpha_summary_overall$value,
linetype_raw_reference = function() private$..linetype_raw_reference$value,
linetype_raw_comparison = function() private$..linetype_raw_comparison$value,
linetype_summary_difference = function() private$..linetype_summary_difference$value,
linetype_raw_unused = function() private$..linetype_raw_unused$value,
color_interval_reference = function() private$..color_interval_reference$value,
color_interval_comparison = function() private$..color_interval_comparison$value,
color_interval_difference = function() private$..color_interval_difference$value,
color_interval_unused = function() private$..color_interval_unused$value,
size_interval_reference = function() private$..size_interval_reference$value,
size_interval_comparison = function() private$..size_interval_comparison$value,
size_interval_difference = function() private$..size_interval_difference$value,
size_interval_unused = function() private$..size_interval_unused$value,
alpha_interval_reference = function() private$..alpha_interval_reference$value,
alpha_interval_comparison = function() private$..alpha_interval_comparison$value,
alpha_interval_difference = function() private$..alpha_interval_difference$value,
alpha_interval_unused = function() private$..alpha_interval_unused$value),
private = list(
..reference_cases = NA,
..reference_ns = NA,
..comparison_cases = NA,
..comparison_ns = NA,
..labels = NA,
..moderator = NA,
..effect_label = NA,
..reported_effect_size = NA,
..conf_level = NA,
..random_effects = NA,
..include_PIs = NA,
..show_details = NA,
..es_plot_width = NA,
..es_plot_height = NA,
..size_base = NA,
..size_multiplier = NA,
..axis.text.y = NA,
..report_CIs = NA,
..meta_diamond_height = NA,
..xlab = NA,
..xmin = NA,
..xmax = NA,
..xbreaks = NA,
..mark_zero = NA,
..axis.text.x = NA,
..axis.title.x = NA,
..dlab = NA,
..dmin = NA,
..dmax = NA,
..dbreaks = NA,
..shape_raw_reference = NA,
..shape_raw_comparison = NA,
..shape_summary_difference = NA,
..shape_raw_unused = NA,
..color_raw_reference = NA,
..color_raw_comparison = NA,
..color_raw_unused = NA,
..color_summary_reference = NA,
..color_summary_comparison = NA,
..color_summary_unused = NA,
..color_summary_difference = NA,
..color_summary_overall = NA,
..fill_raw_reference = NA,
..fill_raw_comparison = NA,
..fill_raw_unused = NA,
..fill_summary_reference = NA,
..fill_summary_comparison = NA,
..fill_summary_unused = NA,
..fill_summary_difference = NA,
..fill_summary_overall = NA,
..alpha_raw_reference = NA,
..alpha_raw_comparison = NA,
..alpha_raw_unused = NA,
..alpha_summary_reference = NA,
..alpha_summary_comparison = NA,
..alpha_summary_unused = NA,
..alpha_summary_difference = NA,
..alpha_summary_overall = NA,
..linetype_raw_reference = NA,
..linetype_raw_comparison = NA,
..linetype_summary_difference = NA,
..linetype_raw_unused = NA,
..color_interval_reference = NA,
..color_interval_comparison = NA,
..color_interval_difference = NA,
..color_interval_unused = NA,
..size_interval_reference = NA,
..size_interval_comparison = NA,
..size_interval_difference = NA,
..size_interval_unused = NA,
..alpha_interval_reference = NA,
..alpha_interval_comparison = NA,
..alpha_interval_difference = NA,
..alpha_interval_unused = NA)
)
jamovimetapdiffResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamovimetapdiffResults",
inherit = jmvcore::Group,
active = list(
debug = function() private$.items[["debug"]],
help = function() private$.items[["help"]],
raw_data = function() private$.items[["raw_data"]],
es_meta = function() private$.items[["es_meta"]],
es_heterogeneity = function() private$.items[["es_heterogeneity"]],
es_meta_difference = function() private$.items[["es_meta_difference"]],
estimation_plot_warnings = function() private$.items[["estimation_plot_warnings"]],
estimation_plots = function() private$.items[["estimation_plots"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Meta-Analysis: Difference in Proportions")
self$add(jmvcore::Html$new(
options=options,
name="debug",
visible=FALSE))
self$add(jmvcore::Html$new(
options=options,
name="help",
visible=FALSE))
self$add(jmvcore::Table$new(
options=options,
name="raw_data",
title="Table of Studies",
rows=1,
clearWith=list(
"reference_cases",
"reference_ns",
"comparison_cases",
"comparison_ns",
"labels",
"moderator",
"effect_label",
"reported_effect_size",
"conf_level",
"random_effects",
"show_details"),
columns=list(
list(
`name`="label",
`title`="Study label",
`type`="text"),
list(
`name`="moderator",
`title`="Moderator level",
`type`="text"),
list(
`name`="effect_size",
`type`="number",
`title`="<i>P</i>"),
list(
`name`="LL",
`title`="LL",
`type`="number"),
list(
`name`="UL",
`title`="UL",
`type`="number"),
list(
`name`="weight",
`title`="Weight",
`type`="number",
`visible`="(show_details)"),
list(
`name`="SE",
`title`="<i>SE</i><sub>proportion<sub>",
`type`="number",
`visible`="(show_details)"),
list(
`name`="sample_variance",
`title`="<i>SE</i><sup>2</sup><sub>proportion<sub>",
`type`="number",
`visible`="(show_details)"),
list(
`name`="reference_P",
`title`="<i>P</i><sub>reference</sub>",
`type`="number"),
list(
`name`="reference_cases",
`title`="Cases<sub>reference</sub>",
`type`="integer",
`visible`="(show_details)"),
list(
`name`="reference_N",
`title`="<i>N</i><sub>reference</sub>",
`type`="integer",
`visible`="(show_details)"),
list(
`name`="comparison_P",
`title`="<i>P</i><sub>comparison</sub>",
`type`="number"),
list(
`name`="comparison_cases",
`title`="Cases<sub>comparison</sub>",
`type`="integer",
`visible`="(show_details)"),
list(
`name`="comparison_N",
`title`="<i>N</i><sub>comparison</sub>",
`type`="integer",
`visible`="(show_details)"))))
self$add(jmvcore::Table$new(
options=options,
name="es_meta",
title="Meta-Analytic Effect Sizes",
refs="metafor",
rows=1,
clearWith=list(
"reference_cases",
"reference_ns",
"comparison_cases",
"comparison_ns",
"labels",
"moderator",
"effect_label",
"reported_effect_size",
"conf_level",
"random_effects",
"show_details"),
columns=list(
list(
`name`="effect_label",
`title`="Effect",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="moderator_variable_name",
`title`="Moderator",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="moderator_variable_level",
`title`="Level",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="effect_size",
`type`="number",
`title`="<i>P</i>"),
list(
`name`="LL",
`title`="LL",
`type`="number"),
list(
`name`="UL",
`title`="UL",
`type`="number"),
list(
`name`="SE",
`title`="<i>SE</i>",
`type`="number",
`visible`="(show_details)"),
list(
`name`="k",
`title`="<i>k</i>",
`type`="integer"),
list(
`name`="PI_LL",
`title`="LL",
`type`="number",
`visible`="(include_PIs & random_effects == 'random_effects')"),
list(
`name`="PI_UL",
`title`="UL",
`type`="number",
`visible`="(include_PIs & random_effects == 'random_effects')"),
list(
`name`="p",
`visible`="(show_details)",
`title`="<i>p</i>, two tailed",
`type`="number",
`format`="zto,pvalue"),
list(
`name`="FE_CI_width",
`type`="number",
`title`="FE CI length",
`visible`="(show_details)"),
list(
`name`="RE_CI_width",
`type`="number",
`title`="RE CI length",
`visible`="(show_details)"))))
self$add(jmvcore::Table$new(
options=options,
name="es_heterogeneity",
title="Effect Size Heterogeneity",
rows=1,
clearWith=list(
"reference_cases",
"reference_ns",
"comparison_cases",
"comparison_ns",
"labels",
"moderator",
"effect_label",
"reported_effect_size",
"conf_level",
"random_effects",
"show_details"),
columns=list(
list(
`name`="measure",
`title`="Measure",
`type`="text",
`combineBelow`=TRUE,
`visible`=FALSE),
list(
`name`="measure_html",
`title`="Measure",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="moderator_level",
`title`="Level",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="estimate",
`type`="number",
`title`="Estimate"),
list(
`name`="LL",
`title`="LL",
`type`="number"),
list(
`name`="UL",
`title`="UL",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="es_meta_difference",
title="Moderator Analysis",
rows=3,
clearWith=list(
"reference_cases",
"reference_ns",
"comparison_cases",
"comparison_ns",
"labels",
"moderator",
"effect_label",
"reported_effect_size",
"conf_level",
"random_effects",
"show_details"),
columns=list(
list(
`name`="effect_label",
`title`="Effect",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="moderator_variable_name",
`title`="Moderator",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="moderator_level",
`title`="Level",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="effect_size",
`type`="number",
`title`="<i>P</i>"),
list(
`name`="LL",
`title`="LL",
`type`="number"),
list(
`name`="UL",
`title`="UL",
`type`="number"),
list(
`name`="SE",
`title`="<i>SE</i>",
`type`="number",
`visible`="(show_details)"),
list(
`name`="p",
`visible`="(show_details)",
`title`="<i>p</i>, two tailed",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Html$new(
options=options,
name="estimation_plot_warnings",
title="Forest Plot Warnings",
visible=TRUE))
self$add(jmvcore::Image$new(
options=options,
name="estimation_plots",
title="Forest Plot",
requiresData=TRUE,
width=400,
height=300,
renderFun=".estimation_plots"))}))
jamovimetapdiffBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamovimetapdiffBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "esci",
name = "jamovimetapdiff",
version = c(1,0,0),
options = options,
results = jamovimetapdiffResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
#' Meta-Analysis: Difference in Proportions
#'
#'
#' @param data .
#' @param reference_cases .
#' @param reference_ns .
#' @param comparison_cases .
#' @param comparison_ns .
#' @param labels .
#' @param moderator .
#' @param effect_label .
#' @param reported_effect_size .
#' @param conf_level .
#' @param random_effects .
#' @param include_PIs .
#' @param show_details .
#' @param es_plot_width .
#' @param es_plot_height .
#' @param size_base .
#' @param size_multiplier .
#' @param axis.text.y .
#' @param report_CIs .
#' @param meta_diamond_height .
#' @param xlab .
#' @param xmin .
#' @param xmax .
#' @param xbreaks .
#' @param mark_zero .
#' @param axis.text.x .
#' @param axis.title.x .
#' @param dlab .
#' @param dmin .
#' @param dmax .
#' @param dbreaks .
#' @param shape_raw_reference .
#' @param shape_raw_comparison .
#' @param shape_summary_difference .
#' @param shape_raw_unused .
#' @param color_raw_reference .
#' @param color_raw_comparison .
#' @param color_raw_unused .
#' @param color_summary_reference .
#' @param color_summary_comparison .
#' @param color_summary_unused .
#' @param color_summary_difference .
#' @param color_summary_overall .
#' @param fill_raw_reference .
#' @param fill_raw_comparison .
#' @param fill_raw_unused .
#' @param fill_summary_reference .
#' @param fill_summary_comparison .
#' @param fill_summary_unused .
#' @param fill_summary_difference .
#' @param fill_summary_overall .
#' @param alpha_raw_reference .
#' @param alpha_raw_comparison .
#' @param alpha_raw_unused .
#' @param alpha_summary_reference .
#' @param alpha_summary_comparison .
#' @param alpha_summary_unused .
#' @param alpha_summary_difference .
#' @param alpha_summary_overall .
#' @param linetype_raw_reference .
#' @param linetype_raw_comparison .
#' @param linetype_summary_difference .
#' @param linetype_raw_unused .
#' @param color_interval_reference .
#' @param color_interval_comparison .
#' @param color_interval_difference .
#' @param color_interval_unused .
#' @param size_interval_reference .
#' @param size_interval_comparison .
#' @param size_interval_difference .
#' @param size_interval_unused .
#' @param alpha_interval_reference .
#' @param alpha_interval_comparison .
#' @param alpha_interval_difference .
#' @param alpha_interval_unused .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$debug} \tab \tab \tab \tab \tab a html \cr
#' \code{results$help} \tab \tab \tab \tab \tab a html \cr
#' \code{results$raw_data} \tab \tab \tab \tab \tab a table \cr
#' \code{results$es_meta} \tab \tab \tab \tab \tab a table \cr
#' \code{results$es_heterogeneity} \tab \tab \tab \tab \tab a table \cr
#' \code{results$es_meta_difference} \tab \tab \tab \tab \tab a table \cr
#' \code{results$estimation_plot_warnings} \tab \tab \tab \tab \tab a html \cr
#' \code{results$estimation_plots} \tab \tab \tab \tab \tab an image \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$raw_data$asDF}
#'
#' \code{as.data.frame(results$raw_data)}
#'
#' @export
jamovimetapdiff <- function(
data,
reference_cases,
reference_ns,
comparison_cases,
comparison_ns,
labels,
moderator,
effect_label = "My effect",
reported_effect_size = "RD",
conf_level = 95,
random_effects = "random_effects",
include_PIs = FALSE,
show_details = FALSE,
es_plot_width = "600",
es_plot_height = "750",
size_base = "2",
size_multiplier = "3",
axis.text.y = "14",
report_CIs = FALSE,
meta_diamond_height = ".25",
xlab = "auto",
xmin = "auto",
xmax = "auto",
xbreaks = "auto",
mark_zero = FALSE,
axis.text.x = "14",
axis.title.x = "15",
dlab = "auto",
dmin = "auto",
dmax = "auto",
dbreaks = "auto",
shape_raw_reference = "square filled",
shape_raw_comparison = "square filled",
shape_summary_difference = "triangle filled",
shape_raw_unused = "square filled",
color_raw_reference = "#008DF9",
color_raw_comparison = "#009F81",
color_raw_unused = "gray65",
color_summary_reference = "#008DF9",
color_summary_comparison = "#009F81",
color_summary_unused = "gray75",
color_summary_difference = "black",
color_summary_overall = "black",
fill_raw_reference = "#008DF9",
fill_raw_comparison = "#009F81",
fill_raw_unused = "gray65",
fill_summary_reference = "#008DF9",
fill_summary_comparison = "#009F81",
fill_summary_unused = "gray75",
fill_summary_difference = "black",
fill_summary_overall = "black",
alpha_raw_reference = "1",
alpha_raw_comparison = "1",
alpha_raw_unused = "1",
alpha_summary_reference = "1",
alpha_summary_comparison = "1",
alpha_summary_unused = "1",
alpha_summary_difference = "1",
alpha_summary_overall = "1",
linetype_raw_reference = "solid",
linetype_raw_comparison = "solid",
linetype_summary_difference = "solid",
linetype_raw_unused = "solid",
color_interval_reference = "black",
color_interval_comparison = "black",
color_interval_difference = "black",
color_interval_unused = "black",
size_interval_reference = ".50",
size_interval_comparison = ".50",
size_interval_difference = ".50",
size_interval_unused = ".50",
alpha_interval_reference = "1",
alpha_interval_comparison = "1",
alpha_interval_difference = "1",
alpha_interval_unused = "1") {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("jamovimetapdiff requires jmvcore to be installed (restart may be required)")
if ( ! missing(reference_cases)) reference_cases <- jmvcore::resolveQuo(jmvcore::enquo(reference_cases))
if ( ! missing(reference_ns)) reference_ns <- jmvcore::resolveQuo(jmvcore::enquo(reference_ns))
if ( ! missing(comparison_cases)) comparison_cases <- jmvcore::resolveQuo(jmvcore::enquo(comparison_cases))
if ( ! missing(comparison_ns)) comparison_ns <- jmvcore::resolveQuo(jmvcore::enquo(comparison_ns))
if ( ! missing(labels)) labels <- jmvcore::resolveQuo(jmvcore::enquo(labels))
if ( ! missing(moderator)) moderator <- jmvcore::resolveQuo(jmvcore::enquo(moderator))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(reference_cases), reference_cases, NULL),
`if`( ! missing(reference_ns), reference_ns, NULL),
`if`( ! missing(comparison_cases), comparison_cases, NULL),
`if`( ! missing(comparison_ns), comparison_ns, NULL),
`if`( ! missing(labels), labels, NULL),
`if`( ! missing(moderator), moderator, NULL))
for (v in labels) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
for (v in moderator) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
options <- jamovimetapdiffOptions$new(
reference_cases = reference_cases,
reference_ns = reference_ns,
comparison_cases = comparison_cases,
comparison_ns = comparison_ns,
labels = labels,
moderator = moderator,
effect_label = effect_label,
reported_effect_size = reported_effect_size,
conf_level = conf_level,
random_effects = random_effects,
include_PIs = include_PIs,
show_details = show_details,
es_plot_width = es_plot_width,
es_plot_height = es_plot_height,
size_base = size_base,
size_multiplier = size_multiplier,
axis.text.y = axis.text.y,
report_CIs = report_CIs,
meta_diamond_height = meta_diamond_height,
xlab = xlab,
xmin = xmin,
xmax = xmax,
xbreaks = xbreaks,
mark_zero = mark_zero,
axis.text.x = axis.text.x,
axis.title.x = axis.title.x,
dlab = dlab,
dmin = dmin,
dmax = dmax,
dbreaks = dbreaks,
shape_raw_reference = shape_raw_reference,
shape_raw_comparison = shape_raw_comparison,
shape_summary_difference = shape_summary_difference,
shape_raw_unused = shape_raw_unused,
color_raw_reference = color_raw_reference,
color_raw_comparison = color_raw_comparison,
color_raw_unused = color_raw_unused,
color_summary_reference = color_summary_reference,
color_summary_comparison = color_summary_comparison,
color_summary_unused = color_summary_unused,
color_summary_difference = color_summary_difference,
color_summary_overall = color_summary_overall,
fill_raw_reference = fill_raw_reference,
fill_raw_comparison = fill_raw_comparison,
fill_raw_unused = fill_raw_unused,
fill_summary_reference = fill_summary_reference,
fill_summary_comparison = fill_summary_comparison,
fill_summary_unused = fill_summary_unused,
fill_summary_difference = fill_summary_difference,
fill_summary_overall = fill_summary_overall,
alpha_raw_reference = alpha_raw_reference,
alpha_raw_comparison = alpha_raw_comparison,
alpha_raw_unused = alpha_raw_unused,
alpha_summary_reference = alpha_summary_reference,
alpha_summary_comparison = alpha_summary_comparison,
alpha_summary_unused = alpha_summary_unused,
alpha_summary_difference = alpha_summary_difference,
alpha_summary_overall = alpha_summary_overall,
linetype_raw_reference = linetype_raw_reference,
linetype_raw_comparison = linetype_raw_comparison,
linetype_summary_difference = linetype_summary_difference,
linetype_raw_unused = linetype_raw_unused,
color_interval_reference = color_interval_reference,
color_interval_comparison = color_interval_comparison,
color_interval_difference = color_interval_difference,
color_interval_unused = color_interval_unused,
size_interval_reference = size_interval_reference,
size_interval_comparison = size_interval_comparison,
size_interval_difference = size_interval_difference,
size_interval_unused = size_interval_unused,
alpha_interval_reference = alpha_interval_reference,
alpha_interval_comparison = alpha_interval_comparison,
alpha_interval_difference = alpha_interval_difference,
alpha_interval_unused = alpha_interval_unused)
analysis <- jamovimetapdiffClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
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