Nothing
R/jamovimagnitude.h.R
In esci: Estimation Statistics with Confidence Intervals
Defines functions
jamovimagnitude
Documented in
jamovimagnitude
# This file is automatically generated, you probably don't want to edit this
jamovimagnitudeOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamovimagnitudeOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
switch = "from_raw",
outcome_variable = NULL,
mean = "",
sd = "",
n = "",
outcome_variable_name = "Outcome variable",
conf_level = 95,
effect_size = "mean",
show_details = FALSE,
show_calculations = FALSE,
evaluate_hypotheses = FALSE,
null_value = "0",
null_boundary = "0",
alpha = 0.05,
null_color = "#A40122",
es_plot_width = "300",
es_plot_height = "400",
ymin = "auto",
ymax = "auto",
breaks = "auto",
ylab = "auto",
xlab = "auto",
axis.text.y = "14",
axis.title.y = "15",
axis.text.x = "14",
axis.title.x = "15",
error_layout = "halfeye",
error_scale = "0.20",
error_nudge = "0.3",
data_layout = "random",
data_spread = "0.25",
shape_raw = "circle filled",
shape_summary = "circle filled",
color_raw = "#008DF9",
color_summary = "#008DF9",
fill_raw = "NA",
fill_summary = "#008DF9",
size_raw = "2",
size_summary = "4",
alpha_raw = "1",
alpha_summary = "1",
linetype_summary = "solid",
color_interval = "black",
size_interval = "3",
alpha_interval = "1",
alpha_error = "1",
fill_error = "gray75", ...) {
super$initialize(
package="esci",
name="jamovimagnitude",
requiresData=TRUE,
...)
private$..switch <- jmvcore::OptionList$new(
"switch",
switch,
default="from_raw",
options=list(
"from_raw",
"from_summary"))
private$..outcome_variable <- jmvcore::OptionVariables$new(
"outcome_variable",
outcome_variable,
suggested=list(
"continuous"),
permitted=list(
"numeric"))
private$..mean <- jmvcore::OptionString$new(
"mean",
mean,
default="")
private$..sd <- jmvcore::OptionString$new(
"sd",
sd,
default="")
private$..n <- jmvcore::OptionString$new(
"n",
n,
default="")
private$..outcome_variable_name <- jmvcore::OptionString$new(
"outcome_variable_name",
outcome_variable_name,
default="Outcome variable")
private$..conf_level <- jmvcore::OptionNumber$new(
"conf_level",
conf_level,
default=95)
private$..effect_size <- jmvcore::OptionList$new(
"effect_size",
effect_size,
default="mean",
options=list(
"mean",
"median"))
private$..show_details <- jmvcore::OptionBool$new(
"show_details",
show_details,
default=FALSE)
private$..show_calculations <- jmvcore::OptionBool$new(
"show_calculations",
show_calculations,
default=FALSE)
private$..evaluate_hypotheses <- jmvcore::OptionBool$new(
"evaluate_hypotheses",
evaluate_hypotheses,
default=FALSE)
private$..null_value <- jmvcore::OptionString$new(
"null_value",
null_value,
default="0")
private$..null_boundary <- jmvcore::OptionString$new(
"null_boundary",
null_boundary,
default="0")
private$..alpha <- jmvcore::OptionNumber$new(
"alpha",
alpha,
default=0.05)
private$..null_color <- jmvcore::OptionList$new(
"null_color",
null_color,
default="#A40122",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..es_plot_width <- jmvcore::OptionString$new(
"es_plot_width",
es_plot_width,
default="300")
private$..es_plot_height <- jmvcore::OptionString$new(
"es_plot_height",
es_plot_height,
default="400")
private$..ymin <- jmvcore::OptionString$new(
"ymin",
ymin,
default="auto")
private$..ymax <- jmvcore::OptionString$new(
"ymax",
ymax,
default="auto")
private$..breaks <- jmvcore::OptionString$new(
"breaks",
breaks,
default="auto")
private$..ylab <- jmvcore::OptionString$new(
"ylab",
ylab,
default="auto")
private$..xlab <- jmvcore::OptionString$new(
"xlab",
xlab,
default="auto")
private$..axis.text.y <- jmvcore::OptionString$new(
"axis.text.y",
axis.text.y,
default="14")
private$..axis.title.y <- jmvcore::OptionString$new(
"axis.title.y",
axis.title.y,
default="15")
private$..axis.text.x <- jmvcore::OptionString$new(
"axis.text.x",
axis.text.x,
default="14")
private$..axis.title.x <- jmvcore::OptionString$new(
"axis.title.x",
axis.title.x,
default="15")
private$..error_layout <- jmvcore::OptionList$new(
"error_layout",
error_layout,
default="halfeye",
options=list(
"halfeye",
"eye",
"none"))
private$..error_scale <- jmvcore::OptionString$new(
"error_scale",
error_scale,
default="0.20")
private$..error_nudge <- jmvcore::OptionString$new(
"error_nudge",
error_nudge,
default="0.3")
private$..data_layout <- jmvcore::OptionList$new(
"data_layout",
data_layout,
default="random",
options=list(
"random",
"swarm",
"none"))
private$..data_spread <- jmvcore::OptionString$new(
"data_spread",
data_spread,
default="0.25")
private$..shape_raw <- jmvcore::OptionList$new(
"shape_raw",
shape_raw,
default="circle filled",
options=list(
"circle filled",
"square filled",
"triangle filled",
"diamond filled"))
private$..shape_summary <- jmvcore::OptionList$new(
"shape_summary",
shape_summary,
default="circle filled",
options=list(
"circle filled",
"square filled",
"triangle filled",
"diamond filled"))
private$..color_raw <- jmvcore::OptionList$new(
"color_raw",
color_raw,
default="#008DF9",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..color_summary <- jmvcore::OptionList$new(
"color_summary",
color_summary,
default="#008DF9",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..fill_raw <- jmvcore::OptionList$new(
"fill_raw",
fill_raw,
default="NA",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..fill_summary <- jmvcore::OptionList$new(
"fill_summary",
fill_summary,
default="#008DF9",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..size_raw <- jmvcore::OptionList$new(
"size_raw",
size_raw,
default="2",
options=list(
"1",
"2",
"3",
"4",
"5",
"6"))
private$..size_summary <- jmvcore::OptionList$new(
"size_summary",
size_summary,
default="4",
options=list(
"1",
"2",
"3",
"4",
"5",
"6"))
private$..alpha_raw <- jmvcore::OptionList$new(
"alpha_raw",
alpha_raw,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_summary <- jmvcore::OptionList$new(
"alpha_summary",
alpha_summary,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..linetype_summary <- jmvcore::OptionList$new(
"linetype_summary",
linetype_summary,
default="solid",
options=list(
"solid",
"dotted",
"dotdash",
"dashed",
"blank"))
private$..color_interval <- jmvcore::OptionList$new(
"color_interval",
color_interval,
default="black",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..size_interval <- jmvcore::OptionList$new(
"size_interval",
size_interval,
default="3",
options=list(
"1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"))
private$..alpha_interval <- jmvcore::OptionList$new(
"alpha_interval",
alpha_interval,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_error <- jmvcore::OptionList$new(
"alpha_error",
alpha_error,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..fill_error <- jmvcore::OptionList$new(
"fill_error",
fill_error,
default="gray75",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
self$.addOption(private$..switch)
self$.addOption(private$..outcome_variable)
self$.addOption(private$..mean)
self$.addOption(private$..sd)
self$.addOption(private$..n)
self$.addOption(private$..outcome_variable_name)
self$.addOption(private$..conf_level)
self$.addOption(private$..effect_size)
self$.addOption(private$..show_details)
self$.addOption(private$..show_calculations)
self$.addOption(private$..evaluate_hypotheses)
self$.addOption(private$..null_value)
self$.addOption(private$..null_boundary)
self$.addOption(private$..alpha)
self$.addOption(private$..null_color)
self$.addOption(private$..es_plot_width)
self$.addOption(private$..es_plot_height)
self$.addOption(private$..ymin)
self$.addOption(private$..ymax)
self$.addOption(private$..breaks)
self$.addOption(private$..ylab)
self$.addOption(private$..xlab)
self$.addOption(private$..axis.text.y)
self$.addOption(private$..axis.title.y)
self$.addOption(private$..axis.text.x)
self$.addOption(private$..axis.title.x)
self$.addOption(private$..error_layout)
self$.addOption(private$..error_scale)
self$.addOption(private$..error_nudge)
self$.addOption(private$..data_layout)
self$.addOption(private$..data_spread)
self$.addOption(private$..shape_raw)
self$.addOption(private$..shape_summary)
self$.addOption(private$..color_raw)
self$.addOption(private$..color_summary)
self$.addOption(private$..fill_raw)
self$.addOption(private$..fill_summary)
self$.addOption(private$..size_raw)
self$.addOption(private$..size_summary)
self$.addOption(private$..alpha_raw)
self$.addOption(private$..alpha_summary)
self$.addOption(private$..linetype_summary)
self$.addOption(private$..color_interval)
self$.addOption(private$..size_interval)
self$.addOption(private$..alpha_interval)
self$.addOption(private$..alpha_error)
self$.addOption(private$..fill_error)
}),
active = list(
switch = function() private$..switch$value,
outcome_variable = function() private$..outcome_variable$value,
mean = function() private$..mean$value,
sd = function() private$..sd$value,
n = function() private$..n$value,
outcome_variable_name = function() private$..outcome_variable_name$value,
conf_level = function() private$..conf_level$value,
effect_size = function() private$..effect_size$value,
show_details = function() private$..show_details$value,
show_calculations = function() private$..show_calculations$value,
evaluate_hypotheses = function() private$..evaluate_hypotheses$value,
null_value = function() private$..null_value$value,
null_boundary = function() private$..null_boundary$value,
alpha = function() private$..alpha$value,
null_color = function() private$..null_color$value,
es_plot_width = function() private$..es_plot_width$value,
es_plot_height = function() private$..es_plot_height$value,
ymin = function() private$..ymin$value,
ymax = function() private$..ymax$value,
breaks = function() private$..breaks$value,
ylab = function() private$..ylab$value,
xlab = function() private$..xlab$value,
axis.text.y = function() private$..axis.text.y$value,
axis.title.y = function() private$..axis.title.y$value,
axis.text.x = function() private$..axis.text.x$value,
axis.title.x = function() private$..axis.title.x$value,
error_layout = function() private$..error_layout$value,
error_scale = function() private$..error_scale$value,
error_nudge = function() private$..error_nudge$value,
data_layout = function() private$..data_layout$value,
data_spread = function() private$..data_spread$value,
shape_raw = function() private$..shape_raw$value,
shape_summary = function() private$..shape_summary$value,
color_raw = function() private$..color_raw$value,
color_summary = function() private$..color_summary$value,
fill_raw = function() private$..fill_raw$value,
fill_summary = function() private$..fill_summary$value,
size_raw = function() private$..size_raw$value,
size_summary = function() private$..size_summary$value,
alpha_raw = function() private$..alpha_raw$value,
alpha_summary = function() private$..alpha_summary$value,
linetype_summary = function() private$..linetype_summary$value,
color_interval = function() private$..color_interval$value,
size_interval = function() private$..size_interval$value,
alpha_interval = function() private$..alpha_interval$value,
alpha_error = function() private$..alpha_error$value,
fill_error = function() private$..fill_error$value),
private = list(
..switch = NA,
..outcome_variable = NA,
..mean = NA,
..sd = NA,
..n = NA,
..outcome_variable_name = NA,
..conf_level = NA,
..effect_size = NA,
..show_details = NA,
..show_calculations = NA,
..evaluate_hypotheses = NA,
..null_value = NA,
..null_boundary = NA,
..alpha = NA,
..null_color = NA,
..es_plot_width = NA,
..es_plot_height = NA,
..ymin = NA,
..ymax = NA,
..breaks = NA,
..ylab = NA,
..xlab = NA,
..axis.text.y = NA,
..axis.title.y = NA,
..axis.text.x = NA,
..axis.title.x = NA,
..error_layout = NA,
..error_scale = NA,
..error_nudge = NA,
..data_layout = NA,
..data_spread = NA,
..shape_raw = NA,
..shape_summary = NA,
..color_raw = NA,
..color_summary = NA,
..fill_raw = NA,
..fill_summary = NA,
..size_raw = NA,
..size_summary = NA,
..alpha_raw = NA,
..alpha_summary = NA,
..linetype_summary = NA,
..color_interval = NA,
..size_interval = NA,
..alpha_interval = NA,
..alpha_error = NA,
..fill_error = NA)
)
jamovimagnitudeResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamovimagnitudeResults",
inherit = jmvcore::Group,
active = list(
debug = function() private$.items[["debug"]],
help = function() private$.items[["help"]],
overview = function() private$.items[["overview"]],
es_smd = function() private$.items[["es_smd"]],
point_null = function() private$.items[["point_null"]],
interval_null = function() private$.items[["interval_null"]],
magnitude_plot_warnings = function() private$.items[["magnitude_plot_warnings"]],
magnitude_plot = function() private$.items[["magnitude_plot"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Means and Medians: Single Group")
self$add(jmvcore::Preformatted$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="overview",
title="Overview",
rows="(outcome_variable)",
clearWith=list(
"outcome_variable",
"mean",
"sd",
"n",
"outcome_variable_name",
"conf_level",
"effect_size",
"show_details",
"show_calculations"),
columns=list(
list(
`name`="outcome_variable_name",
`title`="Outcome variable",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="mean",
`type`="number",
`title`="<i>M</i>"),
list(
`name`="mean_LL",
`title`="LL",
`type`="number",
`visible`="(effect_size == 'mean' | switch == 'from_summary')"),
list(
`name`="mean_UL",
`title`="UL",
`type`="number",
`visible`="(effect_size == 'mean' | switch == 'from_summary')"),
list(
`name`="moe",
`type`="number",
`title`="<i>MoE</i>",
`visible`="(show_details & effect_size == 'mean')"),
list(
`name`="mean_SE",
`title`="<i>SE</i><sub>Mean</sub>",
`type`="number",
`visible`="(show_details & effect_size == 'mean')"),
list(
`name`="median",
`title`="<i>Mdn</i>",
`type`="number",
`visible`="(switch == 'from_raw')"),
list(
`name`="median_LL",
`title`="LL",
`type`="number",
`visible`="(effect_size == 'median' & switch == 'from_raw')"),
list(
`name`="median_UL",
`title`="UL",
`type`="number",
`visible`="(effect_size == 'median' & switch == 'from_raw')"),
list(
`name`="median_SE",
`type`="number",
`title`="<i>SE</i><sub>Median</sub>",
`visible`="(show_details & effect_size == 'median' & switch == 'from_raw')"),
list(
`name`="sd",
`type`="number",
`title`="<i>s</i>"),
list(
`name`="min",
`title`="Minimum",
`type`="number",
`visible`="(switch == 'from_raw' & show_details)"),
list(
`name`="max",
`title`="Maximum",
`type`="number",
`visible`="(switch == 'from_raw' & show_details)"),
list(
`name`="q1",
`title`="25th",
`type`="number",
`superTitle`="Percentile",
`visible`="(switch == 'from_raw' & show_details)"),
list(
`name`="q3",
`title`="75th",
`type`="number",
`superTitle`="Percentile",
`visible`="(switch == 'from_raw' & show_details)"),
list(
`name`="n",
`title`="<i>N</i>",
`type`="integer"),
list(
`name`="missing",
`type`="integer",
`title`="Missing",
`visible`="(switch == 'from_raw')"),
list(
`name`="df_i",
`title`="<i>df</i>",
`type`="integer",
`visible`="(show_details & effect_size == 'mean')"),
list(
`name`="t_multiplier",
`type`="number",
`title`="<i>t</i>",
`superTitle`="Calculation component",
`visible`="(show_calculations & effect_size == 'mean')"),
list(
`name`="s_component",
`type`="number",
`title`="Variability",
`superTitle`="Calculation component",
`visible`="(show_calculations & effect_size == 'mean')"),
list(
`name`="n_component",
`type`="number",
`title`="Sample size",
`superTitle`="Calculation component",
`visible`="(show_calculations & effect_size == 'mean')"))))
self$add(jmvcore::Table$new(
options=options,
name="es_smd",
title="Standardized Mean Difference",
rows="(outcome_variable)",
visible="(effect_size == 'mean' & evaluate_hypotheses)",
clearWith=list(
"outcome_variable",
"mean",
"sd",
"n",
"outcome_variable_name",
"conf_level",
"effect_size",
"show_details",
"show_calculations"),
columns=list(
list(
`name`="outcome_variable_name",
`title`="Outcome variable",
`type`="text",
`combineBelow`=TRUE,
`visible`=FALSE),
list(
`name`="effect",
`title`="Effect",
`type`="text"),
list(
`name`="mean",
`title`="<i>M</i>",
`type`="number"),
list(
`name`="reference_value",
`title`="Reference value",
`type`="number"),
list(
`name`="numerator",
`title`="<i>M</i> – Reference",
`superTitle`="Numerator",
`type`="number"),
list(
`name`="denominator",
`title`="Standardizer",
`superTitle`="Standardizer",
`type`="number"),
list(
`name`="effect_size",
`type`="number",
`title`="<i>d</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`="df",
`title`="<i>df</i>",
`type`="integer",
`visible`="(show_details)"),
list(
`name`="d_biased",
`title`="<i>d</i><sub>biased</sub>",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="point_null",
title="Hypothesis Evaluation",
rows=1,
visible="(evaluate_hypotheses & null_boundary == 0)",
clearWith=list(
"outcome_variable",
"mean",
"sd",
"n",
"outcome_variable_name",
"conf_level",
"effect_size",
"show_details",
"show_calculations",
"null_value",
"null_boundary"),
columns=list(
list(
`name`="effect",
`title`="Effect",
`type`="text",
`combineBelow`=FALSE),
list(
`name`="null_words",
`title`="<i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="CI",
`title`="CI",
`type`="text"),
list(
`name`="CI_compare",
`title`="Compare CI with <i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="t",
`title`="<i>t</i>",
`type`="number",
`visible`="(effect_size == 'mean')"),
list(
`name`="df",
`title`="<i>df</i>",
`type`="integer",
`visible`="(effect_size == 'mean')"),
list(
`name`="p",
`title`="<i>p</i>, two tailed",
`type`="number",
`format`="zto,pvalue",
`visible`="(effect_size == 'mean')"),
list(
`name`="p_result",
`title`="<i>p</i>, two-tailed",
`type`="text",
`visible`="(effect_size == 'median')"),
list(
`name`="null_decision",
`title`="<i>H</i><sub>0</sub> decision"),
list(
`name`="conclusion",
`title`="Conclusion",
`type`="text"))))
self$add(jmvcore::Table$new(
options=options,
name="interval_null",
title="Hypothesis Evaluation",
rows=1,
visible="(evaluate_hypotheses & null_boundary != 0)",
clearWith=list(
"outcome_variable",
"mean",
"sd",
"n",
"outcome_variable_name",
"conf_level",
"effect_size",
"show_details",
"show_calculations",
"null_value",
"null_boundary"),
columns=list(
list(
`name`="effect",
`title`="Effect",
`type`="text",
`combineBelow`=FALSE),
list(
`name`="rope",
`title`="<i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="CI",
`title`="CI",
`type`="text"),
list(
`name`="rope_compare",
`title`="Compare CI with <i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="p_result",
`title`="<i>p</i>, two tailed",
`type`="text"),
list(
`name`="conclusion",
`title`="Conclusion",
`type`="text"))))
self$add(jmvcore::Html$new(
options=options,
name="magnitude_plot_warnings",
title="Figure Warnings",
visible=TRUE))
self$add(jmvcore::Image$new(
options=options,
name="magnitude_plot",
title="Estimation Figure",
requiresData=TRUE,
width=400,
height=300,
renderFun=".magnitude_plot",
refs="ggdist"))}))
jamovimagnitudeBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamovimagnitudeBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "esci",
name = "jamovimagnitude",
version = c(1,0,0),
options = options,
results = jamovimagnitudeResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
#' Means and Medians: Single Group
#'
#'
#' @param switch .
#' @param data .
#' @param outcome_variable .
#' @param mean .
#' @param sd .
#' @param n .
#' @param outcome_variable_name .
#' @param conf_level .
#' @param effect_size .
#' @param show_details .
#' @param show_calculations .
#' @param evaluate_hypotheses .
#' @param null_value .
#' @param null_boundary .
#' @param alpha .
#' @param null_color .
#' @param es_plot_width .
#' @param es_plot_height .
#' @param ymin .
#' @param ymax .
#' @param breaks .
#' @param ylab .
#' @param xlab .
#' @param axis.text.y .
#' @param axis.title.y .
#' @param axis.text.x .
#' @param axis.title.x .
#' @param error_layout .
#' @param error_scale .
#' @param error_nudge .
#' @param data_layout .
#' @param data_spread .
#' @param shape_raw .
#' @param shape_summary .
#' @param color_raw .
#' @param color_summary .
#' @param fill_raw .
#' @param fill_summary .
#' @param size_raw .
#' @param size_summary .
#' @param alpha_raw .
#' @param alpha_summary .
#' @param linetype_summary .
#' @param color_interval .
#' @param size_interval .
#' @param alpha_interval .
#' @param alpha_error .
#' @param fill_error .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$debug} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$help} \tab \tab \tab \tab \tab a html \cr
#' \code{results$overview} \tab \tab \tab \tab \tab a table \cr
#' \code{results$es_smd} \tab \tab \tab \tab \tab a table \cr
#' \code{results$point_null} \tab \tab \tab \tab \tab a table \cr
#' \code{results$interval_null} \tab \tab \tab \tab \tab a table \cr
#' \code{results$magnitude_plot_warnings} \tab \tab \tab \tab \tab a html \cr
#' \code{results$magnitude_plot} \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$overview$asDF}
#'
#' \code{as.data.frame(results$overview)}
#'
#' @export
jamovimagnitude <- function(
switch = "from_raw",
data,
outcome_variable,
mean = "",
sd = "",
n = "",
outcome_variable_name = "Outcome variable",
conf_level = 95,
effect_size = "mean",
show_details = FALSE,
show_calculations = FALSE,
evaluate_hypotheses = FALSE,
null_value = "0",
null_boundary = "0",
alpha = 0.05,
null_color = "#A40122",
es_plot_width = "300",
es_plot_height = "400",
ymin = "auto",
ymax = "auto",
breaks = "auto",
ylab = "auto",
xlab = "auto",
axis.text.y = "14",
axis.title.y = "15",
axis.text.x = "14",
axis.title.x = "15",
error_layout = "halfeye",
error_scale = "0.20",
error_nudge = "0.3",
data_layout = "random",
data_spread = "0.25",
shape_raw = "circle filled",
shape_summary = "circle filled",
color_raw = "#008DF9",
color_summary = "#008DF9",
fill_raw = "NA",
fill_summary = "#008DF9",
size_raw = "2",
size_summary = "4",
alpha_raw = "1",
alpha_summary = "1",
linetype_summary = "solid",
color_interval = "black",
size_interval = "3",
alpha_interval = "1",
alpha_error = "1",
fill_error = "gray75") {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("jamovimagnitude requires jmvcore to be installed (restart may be required)")
if ( ! missing(outcome_variable)) outcome_variable <- jmvcore::resolveQuo(jmvcore::enquo(outcome_variable))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(outcome_variable), outcome_variable, NULL))
options <- jamovimagnitudeOptions$new(
switch = switch,
outcome_variable = outcome_variable,
mean = mean,
sd = sd,
n = n,
outcome_variable_name = outcome_variable_name,
conf_level = conf_level,
effect_size = effect_size,
show_details = show_details,
show_calculations = show_calculations,
evaluate_hypotheses = evaluate_hypotheses,
null_value = null_value,
null_boundary = null_boundary,
alpha = alpha,
null_color = null_color,
es_plot_width = es_plot_width,
es_plot_height = es_plot_height,
ymin = ymin,
ymax = ymax,
breaks = breaks,
ylab = ylab,
xlab = xlab,
axis.text.y = axis.text.y,
axis.title.y = axis.title.y,
axis.text.x = axis.text.x,
axis.title.x = axis.title.x,
error_layout = error_layout,
error_scale = error_scale,
error_nudge = error_nudge,
data_layout = data_layout,
data_spread = data_spread,
shape_raw = shape_raw,
shape_summary = shape_summary,
color_raw = color_raw,
color_summary = color_summary,
fill_raw = fill_raw,
fill_summary = fill_summary,
size_raw = size_raw,
size_summary = size_summary,
alpha_raw = alpha_raw,
alpha_summary = alpha_summary,
linetype_summary = linetype_summary,
color_interval = color_interval,
size_interval = size_interval,
alpha_interval = alpha_interval,
alpha_error = alpha_error,
fill_error = fill_error)
analysis <- jamovimagnitudeClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
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Defines functions jamovimagnitude
Documented in jamovimagnitude
# This file is automatically generated, you probably don't want to edit this
jamovimagnitudeOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamovimagnitudeOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
switch = "from_raw",
outcome_variable = NULL,
mean = "",
sd = "",
n = "",
outcome_variable_name = "Outcome variable",
conf_level = 95,
effect_size = "mean",
show_details = FALSE,
show_calculations = FALSE,
evaluate_hypotheses = FALSE,
null_value = "0",
null_boundary = "0",
alpha = 0.05,
null_color = "#A40122",
es_plot_width = "300",
es_plot_height = "400",
ymin = "auto",
ymax = "auto",
breaks = "auto",
ylab = "auto",
xlab = "auto",
axis.text.y = "14",
axis.title.y = "15",
axis.text.x = "14",
axis.title.x = "15",
error_layout = "halfeye",
error_scale = "0.20",
error_nudge = "0.3",
data_layout = "random",
data_spread = "0.25",
shape_raw = "circle filled",
shape_summary = "circle filled",
color_raw = "#008DF9",
color_summary = "#008DF9",
fill_raw = "NA",
fill_summary = "#008DF9",
size_raw = "2",
size_summary = "4",
alpha_raw = "1",
alpha_summary = "1",
linetype_summary = "solid",
color_interval = "black",
size_interval = "3",
alpha_interval = "1",
alpha_error = "1",
fill_error = "gray75", ...) {
super$initialize(
package="esci",
name="jamovimagnitude",
requiresData=TRUE,
...)
private$..switch <- jmvcore::OptionList$new(
"switch",
switch,
default="from_raw",
options=list(
"from_raw",
"from_summary"))
private$..outcome_variable <- jmvcore::OptionVariables$new(
"outcome_variable",
outcome_variable,
suggested=list(
"continuous"),
permitted=list(
"numeric"))
private$..mean <- jmvcore::OptionString$new(
"mean",
mean,
default="")
private$..sd <- jmvcore::OptionString$new(
"sd",
sd,
default="")
private$..n <- jmvcore::OptionString$new(
"n",
n,
default="")
private$..outcome_variable_name <- jmvcore::OptionString$new(
"outcome_variable_name",
outcome_variable_name,
default="Outcome variable")
private$..conf_level <- jmvcore::OptionNumber$new(
"conf_level",
conf_level,
default=95)
private$..effect_size <- jmvcore::OptionList$new(
"effect_size",
effect_size,
default="mean",
options=list(
"mean",
"median"))
private$..show_details <- jmvcore::OptionBool$new(
"show_details",
show_details,
default=FALSE)
private$..show_calculations <- jmvcore::OptionBool$new(
"show_calculations",
show_calculations,
default=FALSE)
private$..evaluate_hypotheses <- jmvcore::OptionBool$new(
"evaluate_hypotheses",
evaluate_hypotheses,
default=FALSE)
private$..null_value <- jmvcore::OptionString$new(
"null_value",
null_value,
default="0")
private$..null_boundary <- jmvcore::OptionString$new(
"null_boundary",
null_boundary,
default="0")
private$..alpha <- jmvcore::OptionNumber$new(
"alpha",
alpha,
default=0.05)
private$..null_color <- jmvcore::OptionList$new(
"null_color",
null_color,
default="#A40122",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..es_plot_width <- jmvcore::OptionString$new(
"es_plot_width",
es_plot_width,
default="300")
private$..es_plot_height <- jmvcore::OptionString$new(
"es_plot_height",
es_plot_height,
default="400")
private$..ymin <- jmvcore::OptionString$new(
"ymin",
ymin,
default="auto")
private$..ymax <- jmvcore::OptionString$new(
"ymax",
ymax,
default="auto")
private$..breaks <- jmvcore::OptionString$new(
"breaks",
breaks,
default="auto")
private$..ylab <- jmvcore::OptionString$new(
"ylab",
ylab,
default="auto")
private$..xlab <- jmvcore::OptionString$new(
"xlab",
xlab,
default="auto")
private$..axis.text.y <- jmvcore::OptionString$new(
"axis.text.y",
axis.text.y,
default="14")
private$..axis.title.y <- jmvcore::OptionString$new(
"axis.title.y",
axis.title.y,
default="15")
private$..axis.text.x <- jmvcore::OptionString$new(
"axis.text.x",
axis.text.x,
default="14")
private$..axis.title.x <- jmvcore::OptionString$new(
"axis.title.x",
axis.title.x,
default="15")
private$..error_layout <- jmvcore::OptionList$new(
"error_layout",
error_layout,
default="halfeye",
options=list(
"halfeye",
"eye",
"none"))
private$..error_scale <- jmvcore::OptionString$new(
"error_scale",
error_scale,
default="0.20")
private$..error_nudge <- jmvcore::OptionString$new(
"error_nudge",
error_nudge,
default="0.3")
private$..data_layout <- jmvcore::OptionList$new(
"data_layout",
data_layout,
default="random",
options=list(
"random",
"swarm",
"none"))
private$..data_spread <- jmvcore::OptionString$new(
"data_spread",
data_spread,
default="0.25")
private$..shape_raw <- jmvcore::OptionList$new(
"shape_raw",
shape_raw,
default="circle filled",
options=list(
"circle filled",
"square filled",
"triangle filled",
"diamond filled"))
private$..shape_summary <- jmvcore::OptionList$new(
"shape_summary",
shape_summary,
default="circle filled",
options=list(
"circle filled",
"square filled",
"triangle filled",
"diamond filled"))
private$..color_raw <- jmvcore::OptionList$new(
"color_raw",
color_raw,
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$..color_summary <- jmvcore::OptionList$new(
"color_summary",
color_summary,
default="#008DF9",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..fill_raw <- jmvcore::OptionList$new(
"fill_raw",
fill_raw,
default="NA",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..fill_summary <- jmvcore::OptionList$new(
"fill_summary",
fill_summary,
default="#008DF9",
options=list(
"black",
"#00C2F9",
"#008DF9",
"#009F81",
"#FF5AAF",
"#9F0162",
"#A40122",
"#00FCCF",
"#FF6E3A",
"#FFB2FD",
"#8400CD",
"#E20134",
"#FFC33B",
"white",
"NA",
"NA",
"gray0",
"gray5",
"gray10",
"gray15",
"gray20",
"gray25",
"gray30",
"gray35",
"gray40",
"gray45",
"gray50",
"gray55",
"gray60",
"gray65",
"gray70",
"gray75",
"gray80",
"gray85",
"gray90",
"gray95",
"gray100"))
private$..size_raw <- jmvcore::OptionList$new(
"size_raw",
size_raw,
default="2",
options=list(
"1",
"2",
"3",
"4",
"5",
"6"))
private$..size_summary <- jmvcore::OptionList$new(
"size_summary",
size_summary,
default="4",
options=list(
"1",
"2",
"3",
"4",
"5",
"6"))
private$..alpha_raw <- jmvcore::OptionList$new(
"alpha_raw",
alpha_raw,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_summary <- jmvcore::OptionList$new(
"alpha_summary",
alpha_summary,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..linetype_summary <- jmvcore::OptionList$new(
"linetype_summary",
linetype_summary,
default="solid",
options=list(
"solid",
"dotted",
"dotdash",
"dashed",
"blank"))
private$..color_interval <- jmvcore::OptionList$new(
"color_interval",
color_interval,
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$..size_interval <- jmvcore::OptionList$new(
"size_interval",
size_interval,
default="3",
options=list(
"1",
"2",
"3",
"4",
"5",
"6",
"7",
"8"))
private$..alpha_interval <- jmvcore::OptionList$new(
"alpha_interval",
alpha_interval,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..alpha_error <- jmvcore::OptionList$new(
"alpha_error",
alpha_error,
default="1",
options=list(
"1",
".75",
".5",
".25",
".20",
".15",
".10",
".05",
"0"))
private$..fill_error <- jmvcore::OptionList$new(
"fill_error",
fill_error,
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"))
self$.addOption(private$..switch)
self$.addOption(private$..outcome_variable)
self$.addOption(private$..mean)
self$.addOption(private$..sd)
self$.addOption(private$..n)
self$.addOption(private$..outcome_variable_name)
self$.addOption(private$..conf_level)
self$.addOption(private$..effect_size)
self$.addOption(private$..show_details)
self$.addOption(private$..show_calculations)
self$.addOption(private$..evaluate_hypotheses)
self$.addOption(private$..null_value)
self$.addOption(private$..null_boundary)
self$.addOption(private$..alpha)
self$.addOption(private$..null_color)
self$.addOption(private$..es_plot_width)
self$.addOption(private$..es_plot_height)
self$.addOption(private$..ymin)
self$.addOption(private$..ymax)
self$.addOption(private$..breaks)
self$.addOption(private$..ylab)
self$.addOption(private$..xlab)
self$.addOption(private$..axis.text.y)
self$.addOption(private$..axis.title.y)
self$.addOption(private$..axis.text.x)
self$.addOption(private$..axis.title.x)
self$.addOption(private$..error_layout)
self$.addOption(private$..error_scale)
self$.addOption(private$..error_nudge)
self$.addOption(private$..data_layout)
self$.addOption(private$..data_spread)
self$.addOption(private$..shape_raw)
self$.addOption(private$..shape_summary)
self$.addOption(private$..color_raw)
self$.addOption(private$..color_summary)
self$.addOption(private$..fill_raw)
self$.addOption(private$..fill_summary)
self$.addOption(private$..size_raw)
self$.addOption(private$..size_summary)
self$.addOption(private$..alpha_raw)
self$.addOption(private$..alpha_summary)
self$.addOption(private$..linetype_summary)
self$.addOption(private$..color_interval)
self$.addOption(private$..size_interval)
self$.addOption(private$..alpha_interval)
self$.addOption(private$..alpha_error)
self$.addOption(private$..fill_error)
}),
active = list(
switch = function() private$..switch$value,
outcome_variable = function() private$..outcome_variable$value,
mean = function() private$..mean$value,
sd = function() private$..sd$value,
n = function() private$..n$value,
outcome_variable_name = function() private$..outcome_variable_name$value,
conf_level = function() private$..conf_level$value,
effect_size = function() private$..effect_size$value,
show_details = function() private$..show_details$value,
show_calculations = function() private$..show_calculations$value,
evaluate_hypotheses = function() private$..evaluate_hypotheses$value,
null_value = function() private$..null_value$value,
null_boundary = function() private$..null_boundary$value,
alpha = function() private$..alpha$value,
null_color = function() private$..null_color$value,
es_plot_width = function() private$..es_plot_width$value,
es_plot_height = function() private$..es_plot_height$value,
ymin = function() private$..ymin$value,
ymax = function() private$..ymax$value,
breaks = function() private$..breaks$value,
ylab = function() private$..ylab$value,
xlab = function() private$..xlab$value,
axis.text.y = function() private$..axis.text.y$value,
axis.title.y = function() private$..axis.title.y$value,
axis.text.x = function() private$..axis.text.x$value,
axis.title.x = function() private$..axis.title.x$value,
error_layout = function() private$..error_layout$value,
error_scale = function() private$..error_scale$value,
error_nudge = function() private$..error_nudge$value,
data_layout = function() private$..data_layout$value,
data_spread = function() private$..data_spread$value,
shape_raw = function() private$..shape_raw$value,
shape_summary = function() private$..shape_summary$value,
color_raw = function() private$..color_raw$value,
color_summary = function() private$..color_summary$value,
fill_raw = function() private$..fill_raw$value,
fill_summary = function() private$..fill_summary$value,
size_raw = function() private$..size_raw$value,
size_summary = function() private$..size_summary$value,
alpha_raw = function() private$..alpha_raw$value,
alpha_summary = function() private$..alpha_summary$value,
linetype_summary = function() private$..linetype_summary$value,
color_interval = function() private$..color_interval$value,
size_interval = function() private$..size_interval$value,
alpha_interval = function() private$..alpha_interval$value,
alpha_error = function() private$..alpha_error$value,
fill_error = function() private$..fill_error$value),
private = list(
..switch = NA,
..outcome_variable = NA,
..mean = NA,
..sd = NA,
..n = NA,
..outcome_variable_name = NA,
..conf_level = NA,
..effect_size = NA,
..show_details = NA,
..show_calculations = NA,
..evaluate_hypotheses = NA,
..null_value = NA,
..null_boundary = NA,
..alpha = NA,
..null_color = NA,
..es_plot_width = NA,
..es_plot_height = NA,
..ymin = NA,
..ymax = NA,
..breaks = NA,
..ylab = NA,
..xlab = NA,
..axis.text.y = NA,
..axis.title.y = NA,
..axis.text.x = NA,
..axis.title.x = NA,
..error_layout = NA,
..error_scale = NA,
..error_nudge = NA,
..data_layout = NA,
..data_spread = NA,
..shape_raw = NA,
..shape_summary = NA,
..color_raw = NA,
..color_summary = NA,
..fill_raw = NA,
..fill_summary = NA,
..size_raw = NA,
..size_summary = NA,
..alpha_raw = NA,
..alpha_summary = NA,
..linetype_summary = NA,
..color_interval = NA,
..size_interval = NA,
..alpha_interval = NA,
..alpha_error = NA,
..fill_error = NA)
)
jamovimagnitudeResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamovimagnitudeResults",
inherit = jmvcore::Group,
active = list(
debug = function() private$.items[["debug"]],
help = function() private$.items[["help"]],
overview = function() private$.items[["overview"]],
es_smd = function() private$.items[["es_smd"]],
point_null = function() private$.items[["point_null"]],
interval_null = function() private$.items[["interval_null"]],
magnitude_plot_warnings = function() private$.items[["magnitude_plot_warnings"]],
magnitude_plot = function() private$.items[["magnitude_plot"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Means and Medians: Single Group")
self$add(jmvcore::Preformatted$new(
options=options,
name="debug",
visible=FALSE))
self$add(jmvcore::Html$new(
options=options,
name="help",
visible=FALSE))
self$add(jmvcore::Table$new(
options=options,
name="overview",
title="Overview",
rows="(outcome_variable)",
clearWith=list(
"outcome_variable",
"mean",
"sd",
"n",
"outcome_variable_name",
"conf_level",
"effect_size",
"show_details",
"show_calculations"),
columns=list(
list(
`name`="outcome_variable_name",
`title`="Outcome variable",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="mean",
`type`="number",
`title`="<i>M</i>"),
list(
`name`="mean_LL",
`title`="LL",
`type`="number",
`visible`="(effect_size == 'mean' | switch == 'from_summary')"),
list(
`name`="mean_UL",
`title`="UL",
`type`="number",
`visible`="(effect_size == 'mean' | switch == 'from_summary')"),
list(
`name`="moe",
`type`="number",
`title`="<i>MoE</i>",
`visible`="(show_details & effect_size == 'mean')"),
list(
`name`="mean_SE",
`title`="<i>SE</i><sub>Mean</sub>",
`type`="number",
`visible`="(show_details & effect_size == 'mean')"),
list(
`name`="median",
`title`="<i>Mdn</i>",
`type`="number",
`visible`="(switch == 'from_raw')"),
list(
`name`="median_LL",
`title`="LL",
`type`="number",
`visible`="(effect_size == 'median' & switch == 'from_raw')"),
list(
`name`="median_UL",
`title`="UL",
`type`="number",
`visible`="(effect_size == 'median' & switch == 'from_raw')"),
list(
`name`="median_SE",
`type`="number",
`title`="<i>SE</i><sub>Median</sub>",
`visible`="(show_details & effect_size == 'median' & switch == 'from_raw')"),
list(
`name`="sd",
`type`="number",
`title`="<i>s</i>"),
list(
`name`="min",
`title`="Minimum",
`type`="number",
`visible`="(switch == 'from_raw' & show_details)"),
list(
`name`="max",
`title`="Maximum",
`type`="number",
`visible`="(switch == 'from_raw' & show_details)"),
list(
`name`="q1",
`title`="25th",
`type`="number",
`superTitle`="Percentile",
`visible`="(switch == 'from_raw' & show_details)"),
list(
`name`="q3",
`title`="75th",
`type`="number",
`superTitle`="Percentile",
`visible`="(switch == 'from_raw' & show_details)"),
list(
`name`="n",
`title`="<i>N</i>",
`type`="integer"),
list(
`name`="missing",
`type`="integer",
`title`="Missing",
`visible`="(switch == 'from_raw')"),
list(
`name`="df_i",
`title`="<i>df</i>",
`type`="integer",
`visible`="(show_details & effect_size == 'mean')"),
list(
`name`="t_multiplier",
`type`="number",
`title`="<i>t</i>",
`superTitle`="Calculation component",
`visible`="(show_calculations & effect_size == 'mean')"),
list(
`name`="s_component",
`type`="number",
`title`="Variability",
`superTitle`="Calculation component",
`visible`="(show_calculations & effect_size == 'mean')"),
list(
`name`="n_component",
`type`="number",
`title`="Sample size",
`superTitle`="Calculation component",
`visible`="(show_calculations & effect_size == 'mean')"))))
self$add(jmvcore::Table$new(
options=options,
name="es_smd",
title="Standardized Mean Difference",
rows="(outcome_variable)",
visible="(effect_size == 'mean' & evaluate_hypotheses)",
clearWith=list(
"outcome_variable",
"mean",
"sd",
"n",
"outcome_variable_name",
"conf_level",
"effect_size",
"show_details",
"show_calculations"),
columns=list(
list(
`name`="outcome_variable_name",
`title`="Outcome variable",
`type`="text",
`combineBelow`=TRUE,
`visible`=FALSE),
list(
`name`="effect",
`title`="Effect",
`type`="text"),
list(
`name`="mean",
`title`="<i>M</i>",
`type`="number"),
list(
`name`="reference_value",
`title`="Reference value",
`type`="number"),
list(
`name`="numerator",
`title`="<i>M</i> – Reference",
`superTitle`="Numerator",
`type`="number"),
list(
`name`="denominator",
`title`="Standardizer",
`superTitle`="Standardizer",
`type`="number"),
list(
`name`="effect_size",
`type`="number",
`title`="<i>d</i>"),
list(
`name`="LL",
`title`="LL",
`type`="number"),
list(
`name`="UL",
`title`="UL",
`type`="number"),
list(
`name`="SE",
`title`="<i>SE</i>",
`type`="number",
`visible`="(show_details)"),
list(
`name`="df",
`title`="<i>df</i>",
`type`="integer",
`visible`="(show_details)"),
list(
`name`="d_biased",
`title`="<i>d</i><sub>biased</sub>",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="point_null",
title="Hypothesis Evaluation",
rows=1,
visible="(evaluate_hypotheses & null_boundary == 0)",
clearWith=list(
"outcome_variable",
"mean",
"sd",
"n",
"outcome_variable_name",
"conf_level",
"effect_size",
"show_details",
"show_calculations",
"null_value",
"null_boundary"),
columns=list(
list(
`name`="effect",
`title`="Effect",
`type`="text",
`combineBelow`=FALSE),
list(
`name`="null_words",
`title`="<i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="CI",
`title`="CI",
`type`="text"),
list(
`name`="CI_compare",
`title`="Compare CI with <i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="t",
`title`="<i>t</i>",
`type`="number",
`visible`="(effect_size == 'mean')"),
list(
`name`="df",
`title`="<i>df</i>",
`type`="integer",
`visible`="(effect_size == 'mean')"),
list(
`name`="p",
`title`="<i>p</i>, two tailed",
`type`="number",
`format`="zto,pvalue",
`visible`="(effect_size == 'mean')"),
list(
`name`="p_result",
`title`="<i>p</i>, two-tailed",
`type`="text",
`visible`="(effect_size == 'median')"),
list(
`name`="null_decision",
`title`="<i>H</i><sub>0</sub> decision"),
list(
`name`="conclusion",
`title`="Conclusion",
`type`="text"))))
self$add(jmvcore::Table$new(
options=options,
name="interval_null",
title="Hypothesis Evaluation",
rows=1,
visible="(evaluate_hypotheses & null_boundary != 0)",
clearWith=list(
"outcome_variable",
"mean",
"sd",
"n",
"outcome_variable_name",
"conf_level",
"effect_size",
"show_details",
"show_calculations",
"null_value",
"null_boundary"),
columns=list(
list(
`name`="effect",
`title`="Effect",
`type`="text",
`combineBelow`=FALSE),
list(
`name`="rope",
`title`="<i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="CI",
`title`="CI",
`type`="text"),
list(
`name`="rope_compare",
`title`="Compare CI with <i>H</i><sub>0</sub>",
`type`="text"),
list(
`name`="p_result",
`title`="<i>p</i>, two tailed",
`type`="text"),
list(
`name`="conclusion",
`title`="Conclusion",
`type`="text"))))
self$add(jmvcore::Html$new(
options=options,
name="magnitude_plot_warnings",
title="Figure Warnings",
visible=TRUE))
self$add(jmvcore::Image$new(
options=options,
name="magnitude_plot",
title="Estimation Figure",
requiresData=TRUE,
width=400,
height=300,
renderFun=".magnitude_plot",
refs="ggdist"))}))
jamovimagnitudeBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jamovimagnitudeBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "esci",
name = "jamovimagnitude",
version = c(1,0,0),
options = options,
results = jamovimagnitudeResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
#' Means and Medians: Single Group
#'
#'
#' @param switch .
#' @param data .
#' @param outcome_variable .
#' @param mean .
#' @param sd .
#' @param n .
#' @param outcome_variable_name .
#' @param conf_level .
#' @param effect_size .
#' @param show_details .
#' @param show_calculations .
#' @param evaluate_hypotheses .
#' @param null_value .
#' @param null_boundary .
#' @param alpha .
#' @param null_color .
#' @param es_plot_width .
#' @param es_plot_height .
#' @param ymin .
#' @param ymax .
#' @param breaks .
#' @param ylab .
#' @param xlab .
#' @param axis.text.y .
#' @param axis.title.y .
#' @param axis.text.x .
#' @param axis.title.x .
#' @param error_layout .
#' @param error_scale .
#' @param error_nudge .
#' @param data_layout .
#' @param data_spread .
#' @param shape_raw .
#' @param shape_summary .
#' @param color_raw .
#' @param color_summary .
#' @param fill_raw .
#' @param fill_summary .
#' @param size_raw .
#' @param size_summary .
#' @param alpha_raw .
#' @param alpha_summary .
#' @param linetype_summary .
#' @param color_interval .
#' @param size_interval .
#' @param alpha_interval .
#' @param alpha_error .
#' @param fill_error .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$debug} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$help} \tab \tab \tab \tab \tab a html \cr
#' \code{results$overview} \tab \tab \tab \tab \tab a table \cr
#' \code{results$es_smd} \tab \tab \tab \tab \tab a table \cr
#' \code{results$point_null} \tab \tab \tab \tab \tab a table \cr
#' \code{results$interval_null} \tab \tab \tab \tab \tab a table \cr
#' \code{results$magnitude_plot_warnings} \tab \tab \tab \tab \tab a html \cr
#' \code{results$magnitude_plot} \tab \tab \tab \tab \tab an image \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$overview$asDF}
#'
#' \code{as.data.frame(results$overview)}
#'
#' @export
jamovimagnitude <- function(
switch = "from_raw",
data,
outcome_variable,
mean = "",
sd = "",
n = "",
outcome_variable_name = "Outcome variable",
conf_level = 95,
effect_size = "mean",
show_details = FALSE,
show_calculations = FALSE,
evaluate_hypotheses = FALSE,
null_value = "0",
null_boundary = "0",
alpha = 0.05,
null_color = "#A40122",
es_plot_width = "300",
es_plot_height = "400",
ymin = "auto",
ymax = "auto",
breaks = "auto",
ylab = "auto",
xlab = "auto",
axis.text.y = "14",
axis.title.y = "15",
axis.text.x = "14",
axis.title.x = "15",
error_layout = "halfeye",
error_scale = "0.20",
error_nudge = "0.3",
data_layout = "random",
data_spread = "0.25",
shape_raw = "circle filled",
shape_summary = "circle filled",
color_raw = "#008DF9",
color_summary = "#008DF9",
fill_raw = "NA",
fill_summary = "#008DF9",
size_raw = "2",
size_summary = "4",
alpha_raw = "1",
alpha_summary = "1",
linetype_summary = "solid",
color_interval = "black",
size_interval = "3",
alpha_interval = "1",
alpha_error = "1",
fill_error = "gray75") {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("jamovimagnitude requires jmvcore to be installed (restart may be required)")
if ( ! missing(outcome_variable)) outcome_variable <- jmvcore::resolveQuo(jmvcore::enquo(outcome_variable))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(outcome_variable), outcome_variable, NULL))
options <- jamovimagnitudeOptions$new(
switch = switch,
outcome_variable = outcome_variable,
mean = mean,
sd = sd,
n = n,
outcome_variable_name = outcome_variable_name,
conf_level = conf_level,
effect_size = effect_size,
show_details = show_details,
show_calculations = show_calculations,
evaluate_hypotheses = evaluate_hypotheses,
null_value = null_value,
null_boundary = null_boundary,
alpha = alpha,
null_color = null_color,
es_plot_width = es_plot_width,
es_plot_height = es_plot_height,
ymin = ymin,
ymax = ymax,
breaks = breaks,
ylab = ylab,
xlab = xlab,
axis.text.y = axis.text.y,
axis.title.y = axis.title.y,
axis.text.x = axis.text.x,
axis.title.x = axis.title.x,
error_layout = error_layout,
error_scale = error_scale,
error_nudge = error_nudge,
data_layout = data_layout,
data_spread = data_spread,
shape_raw = shape_raw,
shape_summary = shape_summary,
color_raw = color_raw,
color_summary = color_summary,
fill_raw = fill_raw,
fill_summary = fill_summary,
size_raw = size_raw,
size_summary = size_summary,
alpha_raw = alpha_raw,
alpha_summary = alpha_summary,
linetype_summary = linetype_summary,
color_interval = color_interval,
size_interval = size_interval,
alpha_interval = alpha_interval,
alpha_error = alpha_error,
fill_error = fill_error)
analysis <- jamovimagnitudeClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
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