# This file is automatically generated, you probably don't want to edit this
gamljgmixedOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"gamljgmixedOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
.caller = "glmer",
.interface = "jamovi",
dep = NULL,
factors = NULL,
covs = NULL,
model_terms = NULL,
fixed_intercept = TRUE,
es = list(
"expb"),
expb_ci = TRUE,
nested_terms = NULL,
comparison = FALSE,
nested_intercept = TRUE,
estimates_ci = FALSE,
re_ci = FALSE,
donotrun = FALSE,
ci_method = "wald",
boot_r = 1000,
ci_width = 95,
contrasts = NULL,
show_contrastnames = FALSE,
show_contrastcodes = FALSE,
plot_x = NULL,
plot_z = NULL,
plot_by = NULL,
plot_raw = FALSE,
plot_yscale = FALSE,
plot_xoriginal = FALSE,
plot_black = FALSE,
plot_around = "none",
plot_re = FALSE,
plot_re_method = "average",
plot_scale = "response",
emmeans = NULL,
posthoc = NULL,
posthoc_ci = FALSE,
simple_x = NULL,
simple_mods = NULL,
simple_interactions = FALSE,
covs_conditioning = "mean_sd",
ccra_steps = 1,
ccm_value = 1,
ccp_value = 25,
covs_scale_labels = "labels",
adjust = list(
"bonf"),
model_type = "logistic",
covs_scale = NULL,
scale_missing = "colwise",
mute = FALSE,
cluster = NULL,
re = list(
list()),
nested_re = list(
list()),
re_corr = "all",
re_modelterms = TRUE,
re_listing = "none",
re_lrt = FALSE, ...) {
super$initialize(
package="GAMLj3",
name="gamljgmixed",
requiresData=TRUE,
...)
private$...caller <- jmvcore::OptionString$new(
".caller",
.caller,
default="glmer",
hidden=TRUE)
private$...interface <- jmvcore::OptionString$new(
".interface",
.interface,
default="jamovi",
hidden=TRUE)
private$..dep <- jmvcore::OptionVariable$new(
"dep",
dep,
default=NULL,
permitted=list(
"factor",
"numeric"))
private$..factors <- jmvcore::OptionVariables$new(
"factors",
factors,
suggested=list(
"nominal"),
permitted=list(
"factor"),
default=NULL)
private$..covs <- jmvcore::OptionVariables$new(
"covs",
covs,
suggested=list(
"continuous",
"ordinal"),
permitted=list(
"numeric"),
default=NULL)
private$..model_terms <- jmvcore::OptionTerms$new(
"model_terms",
model_terms,
default=NULL)
private$..fixed_intercept <- jmvcore::OptionBool$new(
"fixed_intercept",
fixed_intercept,
default=TRUE)
private$..es <- jmvcore::OptionNMXList$new(
"es",
es,
options=list(
"expb",
"RR",
"marginals"),
default=list(
"expb"))
private$..expb_ci <- jmvcore::OptionBool$new(
"expb_ci",
expb_ci,
default=TRUE)
private$..nested_terms <- jmvcore::OptionTerms$new(
"nested_terms",
nested_terms,
default=NULL)
private$..comparison <- jmvcore::OptionBool$new(
"comparison",
comparison,
default=FALSE)
private$..nested_intercept <- jmvcore::OptionBool$new(
"nested_intercept",
nested_intercept,
default=TRUE)
private$..estimates_ci <- jmvcore::OptionBool$new(
"estimates_ci",
estimates_ci,
default=FALSE)
private$..re_ci <- jmvcore::OptionBool$new(
"re_ci",
re_ci,
default=FALSE)
private$..donotrun <- jmvcore::OptionBool$new(
"donotrun",
donotrun,
default=FALSE)
private$..ci_method <- jmvcore::OptionList$new(
"ci_method",
ci_method,
default="wald",
options=list(
"wald",
"profile",
"quantile"))
private$..boot_r <- jmvcore::OptionNumber$new(
"boot_r",
boot_r,
min=1,
default=1000)
private$..ci_width <- jmvcore::OptionNumber$new(
"ci_width",
ci_width,
min=50,
max=99.9,
default=95)
private$..contrasts <- jmvcore::OptionArray$new(
"contrasts",
contrasts,
items="(factors)",
default=NULL,
template=jmvcore::OptionGroup$new(
"contrasts",
NULL,
elements=list(
jmvcore::OptionVariable$new(
"var",
NULL,
content="$key"),
jmvcore::OptionList$new(
"type",
NULL,
options=list(
"simple",
"deviation",
"dummy",
"difference",
"helmert",
"repeated",
"polynomial"),
default="simple"))))
private$..show_contrastnames <- jmvcore::OptionBool$new(
"show_contrastnames",
show_contrastnames,
default=FALSE)
private$..show_contrastcodes <- jmvcore::OptionBool$new(
"show_contrastcodes",
show_contrastcodes,
default=FALSE)
private$..plot_x <- jmvcore::OptionVariable$new(
"plot_x",
plot_x,
default=NULL)
private$..plot_z <- jmvcore::OptionVariable$new(
"plot_z",
plot_z,
default=NULL)
private$..plot_by <- jmvcore::OptionVariables$new(
"plot_by",
plot_by,
default=NULL)
private$..plot_raw <- jmvcore::OptionBool$new(
"plot_raw",
plot_raw,
default=FALSE)
private$..plot_yscale <- jmvcore::OptionBool$new(
"plot_yscale",
plot_yscale,
default=FALSE)
private$..plot_xoriginal <- jmvcore::OptionBool$new(
"plot_xoriginal",
plot_xoriginal,
default=FALSE)
private$..plot_black <- jmvcore::OptionBool$new(
"plot_black",
plot_black,
default=FALSE)
private$..plot_around <- jmvcore::OptionList$new(
"plot_around",
plot_around,
options=list(
"none",
"ci",
"se"),
default="none")
private$..plot_re <- jmvcore::OptionBool$new(
"plot_re",
plot_re,
default=FALSE)
private$..plot_re_method <- jmvcore::OptionList$new(
"plot_re_method",
plot_re_method,
default="average",
options=list(
"average",
"full"))
private$..plot_scale <- jmvcore::OptionList$new(
"plot_scale",
plot_scale,
options=list(
"response",
"link",
"mean.class"),
default="response")
private$..emmeans <- jmvcore::OptionTerms$new(
"emmeans",
emmeans,
default=NULL)
private$..posthoc <- jmvcore::OptionTerms$new(
"posthoc",
posthoc,
default=NULL)
private$..posthoc_ci <- jmvcore::OptionBool$new(
"posthoc_ci",
posthoc_ci,
default=FALSE)
private$..simple_x <- jmvcore::OptionVariable$new(
"simple_x",
simple_x,
default=NULL)
private$..simple_mods <- jmvcore::OptionVariables$new(
"simple_mods",
simple_mods,
default=NULL)
private$..simple_interactions <- jmvcore::OptionBool$new(
"simple_interactions",
simple_interactions,
default=FALSE)
private$..covs_conditioning <- jmvcore::OptionList$new(
"covs_conditioning",
covs_conditioning,
options=list(
"mean_sd",
"percent",
"range"),
default="mean_sd")
private$..ccra_steps <- jmvcore::OptionNumber$new(
"ccra_steps",
ccra_steps,
default=1,
min=1,
max=50)
private$..ccm_value <- jmvcore::OptionNumber$new(
"ccm_value",
ccm_value,
default=1)
private$..ccp_value <- jmvcore::OptionNumber$new(
"ccp_value",
ccp_value,
default=25,
min=5,
max=50)
private$..covs_scale_labels <- jmvcore::OptionList$new(
"covs_scale_labels",
covs_scale_labels,
options=list(
"labels",
"values",
"values_labels",
"uvalues",
"uvalues_labels"),
default="labels")
private$..adjust <- jmvcore::OptionNMXList$new(
"adjust",
adjust,
options=list(
"none",
"bonf",
"tukey",
"holm",
"scheffe",
"sidak"),
default=list(
"bonf"))
private$..predicted <- jmvcore::OptionOutput$new(
"predicted")
private$..residuals <- jmvcore::OptionOutput$new(
"residuals")
private$..model_type <- jmvcore::OptionList$new(
"model_type",
model_type,
options=list(
"logistic",
"probit",
"poisson",
"nb",
"ordinal",
"multinomial"),
default="logistic")
private$..covs_scale <- jmvcore::OptionArray$new(
"covs_scale",
covs_scale,
items="(covs)",
default=NULL,
template=jmvcore::OptionGroup$new(
"covs_scale",
NULL,
elements=list(
jmvcore::OptionVariable$new(
"var",
NULL,
content="$key"),
jmvcore::OptionList$new(
"type",
NULL,
options=list(
"centered",
"standardized",
"clusterbasedcentered",
"clustermeans",
"clusterbasedstandardized",
"none"),
default="centered"))))
private$..scale_missing <- jmvcore::OptionList$new(
"scale_missing",
scale_missing,
options=list(
"colwise",
"complete"),
default="colwise")
private$..mute <- jmvcore::OptionBool$new(
"mute",
mute,
default=FALSE)
private$..cluster <- jmvcore::OptionVariables$new(
"cluster",
cluster,
default=NULL,
suggested=list(
"nominal"))
private$..re <- jmvcore::OptionArray$new(
"re",
re,
default=list(
list()),
template=jmvcore::OptionTerms$new(
"re",
NULL))
private$..nested_re <- jmvcore::OptionArray$new(
"nested_re",
nested_re,
default=list(
list()),
template=jmvcore::OptionTerms$new(
"nested_re",
NULL))
private$..re_corr <- jmvcore::OptionList$new(
"re_corr",
re_corr,
options=list(
"all",
"none",
"block"),
default="all")
private$..re_modelterms <- jmvcore::OptionBool$new(
"re_modelterms",
re_modelterms,
default=TRUE)
private$..re_listing <- jmvcore::OptionList$new(
"re_listing",
re_listing,
options=list(
"none",
"main",
"way2",
"way3",
"all"),
default="none")
private$..re_lrt <- jmvcore::OptionBool$new(
"re_lrt",
re_lrt,
default=FALSE)
self$.addOption(private$...caller)
self$.addOption(private$...interface)
self$.addOption(private$..dep)
self$.addOption(private$..factors)
self$.addOption(private$..covs)
self$.addOption(private$..model_terms)
self$.addOption(private$..fixed_intercept)
self$.addOption(private$..es)
self$.addOption(private$..expb_ci)
self$.addOption(private$..nested_terms)
self$.addOption(private$..comparison)
self$.addOption(private$..nested_intercept)
self$.addOption(private$..estimates_ci)
self$.addOption(private$..re_ci)
self$.addOption(private$..donotrun)
self$.addOption(private$..ci_method)
self$.addOption(private$..boot_r)
self$.addOption(private$..ci_width)
self$.addOption(private$..contrasts)
self$.addOption(private$..show_contrastnames)
self$.addOption(private$..show_contrastcodes)
self$.addOption(private$..plot_x)
self$.addOption(private$..plot_z)
self$.addOption(private$..plot_by)
self$.addOption(private$..plot_raw)
self$.addOption(private$..plot_yscale)
self$.addOption(private$..plot_xoriginal)
self$.addOption(private$..plot_black)
self$.addOption(private$..plot_around)
self$.addOption(private$..plot_re)
self$.addOption(private$..plot_re_method)
self$.addOption(private$..plot_scale)
self$.addOption(private$..emmeans)
self$.addOption(private$..posthoc)
self$.addOption(private$..posthoc_ci)
self$.addOption(private$..simple_x)
self$.addOption(private$..simple_mods)
self$.addOption(private$..simple_interactions)
self$.addOption(private$..covs_conditioning)
self$.addOption(private$..ccra_steps)
self$.addOption(private$..ccm_value)
self$.addOption(private$..ccp_value)
self$.addOption(private$..covs_scale_labels)
self$.addOption(private$..adjust)
self$.addOption(private$..predicted)
self$.addOption(private$..residuals)
self$.addOption(private$..model_type)
self$.addOption(private$..covs_scale)
self$.addOption(private$..scale_missing)
self$.addOption(private$..mute)
self$.addOption(private$..cluster)
self$.addOption(private$..re)
self$.addOption(private$..nested_re)
self$.addOption(private$..re_corr)
self$.addOption(private$..re_modelterms)
self$.addOption(private$..re_listing)
self$.addOption(private$..re_lrt)
}),
active = list(
.caller = function() private$...caller$value,
.interface = function() private$...interface$value,
dep = function() private$..dep$value,
factors = function() private$..factors$value,
covs = function() private$..covs$value,
model_terms = function() private$..model_terms$value,
fixed_intercept = function() private$..fixed_intercept$value,
es = function() private$..es$value,
expb_ci = function() private$..expb_ci$value,
nested_terms = function() private$..nested_terms$value,
comparison = function() private$..comparison$value,
nested_intercept = function() private$..nested_intercept$value,
estimates_ci = function() private$..estimates_ci$value,
re_ci = function() private$..re_ci$value,
donotrun = function() private$..donotrun$value,
ci_method = function() private$..ci_method$value,
boot_r = function() private$..boot_r$value,
ci_width = function() private$..ci_width$value,
contrasts = function() private$..contrasts$value,
show_contrastnames = function() private$..show_contrastnames$value,
show_contrastcodes = function() private$..show_contrastcodes$value,
plot_x = function() private$..plot_x$value,
plot_z = function() private$..plot_z$value,
plot_by = function() private$..plot_by$value,
plot_raw = function() private$..plot_raw$value,
plot_yscale = function() private$..plot_yscale$value,
plot_xoriginal = function() private$..plot_xoriginal$value,
plot_black = function() private$..plot_black$value,
plot_around = function() private$..plot_around$value,
plot_re = function() private$..plot_re$value,
plot_re_method = function() private$..plot_re_method$value,
plot_scale = function() private$..plot_scale$value,
emmeans = function() private$..emmeans$value,
posthoc = function() private$..posthoc$value,
posthoc_ci = function() private$..posthoc_ci$value,
simple_x = function() private$..simple_x$value,
simple_mods = function() private$..simple_mods$value,
simple_interactions = function() private$..simple_interactions$value,
covs_conditioning = function() private$..covs_conditioning$value,
ccra_steps = function() private$..ccra_steps$value,
ccm_value = function() private$..ccm_value$value,
ccp_value = function() private$..ccp_value$value,
covs_scale_labels = function() private$..covs_scale_labels$value,
adjust = function() private$..adjust$value,
predicted = function() private$..predicted$value,
residuals = function() private$..residuals$value,
model_type = function() private$..model_type$value,
covs_scale = function() private$..covs_scale$value,
scale_missing = function() private$..scale_missing$value,
mute = function() private$..mute$value,
cluster = function() private$..cluster$value,
re = function() private$..re$value,
nested_re = function() private$..nested_re$value,
re_corr = function() private$..re_corr$value,
re_modelterms = function() private$..re_modelterms$value,
re_listing = function() private$..re_listing$value,
re_lrt = function() private$..re_lrt$value),
private = list(
...caller = NA,
...interface = NA,
..dep = NA,
..factors = NA,
..covs = NA,
..model_terms = NA,
..fixed_intercept = NA,
..es = NA,
..expb_ci = NA,
..nested_terms = NA,
..comparison = NA,
..nested_intercept = NA,
..estimates_ci = NA,
..re_ci = NA,
..donotrun = NA,
..ci_method = NA,
..boot_r = NA,
..ci_width = NA,
..contrasts = NA,
..show_contrastnames = NA,
..show_contrastcodes = NA,
..plot_x = NA,
..plot_z = NA,
..plot_by = NA,
..plot_raw = NA,
..plot_yscale = NA,
..plot_xoriginal = NA,
..plot_black = NA,
..plot_around = NA,
..plot_re = NA,
..plot_re_method = NA,
..plot_scale = NA,
..emmeans = NA,
..posthoc = NA,
..posthoc_ci = NA,
..simple_x = NA,
..simple_mods = NA,
..simple_interactions = NA,
..covs_conditioning = NA,
..ccra_steps = NA,
..ccm_value = NA,
..ccp_value = NA,
..covs_scale_labels = NA,
..adjust = NA,
..predicted = NA,
..residuals = NA,
..model_type = NA,
..covs_scale = NA,
..scale_missing = NA,
..mute = NA,
..cluster = NA,
..re = NA,
..nested_re = NA,
..re_corr = NA,
..re_modelterms = NA,
..re_listing = NA,
..re_lrt = NA)
)
gamljgmixedResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"gamljgmixedResults",
inherit = jmvcore::Group,
active = list(
model = function() private$..model,
info = function() private$.items[["info"]],
main = function() private$.items[["main"]],
posthoc = function() private$.items[["posthoc"]],
simpleEffects = function() private$.items[["simpleEffects"]],
simpleInteractions = function() private$.items[["simpleInteractions"]],
emmeans = function() private$.items[["emmeans"]],
mainPlots = function() private$.items[["mainPlots"]],
plotnotes = function() private$.items[["plotnotes"]],
predicted = function() private$.items[["predicted"]],
residuals = function() private$.items[["residuals"]]),
private = list(
..model = NA),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Generalized Mixed Model")
private$..model <- NULL
self$add(jmvcore::Table$new(
options=options,
name="info",
title="Model Info",
columns=list(
list(
`name`="info",
`type`="text",
`title`="Info"),
list(
`name`="value",
`type`="text",
`title`=""),
list(
`name`="specs",
`type`="text",
`title`="")),
refs="gamlj"))
self$add(R6::R6Class(
inherit = jmvcore::Group,
active = list(
r2 = function() private$.items[["r2"]],
fit = function() private$.items[["fit"]],
anova = function() private$.items[["anova"]],
coefficients = function() private$.items[["coefficients"]],
contrastCodeTables = function() private$.items[["contrastCodeTables"]],
marginals = function() private$.items[["marginals"]],
relativerisk = function() private$.items[["relativerisk"]],
random = function() private$.items[["random"]],
randomcov = function() private$.items[["randomcov"]],
multirandom = function() private$.items[["multirandom"]],
ranova = function() private$.items[["ranova"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="main",
title="Model Results")
self$add(jmvcore::Table$new(
options=options,
name="r2",
title="Model Fit",
clearWith=list(
"dep",
"factors",
"covs",
"covs_scale",
"scale_missing",
"model_terms",
"fixed_intercept",
"se_method",
"mute",
"re",
"re_corr",
"df_method",
"relm",
"contrasts",
"covs_scale",
"mute",
"model_type",
"nested_terms",
"nested_re",
"nested_intercept",
"comparison"),
columns=list(
list(
`name`="model",
`title`="Model",
`visible`="(comparison)"),
list(
`name`="type",
`type`="text",
`title`="Type"),
list(
`name`="r2",
`title`="R\u00B2",
`type`="number",
`format`="zto"),
list(
`name`="df1",
`title`="df",
`type`="integer",
`format`="zto"),
list(
`name`="test",
`title`="LRT X\u00B2",
`type`="number",
`format`="zto"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue")),
refs="goodness"))
self$add(jmvcore::Table$new(
options=options,
name="fit",
title="Additional Indices",
visible=TRUE,
clearWith=list(
"dep",
"factors",
"covs",
"covs_scale",
"scale_missing",
"model_terms",
"fixed_intercept",
"se_method",
"mute",
"re",
"re_corr",
"df_method",
"relm",
"contrasts",
"covs_scale",
"mute",
"model_type",
"nested_terms",
"nested_re",
"nested_intercept",
"comparison"),
columns=list(
list(
`name`="info",
`type`="text",
`title`="Info"),
list(
`name`="value",
`type`="text",
`title`="Model Value",
`format`="zto"),
list(
`name`="nested",
`type`="text",
`title`="Nested Model",
`visible`="(comparison)",
`format`="zto"),
list(
`name`="diff",
`type`="text",
`title`="\u0394",
`visible`="(comparison)",
`format`="zto"),
list(
`name`="specs",
`type`="text",
`title`="Comment"))))
self$add(jmvcore::Table$new(
options=options,
name="anova",
title="Fixed Effects Omnibus Tests",
visible=FALSE,
clearWith=list(
"dep",
"factors",
"covs",
"covs_scale",
"scale_missing",
"model_terms",
"fixed_intercept",
"se_method",
"mute",
"re",
"re_corr",
"df_method",
"relm",
"contrasts",
"covs_scale",
"mute",
"model_type"),
columns=list(
list(
`name`="source",
`title`="",
`type`="text"),
list(
`name`="test",
`title`="X\u00B2",
`type`="number"),
list(
`name`="df",
`title`="df",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="coefficients",
title="Parameter Estimates (Fixed Coefficients)",
clearWith=list(
"dep",
"factors",
"covs",
"covs_scale",
"scale_missing",
"model_terms",
"fixed_intercept",
"se_method",
"mute",
"re",
"re_corr",
"df_method",
"relm",
"contrasts",
"covs_scale",
"mute",
"model_type",
"ci_width",
"ci_method",
"boot_r"),
columns=list(
list(
`name`="response",
`title`="Response",
`type`="text",
`visible`="(model_type:multinomial)"),
list(
`name`="source",
`title`="Names",
`type`="text"),
list(
`name`="label",
`title`="Effect",
`type`="text",
`visible`="(show_contrastnames)"),
list(
`name`="estimate",
`title`="Estimate",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"),
list(
`name`="est.ci.lower",
`type`="number",
`title`="Lower",
`visible`="(estimates_ci)"),
list(
`name`="est.ci.upper",
`type`="number",
`title`="Upper",
`visible`="(estimates_ci)"),
list(
`name`="expb",
`type`="number",
`title`="Exp(B)",
`visible`="(es:expb)"),
list(
`name`="expb.ci.lower",
`type`="number",
`title`="Lower",
`visible`="(es:expb & expb_ci)"),
list(
`name`="expb.ci.upper",
`type`="number",
`title`="Upper",
`visible`="(es:expb & expb_ci)"),
list(
`name`="test",
`title`="z",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue")),
refs="parameters"))
self$add(jmvcore::Array$new(
options=options,
name="contrastCodeTables",
title="Contrast Coefficients",
visible="(show_contrastcodes)",
items="(factors)",
clearWith=list(
"contrasts"),
template=jmvcore::Table$new(
options=options,
title="Factor: ___key___",
columns=list(
list(
`name`="cname",
`title`="Name",
`type`="text",
`visible`="(show_contrastnames)"),
list(
`name`="clab",
`title`="Contrast",
`type`="text"),
list(
`name`="bogus",
`title`="bogus",
`type`="text",
`visible`=FALSE)))))
self$add(jmvcore::Table$new(
options=options,
name="marginals",
title="Marginal Effects",
visible="(es:marginals)",
clearWith=list(
"dep",
"factors",
"covs",
"covs_scale",
"scale_missing",
"model_terms",
"fixed_intercept",
"se_method",
"mute",
"re",
"re_corr",
"df_method",
"relm",
"contrasts",
"covs_scale",
"mute",
"model_type",
"ci_width",
"ci_method",
"boot_r"),
columns=list(
list(
`name`="response",
`title`="Response",
`type`="text",
`combineBelow`=TRUE,
`visible`="(model_type:multinomial)"),
list(
`name`="source",
`title`="Name",
`type`="text"),
list(
`name`="contrast",
`title`="Effect",
`type`="text"),
list(
`name`="estimate",
`title`="AME",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"),
list(
`name`="est.ci.lower",
`type`="number",
`title`="Lower"),
list(
`name`="est.ci.upper",
`type`="number",
`title`="Upper"),
list(
`name`="test",
`title`="z",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="relativerisk",
title="Relative risk",
visible="(es:RR)",
clearWith=list(
"dep",
"factors",
"covs",
"covs_scale",
"scale_missing",
"model_terms",
"fixed_intercept",
"se_method",
"mute",
"re",
"re_corr",
"df_method",
"relm",
"contrasts",
"covs_scale",
"mute",
"model_type",
"ci_width",
"ci_method",
"boot_r"),
columns=list(
list(
`name`="source",
`title`="Name",
`type`="text",
`visible`="(show_contrastnames)"),
list(
`name`="label",
`title`="Effect",
`type`="text"),
list(
`name`="estimate",
`title`="RR",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"),
list(
`name`="est.ci.lower",
`type`="number",
`title`="Lower",
`visible`="(expb_ci | estimates_ci)"),
list(
`name`="est.ci.upper",
`type`="number",
`title`="Upper",
`visible`="(expb_ci | estimates_ci)"),
list(
`name`="test",
`title`="z",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="random",
title="Random Components",
visible=FALSE,
clearWith=list(
"dep",
"factors",
"covs",
"covs_scale",
"scale_missing",
"model_terms",
"fixed_intercept",
"se_method",
"mute",
"re",
"re_corr",
"df_method",
"relm",
"contrasts",
"covs_scale",
"mute",
"model_type",
"ci_width",
"ci_method",
"boot_r",
"re_ci"),
columns=list(
list(
`name`="groups",
`title`="Groups",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="var1",
`title`="Name",
`type`="text"),
list(
`name`="vcov",
`title`="Variance",
`type`="number"),
list(
`name`="sdcor",
`title`="SD",
`type`="number"),
list(
`name`="sd.ci.lower",
`type`="number",
`title`="Lower",
`visible`="(re_ci)",
`superTitle`="SD Confidence Intervals"),
list(
`name`="sd.ci.upper",
`type`="number",
`title`="Upper",
`visible`="(re_ci)",
`superTitle`="SD Confidence Intervals"),
list(
`name`="icc",
`title`="ICC",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="randomcov",
title="Random Parameters correlations",
visible=FALSE,
clearWith=list(
"dep",
"factors",
"covs",
"covs_scale",
"scale_missing",
"model_terms",
"fixed_intercept",
"se_method",
"mute",
"re",
"re_corr",
"df_method",
"relm",
"contrasts",
"covs_scale",
"mute",
"model_type"),
columns=list(
list(
`name`="groups",
`title`="Groups",
`combineBelow`=TRUE,
`type`="text"),
list(
`name`="var1",
`title`="name",
`type`="text"),
list(
`name`="var2",
`title`="name2",
`type`="text"),
list(
`name`="vcov",
`title`="Cov.",
`type`="number"),
list(
`name`="sdcor",
`title`="Corr.",
`type`="number"),
list(
`name`="sd.ci.lower",
`type`="number",
`title`="Lower",
`visible`="(re_ci)",
`superTitle`="Corr. Confidence Intervals"),
list(
`name`="sd.ci.upper",
`type`="number",
`title`="Upper",
`visible`="(re_ci)",
`superTitle`="Corr. Confidence Intervals"))))
self$add(jmvcore::Array$new(
options=options,
name="multirandom",
title="Random Parameters covariances",
visible=TRUE,
clearWith=list(
"dep",
"factors",
"covs",
"covs_scale",
"scale_missing",
"model_terms",
"fixed_intercept",
"se_method",
"mute",
"re",
"re_corr",
"df_method",
"relm",
"contrasts",
"covs_scale",
"mute",
"model_type"),
template=jmvcore::Table$new(
options=options,
title="Covariances for: ___key___",
columns=list(
list(
`name`="name",
`title`="name",
`type`="text")))))
self$add(jmvcore::Table$new(
options=options,
name="ranova",
title="Random Effect LRT",
visible="(re_lrt)",
clearWith=list(
"dep",
"factors",
"covs",
"covs_scale",
"scale_missing",
"model_terms",
"fixed_intercept",
"se_method",
"mute",
"re",
"re_corr",
"df_method",
"relm",
"contrasts",
"covs_scale",
"mute",
"model_type"),
columns=list(
list(
`name`="test",
`title`="Test",
`combineBelow`=TRUE,
`type`="text"),
list(
`name`="npar",
`title`="N. par",
`type`="number"),
list(
`name`="AIC",
`title`="AIC",
`type`="number"),
list(
`name`="LRT",
`title`="LRT",
`type`="number"),
list(
`name`="df",
`title`="df",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))}))$new(options=options))
self$add(jmvcore::Array$new(
options=options,
name="posthoc",
title="Post Hoc Tests",
items="(posthoc)",
template=jmvcore::Table$new(
options=options,
title="Post Hoc comparison: ___key___",
clearWith=list(
"dep",
"factors",
"covs",
"covs_scale",
"scale_missing",
"model_terms",
"fixed_intercept",
"se_method",
"mute",
"re",
"re_corr",
"df_method",
"relm",
"contrasts",
"covs_scale",
"mute",
"model_type",
"ci_width",
"ci_method",
"boot_r",
"adjust"),
columns=list(
list(
`name`="response",
`title`="Response",
`type`="text",
`visible`="(model_type:multinomial)",
`combineBelow`=TRUE),
list(
`name`="estimate",
`title`="Difference",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"),
list(
`name`="est.ci.lower",
`type`="number",
`title`="Lower",
`visible`="(posthoc_ci)"),
list(
`name`="est.ci.upper",
`type`="number",
`title`="Upper",
`visible`="(posthoc_ci)"),
list(
`name`="test",
`title`="z",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(adjust:none)"),
list(
`name`="bonf",
`title`="p<sub>bonferroni</sub>",
`type`="number",
`format`="zto,pvalue",
`visible`="(adjust:bonf)"),
list(
`name`="tukey",
`title`="p<sub>tukey</sub>",
`type`="number",
`format`="zto,pvalue",
`visible`="(adjust:tukey)"),
list(
`name`="holm",
`title`="p<sub>holm</sub>",
`type`="number",
`format`="zto,pvalue",
`visible`="(adjust:holm)"),
list(
`name`="scheffe",
`title`="p<sub>scheffe</sub>",
`type`="number",
`format`="zto,pvalue",
`visible`="(adjust:scheffe)"),
list(
`name`="sidak",
`title`="p<sub>sidak</sub>",
`type`="number",
`format`="zto,pvalue",
`visible`="(adjust:sidak)")))))
self$add(R6::R6Class(
inherit = jmvcore::Group,
active = list(
anova = function() private$.items[["anova"]],
coefficients = function() private$.items[["coefficients"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="simpleEffects",
title="Simple Effects")
self$add(jmvcore::Table$new(
options=options,
name="anova",
title="ANOVA for Simple Effects of ___key___",
visible=FALSE,
clearWith=list(
"dep",
"factors",
"covs",
"covs_scale",
"scale_missing",
"model_terms",
"fixed_intercept",
"se_method",
"mute",
"re",
"re_corr",
"df_method",
"relm",
"contrasts",
"covs_scale",
"mute",
"model_type",
"ci_width",
"ci_method",
"boot_r",
"simple_x",
"simple_mods",
"simple_scale",
"ccm_value",
"ccp_value",
"ccra_steps",
"covs_scale_labels",
"covs_conditioning"),
columns=list(
list(
`name`="test",
`title`="X\u00B2",
`type`="number"),
list(
`name`="df1",
`title`="df",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="coefficients",
title="Parameter Estimates for simple effects of ___key___",
visible=FALSE,
clearWith=list(
"dep",
"factors",
"covs",
"covs_scale",
"scale_missing",
"model_terms",
"fixed_intercept",
"se_method",
"mute",
"re",
"re_corr",
"df_method",
"relm",
"contrasts",
"covs_scale",
"mute",
"model_type",
"ci_width",
"ci_method",
"boot_r",
"simple_x",
"simple_mods",
"simple_scale",
"ccm_value",
"ccp_value",
"ccra_steps",
"covs_scale_labels",
"covs_conditioning"),
columns=list(
list(
`name`="response",
`title`="Response",
`type`="text",
`combineBelow`=TRUE,
`visible`="(model_type:multinomial)"),
list(
`name`="contrast",
`title`="Effect",
`type`="text"),
list(
`name`="estimate",
`title`="Estimate",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"),
list(
`name`="est.ci.lower",
`type`="number",
`title`="Lower",
`visible`="(estimates_ci)"),
list(
`name`="est.ci.upper",
`type`="number",
`title`="Upper",
`visible`="(estimates_ci)"),
list(
`name`="expb",
`type`="number",
`title`="Exp(B)",
`visible`="(es:expb)"),
list(
`name`="expb.ci.lower",
`type`="number",
`title`="Lower",
`visible`="(es:expb & expb_ci)"),
list(
`name`="expb.ci.upper",
`type`="number",
`title`="Upper",
`visible`="(es:expb & expb_ci)"),
list(
`name`="test",
`title`="z",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))}))$new(options=options))
self$add(jmvcore::Array$new(
options=options,
name="simpleInteractions",
title="Simple Interactions",
visible="(simple_interactions)",
template=R6::R6Class(
inherit = jmvcore::Group,
active = list(
anova = function() private$.items[["anova"]],
coefficients = function() private$.items[["coefficients"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="undefined",
title="Interaction: ___key___",
clearWith=list())
self$add(jmvcore::Table$new(
options=options,
name="anova",
title="ANOVA",
clearWith=list(
"dep",
"factors",
"covs",
"covs_scale",
"scale_missing",
"model_terms",
"fixed_intercept",
"se_method",
"mute",
"re",
"re_corr",
"df_method",
"relm",
"contrasts",
"covs_scale",
"mute",
"model_type",
"ci_width",
"ci_method",
"boot_r",
"simple_x",
"simple_mods",
"simple_scale",
"ccm_value",
"ccp_value",
"ccra_steps",
"covs_scale_labels",
"covs_conditioning"),
columns=list(
list(
`name`="effect",
`title`="Effect",
`type`="text"),
list(
`name`="test",
`title`="X\u00B2",
`type`="number"),
list(
`name`="df1",
`title`="df1",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="coefficients",
title="Parameter Estimates",
clearWith=list(
"dep",
"factors",
"covs",
"covs_scale",
"scale_missing",
"model_terms",
"fixed_intercept",
"se_method",
"mute",
"re",
"re_corr",
"df_method",
"relm",
"contrasts",
"covs_scale",
"mute",
"model_type",
"ci_width",
"ci_method",
"boot_r",
"simple_x",
"simple_mods",
"simple_scale",
"ccm_value",
"ccp_value",
"ccra_steps",
"covs_scale_labels",
"covs_conditioning"),
columns=list(
list(
`name`="effect",
`title`="Effect",
`type`="text"),
list(
`name`="estimate",
`title`="Estimate",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"),
list(
`name`="est.ci.lower",
`title`="Lower",
`type`="number",
`visible`="(estimates_ci)"),
list(
`name`="est.ci.upper",
`title`="Upper",
`type`="number",
`visible`="(estimates_ci)"),
list(
`name`="expb",
`type`="number",
`title`="Exp(B)",
`visible`="(es:expb)"),
list(
`name`="expb.ci.lower",
`type`="number",
`title`="Lower",
`visible`="(es:expb & expb_ci)",
`superTitle`="Exp(B) Confidence Intervals"),
list(
`name`="expb.ci.upper",
`type`="number",
`title`="Upper",
`visible`="(es:expb & expb_ci)",
`superTitle`="Exp(B) Confidence Intervals"),
list(
`name`="test",
`title`="z",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))}))$new(options=options)))
self$add(jmvcore::Array$new(
options=options,
name="emmeans",
title="Estimated Marginal Means",
visible=FALSE,
items="(emmeans)",
template=jmvcore::Table$new(
options=options,
title="Estimate Marginal Means - ___key___",
clearWith=list(
"dep",
"factors",
"covs",
"covs_scale",
"scale_missing",
"model_terms",
"fixed_intercept",
"se_method",
"mute",
"re",
"re_corr",
"df_method",
"relm",
"contrasts",
"covs_scale",
"mute",
"model_type",
"ci_width",
"ci_method",
"boot_r",
"simple_x",
"simple_mods",
"simple_scale",
"ccm_value",
"ccp_value",
"ccra_steps",
"covs_scale_labels",
"covs_conditioning"),
columns=list(
list(
`name`="estimate",
`title`="Mean",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"),
list(
`name`="est.ci.lower",
`title`="Lower",
`type`="number"),
list(
`name`="est.ci.upper",
`title`="Upper",
`type`="number")))))
self$add(jmvcore::Array$new(
options=options,
name="mainPlots",
title="Results Plots",
template=jmvcore::Image$new(
options=options,
title="",
renderFun=".mainPlot",
width=600,
height=400)))
self$add(jmvcore::Html$new(
options=options,
name="plotnotes",
visible=FALSE))
self$add(jmvcore::Output$new(
options=options,
name="predicted",
title="Predicted Vales",
varTitle="`GZMIXED_${ dep }_PRED`",
varDescription="Predicted values",
clearWith=list(
"dep",
"factors",
"covs",
"covs_scale",
"scale_missing",
"model_terms",
"fixed_intercept",
"se_method",
"mute",
"re",
"re_corr",
"df_method",
"relm",
"contrasts",
"covs_scale",
"mute",
"model_type")))
self$add(jmvcore::Output$new(
options=options,
name="residuals",
title="Residuals Vales",
varTitle="`GZMIXED_${ dep }_RES`",
varDescription="Residuals values",
clearWith=list(
"dep",
"factors",
"covs",
"covs_scale",
"scale_missing",
"model_terms",
"fixed_intercept",
"se_method",
"mute",
"re",
"re_corr",
"df_method",
"relm",
"contrasts",
"covs_scale",
"mute",
"model_type")))},
.setModel=function(x) private$..model <- x))
gamljgmixedBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"gamljgmixedBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "GAMLj3",
name = "gamljgmixed",
version = c(3,0,0),
options = options,
results = gamljgmixedResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = TRUE,
requiresMissings = FALSE,
weightsSupport = 'none')
}))
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