R/jammglm.h.R
In jamovi-amm/jamm: Advanced Mediational Models
# This file is automatically generated, you probably don't want to edit this
jammGLMOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jammGLMOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
dep = NULL,
mediators = NULL,
factors = NULL,
covs = NULL,
modelTerms = NULL,
ciType = "standard",
ciWidth = 95,
bootN = 1000,
contrasts = NULL,
showRealNames = TRUE,
showContrastCode = FALSE,
simpleScale = "mean_sd",
cvalue = 1,
percvalue = 25,
simpleScaleLabels = "labels",
scaling = NULL,
tableOptions = list(
"beta",
"component"),
pathOptions = list(
"suggested"),
mediatorsTerms = list(
list()),
moderatorsTerms = list(
list()),
missing = "listwise",
diagram = "conceptual",
diag_paths = "est",
diag_labsize = "medium",
diag_shape = "rectangle",
diag_abbrev = "0",
diag_offset = FALSE, ...) {
super$initialize(
package="jamm",
name="jammGLM",
requiresData=TRUE,
...)
private$..dep <- jmvcore::OptionVariable$new(
"dep",
dep,
default=NULL,
suggested=list(
"continuous",
"ordinal"),
permitted=list(
"numeric"))
private$..mediators <- jmvcore::OptionVariables$new(
"mediators",
mediators,
suggested=list(
"continuous",
"ordinal"),
permitted=list(
"numeric"),
default=NULL)
private$..factors <- jmvcore::OptionVariables$new(
"factors",
factors,
suggested=list(
"nominal",
"ordinal"),
permitted=list(
"factor"),
default=NULL)
private$..covs <- jmvcore::OptionVariables$new(
"covs",
covs,
suggested=list(
"continuous",
"ordinal"),
permitted=list(
"numeric"),
default=NULL)
private$..modelTerms <- jmvcore::OptionTerms$new(
"modelTerms",
modelTerms,
default=NULL)
private$..ciType <- jmvcore::OptionList$new(
"ciType",
ciType,
options=list(
"standard",
"bca",
"perc",
"none"),
default="standard")
private$..ciWidth <- jmvcore::OptionNumber$new(
"ciWidth",
ciWidth,
min=50,
max=99.9,
default=95)
private$..bootN <- jmvcore::OptionNumber$new(
"bootN",
bootN,
min=50,
default=1000)
private$..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$new(
"type",
NULL,
options=list(
"simple",
"deviation",
"dummy",
"difference",
"helmert",
"repeated",
"polynomial"),
default="simple"))))
private$..showRealNames <- jmvcore::OptionBool$new(
"showRealNames",
showRealNames,
default=TRUE)
private$..showContrastCode <- jmvcore::OptionBool$new(
"showContrastCode",
showContrastCode,
default=FALSE)
private$..simpleScale <- jmvcore::OptionList$new(
"simpleScale",
simpleScale,
options=list(
"mean_sd",
"percent"),
default="mean_sd")
private$..cvalue <- jmvcore::OptionNumber$new(
"cvalue",
cvalue,
default=1)
private$..percvalue <- jmvcore::OptionNumber$new(
"percvalue",
percvalue,
default=25,
min=5,
max=50)
private$..simpleScaleLabels <- jmvcore::OptionList$new(
"simpleScaleLabels",
simpleScaleLabels,
options=list(
"labels",
"values",
"values_labels"),
default="labels")
private$..scaling <- jmvcore::OptionArray$new(
"scaling",
scaling,
items="(covs)",
default=NULL,
template=jmvcore::OptionGroup$new(
"scaling",
NULL,
elements=list(
jmvcore::OptionVariable$new(
"var",
NULL,
content="$key"),
jmvcore::OptionList$new(
"type",
NULL,
options=list(
"centered",
"standardized",
"none"),
default="centered"))))
private$..tableOptions <- jmvcore::OptionNMXList$new(
"tableOptions",
tableOptions,
options=list(
"component",
"beta",
"regression"),
default=list(
"beta",
"component"))
private$..pathOptions <- jmvcore::OptionNMXList$new(
"pathOptions",
pathOptions,
options=list(
"suggested"),
default=list(
"suggested"))
private$..mediatorsTerms <- jmvcore::OptionArray$new(
"mediatorsTerms",
mediatorsTerms,
default=list(
list()),
template=jmvcore::OptionTerms$new(
"mediatorsTerms",
NULL))
private$..moderatorsTerms <- jmvcore::OptionArray$new(
"moderatorsTerms",
moderatorsTerms,
default=list(
list()),
template=jmvcore::OptionTerms$new(
"moderatorsTerms",
NULL))
private$..missing <- jmvcore::OptionList$new(
"missing",
missing,
options=list(
"listwise",
"ml"),
default="listwise")
private$..diagram <- jmvcore::OptionList$new(
"diagram",
diagram,
options=list(
"conceptual",
"statistical"),
default="conceptual")
private$..diag_paths <- jmvcore::OptionList$new(
"diag_paths",
diag_paths,
options=list(
"est",
"stand",
"hide"),
default="est")
private$..diag_labsize <- jmvcore::OptionList$new(
"diag_labsize",
diag_labsize,
options=list(
"small",
"medium",
"large",
"vlarge"),
default="medium")
private$..diag_shape <- jmvcore::OptionList$new(
"diag_shape",
diag_shape,
options=list(
"rectangle",
"square",
"circle",
"ellipse",
"diamond"),
default="rectangle")
private$..diag_abbrev <- jmvcore::OptionList$new(
"diag_abbrev",
diag_abbrev,
options=list(
"0",
"5",
"10",
"15",
"20",
"25"),
default="0")
private$..diag_offset <- jmvcore::OptionBool$new(
"diag_offset",
diag_offset,
default=FALSE)
self$.addOption(private$..dep)
self$.addOption(private$..mediators)
self$.addOption(private$..factors)
self$.addOption(private$..covs)
self$.addOption(private$..modelTerms)
self$.addOption(private$..ciType)
self$.addOption(private$..ciWidth)
self$.addOption(private$..bootN)
self$.addOption(private$..contrasts)
self$.addOption(private$..showRealNames)
self$.addOption(private$..showContrastCode)
self$.addOption(private$..simpleScale)
self$.addOption(private$..cvalue)
self$.addOption(private$..percvalue)
self$.addOption(private$..simpleScaleLabels)
self$.addOption(private$..scaling)
self$.addOption(private$..tableOptions)
self$.addOption(private$..pathOptions)
self$.addOption(private$..mediatorsTerms)
self$.addOption(private$..moderatorsTerms)
self$.addOption(private$..missing)
self$.addOption(private$..diagram)
self$.addOption(private$..diag_paths)
self$.addOption(private$..diag_labsize)
self$.addOption(private$..diag_shape)
self$.addOption(private$..diag_abbrev)
self$.addOption(private$..diag_offset)
}),
active = list(
dep = function() private$..dep$value,
mediators = function() private$..mediators$value,
factors = function() private$..factors$value,
covs = function() private$..covs$value,
modelTerms = function() private$..modelTerms$value,
ciType = function() private$..ciType$value,
ciWidth = function() private$..ciWidth$value,
bootN = function() private$..bootN$value,
contrasts = function() private$..contrasts$value,
showRealNames = function() private$..showRealNames$value,
showContrastCode = function() private$..showContrastCode$value,
simpleScale = function() private$..simpleScale$value,
cvalue = function() private$..cvalue$value,
percvalue = function() private$..percvalue$value,
simpleScaleLabels = function() private$..simpleScaleLabels$value,
scaling = function() private$..scaling$value,
tableOptions = function() private$..tableOptions$value,
pathOptions = function() private$..pathOptions$value,
mediatorsTerms = function() private$..mediatorsTerms$value,
moderatorsTerms = function() private$..moderatorsTerms$value,
missing = function() private$..missing$value,
diagram = function() private$..diagram$value,
diag_paths = function() private$..diag_paths$value,
diag_labsize = function() private$..diag_labsize$value,
diag_shape = function() private$..diag_shape$value,
diag_abbrev = function() private$..diag_abbrev$value,
diag_offset = function() private$..diag_offset$value),
private = list(
..dep = NA,
..mediators = NA,
..factors = NA,
..covs = NA,
..modelTerms = NA,
..ciType = NA,
..ciWidth = NA,
..bootN = NA,
..contrasts = NA,
..showRealNames = NA,
..showContrastCode = NA,
..simpleScale = NA,
..cvalue = NA,
..percvalue = NA,
..simpleScaleLabels = NA,
..scaling = NA,
..tableOptions = NA,
..pathOptions = NA,
..mediatorsTerms = NA,
..moderatorsTerms = NA,
..missing = NA,
..diagram = NA,
..diag_paths = NA,
..diag_labsize = NA,
..diag_shape = NA,
..diag_abbrev = NA,
..diag_offset = NA)
)
jammGLMResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jammGLMResults",
inherit = jmvcore::Group,
active = list(
info = function() private$.items[["info"]],
pathmodelgroup = function() private$.items[["pathmodelgroup"]],
models = function() private$.items[["models"]],
regressions = function() private$.items[["regressions"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="GLM Mediation Analysis")
self$add(jmvcore::Table$new(
options=options,
name="info",
title="Models Info",
columns=list(
list(
`name`="info",
`type`="text",
`title`="",
`combineBelow`=TRUE),
list(
`name`="specs",
`type`="text",
`title`=""),
list(
`name`="value",
`type`="text",
`title`="")),
refs="jamm"))
self$add(R6::R6Class(
inherit = jmvcore::Group,
active = list(
pathmodel = function() private$.items[["pathmodel"]],
statmodel = function() private$.items[["statmodel"]],
pathnotes = function() private$.items[["pathnotes"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="pathmodelgroup",
title="Path Model",
clearWith=list(
"dep",
"mediatorsTerms",
"modelTerms",
"moderatorsTerms"))
self$add(jmvcore::Image$new(
options=options,
name="pathmodel",
title="Conceptual Diagram",
width=800,
height=600,
renderFun=".showConceptualDiagram",
clearWith=list(
"dep",
"mediatorsTerms",
"modelTerms",
"moderatorsTerms",
"pathOptions",
"diagram",
"diag_labsize",
"diag_shape",
"diag_abbrev"),
refs="diagram",
visible="(diagram:conceptual)"))
self$add(jmvcore::Image$new(
options=options,
name="statmodel",
title="Statistical Diagram",
width=800,
height=600,
renderFun=".showStatDiagram",
clearWith=list(
"dep",
"mediatorsTerms",
"modelTerms",
"moderatorsTerms",
"pathOptions",
"diagram",
"diag_offset",
"diag_labsize",
"diag_shape",
"diag_abbrev",
"diag_paths"),
refs="diagram",
visible="(diagram:statistical)"))
self$add(jmvcore::Table$new(
options=options,
name="pathnotes",
title="",
visible=FALSE,
columns=list(
list(
`name`="info",
`type`="text",
`title`="Diagram notes"))))}))$new(options=options))
self$add(R6::R6Class(
inherit = jmvcore::Group,
active = list(
moderationEffects = function() private$.items[["moderationEffects"]],
main = function() private$.items[["main"]],
contrastCodeTables = function() private$.items[["contrastCodeTables"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="models",
title="Mediation",
clearWith=list(
"dep",
"mediators",
"factors",
"covs"))
self$add(jmvcore::Table$new(
options=options,
name="moderationEffects",
title="Moderation effects (interactions)",
visible=FALSE,
clearWith=list(
"dep",
"modelTerms",
"contrasts",
"fixedIntercept",
"simpleScale"),
columns=list(
list(
`name`="mod",
`title`="Moderator",
`combineBelow`=TRUE,
`type`="text"),
list(
`name`="target",
`title`="Interaction",
`type`="text"),
list(
`name`="label",
`title`="Contrasts",
`visible`=FALSE,
`type`="text"),
list(
`name`="est",
`title`="Estimate",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"),
list(
`name`="ci.lower",
`type`="number",
`title`="Lower",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="ci.upper",
`type`="number",
`title`="Upper",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="std.all",
`type`="number",
`title`="\u03B2",
`visible`="(tableOptions:beta)"),
list(
`name`="z",
`title`="z",
`type`="number"),
list(
`name`="pvalue",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="main",
title="Indirect and Total Effects",
refs="lavaan",
clearWith=list(
"dep",
"modelTerms",
"contrasts",
"fixedIntercept",
"simpleScale",
"ciType"),
columns=list(
list(
`name`="type",
`title`="Type",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="source",
`title`="Effect",
`type`="text"),
list(
`name`="label",
`title`="Contrasts",
`visible`=FALSE,
`type`="text"),
list(
`name`="est",
`title`="Estimate",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"),
list(
`name`="ci.lower",
`type`="number",
`title`="Lower",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="ci.upper",
`type`="number",
`title`="Upper",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="std.all",
`type`="number",
`title`="\u03B2",
`visible`="(tableOptions:beta)"),
list(
`name`="z",
`title`="z",
`type`="number"),
list(
`name`="pvalue",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Array$new(
options=options,
name="contrastCodeTables",
title="Contrast Coefficients",
visible="(showContrastCode)",
clearWith=list(
"contrasts",
"showContrastCode"),
template=jmvcore::Table$new(
options=options,
title="$key",
visible="(showContrastCode)",
columns=list(
list(
`name`="rnames",
`title`="Name",
`type`="text"),
list(
`name`="clabs",
`title`="Contrast",
`type`="text")))))}))$new(options=options))
self$add(R6::R6Class(
inherit = jmvcore::Group,
active = list(
overall = function() private$.items[["overall"]],
mediator_regressions = function() private$.items[["mediator_regressions"]],
full = function() private$.items[["full"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="regressions",
title="",
clearWith=list(
"dep",
"contrasts",
"scaling"))
self$add(R6::R6Class(
inherit = jmvcore::Group,
active = list(
anova = function() private$.items[["anova"]],
regression = function() private$.items[["regression"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="overall",
title="Total effects",
clearWith=list(
"dep",
"contrasts",
"scaling"))
self$add(jmvcore::Table$new(
options=options,
name="anova",
title="ANOVA Table",
visible="(tableOptions:regression)",
columns=list(
list(
`name`="rsquared",
`title`="R-squared",
`type`="number"),
list(
`name`="f",
`type`="number",
`title`="F"),
list(
`name`="df1",
`title`="df1",
`type`="number"),
list(
`name`="df2",
`title`="df2",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="regression",
title="Regression Table",
visible="(tableOptions:regression)",
columns=list(
list(
`name`="source",
`title`="Names",
`type`="text",
`visible`="(showRealNames)"),
list(
`name`="label",
`title`="Effect",
`type`="text"),
list(
`name`="estimate",
`title`="Estimate",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"),
list(
`name`="cilow",
`type`="number",
`title`="Lower",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="cihig",
`type`="number",
`title`="Upper",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="beta",
`type`="number",
`title`="\u03B2",
`visible`="(tableOptions:beta)"),
list(
`name`="df",
`title`="df",
`type`="number"),
list(
`name`="t",
`title`="t",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))}))$new(options=options))
self$add(jmvcore::Array$new(
options=options,
name="mediator_regressions",
title="Mediator Model",
clearWith=list(
"dep",
"contrasts",
"scaling"),
template=R6::R6Class(
inherit = jmvcore::Group,
active = list(
anova = function() private$.items[["anova"]],
regression = function() private$.items[["regression"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="undefined",
title="",
clearWith=list())
self$add(jmvcore::Table$new(
options=options,
name="anova",
title="ANOVA",
columns=list(
list(
`name`="rsquared",
`title`="R-squared",
`type`="number"),
list(
`name`="f",
`type`="number",
`title`="F"),
list(
`name`="df1",
`title`="df1",
`type`="number"),
list(
`name`="df2",
`title`="df2",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="regression",
title="Regression",
visible="(tableOptions:regression)",
columns=list(
list(
`name`="source",
`title`="Names",
`type`="text",
`visible`="(showRealNames)"),
list(
`name`="label",
`title`="Effect",
`type`="text"),
list(
`name`="estimate",
`title`="Estimate",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"),
list(
`name`="cilow",
`type`="number",
`title`="Lower",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="cihig",
`type`="number",
`title`="Upper",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="beta",
`type`="number",
`title`="\u03B2",
`visible`="(tableOptions:beta)"),
list(
`name`="df",
`title`="df",
`type`="number"),
list(
`name`="t",
`title`="t",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))}))$new(options=options)))
self$add(R6::R6Class(
inherit = jmvcore::Group,
active = list(
anova = function() private$.items[["anova"]],
regression = function() private$.items[["regression"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="full",
title="Full model effects",
clearWith=list(
"dep",
"contrasts",
"scaling"))
self$add(jmvcore::Table$new(
options=options,
name="anova",
title="ANOVA Table",
visible="(tableOptions:regression)",
columns=list(
list(
`name`="rsquared",
`title`="R-squared",
`type`="number"),
list(
`name`="f",
`type`="number",
`title`="F"),
list(
`name`="df1",
`title`="df1",
`type`="number"),
list(
`name`="df2",
`title`="df2",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="regression",
title="Regression Table",
visible="(tableOptions:regression)",
columns=list(
list(
`name`="source",
`title`="Names",
`type`="text",
`visible`="(showRealNames)"),
list(
`name`="label",
`title`="Effect",
`type`="text"),
list(
`name`="estimate",
`title`="Estimate",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"),
list(
`name`="cilow",
`type`="number",
`title`="Lower",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="cihig",
`type`="number",
`title`="Upper",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="beta",
`type`="number",
`title`="\u03B2",
`visible`="(tableOptions:beta)"),
list(
`name`="df",
`title`="df",
`type`="number"),
list(
`name`="t",
`title`="t",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))}))$new(options=options))}))$new(options=options))}))
jammGLMBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jammGLMBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "jamm",
name = "jammGLM",
version = c(1,1,0),
options = options,
results = jammGLMResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
jamovi-amm/jamm documentation built on Nov. 15, 2023, 9:18 p.m.
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# This file is automatically generated, you probably don't want to edit this
jammGLMOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jammGLMOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
dep = NULL,
mediators = NULL,
factors = NULL,
covs = NULL,
modelTerms = NULL,
ciType = "standard",
ciWidth = 95,
bootN = 1000,
contrasts = NULL,
showRealNames = TRUE,
showContrastCode = FALSE,
simpleScale = "mean_sd",
cvalue = 1,
percvalue = 25,
simpleScaleLabels = "labels",
scaling = NULL,
tableOptions = list(
"beta",
"component"),
pathOptions = list(
"suggested"),
mediatorsTerms = list(
list()),
moderatorsTerms = list(
list()),
missing = "listwise",
diagram = "conceptual",
diag_paths = "est",
diag_labsize = "medium",
diag_shape = "rectangle",
diag_abbrev = "0",
diag_offset = FALSE, ...) {
super$initialize(
package="jamm",
name="jammGLM",
requiresData=TRUE,
...)
private$..dep <- jmvcore::OptionVariable$new(
"dep",
dep,
default=NULL,
suggested=list(
"continuous",
"ordinal"),
permitted=list(
"numeric"))
private$..mediators <- jmvcore::OptionVariables$new(
"mediators",
mediators,
suggested=list(
"continuous",
"ordinal"),
permitted=list(
"numeric"),
default=NULL)
private$..factors <- jmvcore::OptionVariables$new(
"factors",
factors,
suggested=list(
"nominal",
"ordinal"),
permitted=list(
"factor"),
default=NULL)
private$..covs <- jmvcore::OptionVariables$new(
"covs",
covs,
suggested=list(
"continuous",
"ordinal"),
permitted=list(
"numeric"),
default=NULL)
private$..modelTerms <- jmvcore::OptionTerms$new(
"modelTerms",
modelTerms,
default=NULL)
private$..ciType <- jmvcore::OptionList$new(
"ciType",
ciType,
options=list(
"standard",
"bca",
"perc",
"none"),
default="standard")
private$..ciWidth <- jmvcore::OptionNumber$new(
"ciWidth",
ciWidth,
min=50,
max=99.9,
default=95)
private$..bootN <- jmvcore::OptionNumber$new(
"bootN",
bootN,
min=50,
default=1000)
private$..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$new(
"type",
NULL,
options=list(
"simple",
"deviation",
"dummy",
"difference",
"helmert",
"repeated",
"polynomial"),
default="simple"))))
private$..showRealNames <- jmvcore::OptionBool$new(
"showRealNames",
showRealNames,
default=TRUE)
private$..showContrastCode <- jmvcore::OptionBool$new(
"showContrastCode",
showContrastCode,
default=FALSE)
private$..simpleScale <- jmvcore::OptionList$new(
"simpleScale",
simpleScale,
options=list(
"mean_sd",
"percent"),
default="mean_sd")
private$..cvalue <- jmvcore::OptionNumber$new(
"cvalue",
cvalue,
default=1)
private$..percvalue <- jmvcore::OptionNumber$new(
"percvalue",
percvalue,
default=25,
min=5,
max=50)
private$..simpleScaleLabels <- jmvcore::OptionList$new(
"simpleScaleLabels",
simpleScaleLabels,
options=list(
"labels",
"values",
"values_labels"),
default="labels")
private$..scaling <- jmvcore::OptionArray$new(
"scaling",
scaling,
items="(covs)",
default=NULL,
template=jmvcore::OptionGroup$new(
"scaling",
NULL,
elements=list(
jmvcore::OptionVariable$new(
"var",
NULL,
content="$key"),
jmvcore::OptionList$new(
"type",
NULL,
options=list(
"centered",
"standardized",
"none"),
default="centered"))))
private$..tableOptions <- jmvcore::OptionNMXList$new(
"tableOptions",
tableOptions,
options=list(
"component",
"beta",
"regression"),
default=list(
"beta",
"component"))
private$..pathOptions <- jmvcore::OptionNMXList$new(
"pathOptions",
pathOptions,
options=list(
"suggested"),
default=list(
"suggested"))
private$..mediatorsTerms <- jmvcore::OptionArray$new(
"mediatorsTerms",
mediatorsTerms,
default=list(
list()),
template=jmvcore::OptionTerms$new(
"mediatorsTerms",
NULL))
private$..moderatorsTerms <- jmvcore::OptionArray$new(
"moderatorsTerms",
moderatorsTerms,
default=list(
list()),
template=jmvcore::OptionTerms$new(
"moderatorsTerms",
NULL))
private$..missing <- jmvcore::OptionList$new(
"missing",
missing,
options=list(
"listwise",
"ml"),
default="listwise")
private$..diagram <- jmvcore::OptionList$new(
"diagram",
diagram,
options=list(
"conceptual",
"statistical"),
default="conceptual")
private$..diag_paths <- jmvcore::OptionList$new(
"diag_paths",
diag_paths,
options=list(
"est",
"stand",
"hide"),
default="est")
private$..diag_labsize <- jmvcore::OptionList$new(
"diag_labsize",
diag_labsize,
options=list(
"small",
"medium",
"large",
"vlarge"),
default="medium")
private$..diag_shape <- jmvcore::OptionList$new(
"diag_shape",
diag_shape,
options=list(
"rectangle",
"square",
"circle",
"ellipse",
"diamond"),
default="rectangle")
private$..diag_abbrev <- jmvcore::OptionList$new(
"diag_abbrev",
diag_abbrev,
options=list(
"0",
"5",
"10",
"15",
"20",
"25"),
default="0")
private$..diag_offset <- jmvcore::OptionBool$new(
"diag_offset",
diag_offset,
default=FALSE)
self$.addOption(private$..dep)
self$.addOption(private$..mediators)
self$.addOption(private$..factors)
self$.addOption(private$..covs)
self$.addOption(private$..modelTerms)
self$.addOption(private$..ciType)
self$.addOption(private$..ciWidth)
self$.addOption(private$..bootN)
self$.addOption(private$..contrasts)
self$.addOption(private$..showRealNames)
self$.addOption(private$..showContrastCode)
self$.addOption(private$..simpleScale)
self$.addOption(private$..cvalue)
self$.addOption(private$..percvalue)
self$.addOption(private$..simpleScaleLabels)
self$.addOption(private$..scaling)
self$.addOption(private$..tableOptions)
self$.addOption(private$..pathOptions)
self$.addOption(private$..mediatorsTerms)
self$.addOption(private$..moderatorsTerms)
self$.addOption(private$..missing)
self$.addOption(private$..diagram)
self$.addOption(private$..diag_paths)
self$.addOption(private$..diag_labsize)
self$.addOption(private$..diag_shape)
self$.addOption(private$..diag_abbrev)
self$.addOption(private$..diag_offset)
}),
active = list(
dep = function() private$..dep$value,
mediators = function() private$..mediators$value,
factors = function() private$..factors$value,
covs = function() private$..covs$value,
modelTerms = function() private$..modelTerms$value,
ciType = function() private$..ciType$value,
ciWidth = function() private$..ciWidth$value,
bootN = function() private$..bootN$value,
contrasts = function() private$..contrasts$value,
showRealNames = function() private$..showRealNames$value,
showContrastCode = function() private$..showContrastCode$value,
simpleScale = function() private$..simpleScale$value,
cvalue = function() private$..cvalue$value,
percvalue = function() private$..percvalue$value,
simpleScaleLabels = function() private$..simpleScaleLabels$value,
scaling = function() private$..scaling$value,
tableOptions = function() private$..tableOptions$value,
pathOptions = function() private$..pathOptions$value,
mediatorsTerms = function() private$..mediatorsTerms$value,
moderatorsTerms = function() private$..moderatorsTerms$value,
missing = function() private$..missing$value,
diagram = function() private$..diagram$value,
diag_paths = function() private$..diag_paths$value,
diag_labsize = function() private$..diag_labsize$value,
diag_shape = function() private$..diag_shape$value,
diag_abbrev = function() private$..diag_abbrev$value,
diag_offset = function() private$..diag_offset$value),
private = list(
..dep = NA,
..mediators = NA,
..factors = NA,
..covs = NA,
..modelTerms = NA,
..ciType = NA,
..ciWidth = NA,
..bootN = NA,
..contrasts = NA,
..showRealNames = NA,
..showContrastCode = NA,
..simpleScale = NA,
..cvalue = NA,
..percvalue = NA,
..simpleScaleLabels = NA,
..scaling = NA,
..tableOptions = NA,
..pathOptions = NA,
..mediatorsTerms = NA,
..moderatorsTerms = NA,
..missing = NA,
..diagram = NA,
..diag_paths = NA,
..diag_labsize = NA,
..diag_shape = NA,
..diag_abbrev = NA,
..diag_offset = NA)
)
jammGLMResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jammGLMResults",
inherit = jmvcore::Group,
active = list(
info = function() private$.items[["info"]],
pathmodelgroup = function() private$.items[["pathmodelgroup"]],
models = function() private$.items[["models"]],
regressions = function() private$.items[["regressions"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="GLM Mediation Analysis")
self$add(jmvcore::Table$new(
options=options,
name="info",
title="Models Info",
columns=list(
list(
`name`="info",
`type`="text",
`title`="",
`combineBelow`=TRUE),
list(
`name`="specs",
`type`="text",
`title`=""),
list(
`name`="value",
`type`="text",
`title`="")),
refs="jamm"))
self$add(R6::R6Class(
inherit = jmvcore::Group,
active = list(
pathmodel = function() private$.items[["pathmodel"]],
statmodel = function() private$.items[["statmodel"]],
pathnotes = function() private$.items[["pathnotes"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="pathmodelgroup",
title="Path Model",
clearWith=list(
"dep",
"mediatorsTerms",
"modelTerms",
"moderatorsTerms"))
self$add(jmvcore::Image$new(
options=options,
name="pathmodel",
title="Conceptual Diagram",
width=800,
height=600,
renderFun=".showConceptualDiagram",
clearWith=list(
"dep",
"mediatorsTerms",
"modelTerms",
"moderatorsTerms",
"pathOptions",
"diagram",
"diag_labsize",
"diag_shape",
"diag_abbrev"),
refs="diagram",
visible="(diagram:conceptual)"))
self$add(jmvcore::Image$new(
options=options,
name="statmodel",
title="Statistical Diagram",
width=800,
height=600,
renderFun=".showStatDiagram",
clearWith=list(
"dep",
"mediatorsTerms",
"modelTerms",
"moderatorsTerms",
"pathOptions",
"diagram",
"diag_offset",
"diag_labsize",
"diag_shape",
"diag_abbrev",
"diag_paths"),
refs="diagram",
visible="(diagram:statistical)"))
self$add(jmvcore::Table$new(
options=options,
name="pathnotes",
title="",
visible=FALSE,
columns=list(
list(
`name`="info",
`type`="text",
`title`="Diagram notes"))))}))$new(options=options))
self$add(R6::R6Class(
inherit = jmvcore::Group,
active = list(
moderationEffects = function() private$.items[["moderationEffects"]],
main = function() private$.items[["main"]],
contrastCodeTables = function() private$.items[["contrastCodeTables"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="models",
title="Mediation",
clearWith=list(
"dep",
"mediators",
"factors",
"covs"))
self$add(jmvcore::Table$new(
options=options,
name="moderationEffects",
title="Moderation effects (interactions)",
visible=FALSE,
clearWith=list(
"dep",
"modelTerms",
"contrasts",
"fixedIntercept",
"simpleScale"),
columns=list(
list(
`name`="mod",
`title`="Moderator",
`combineBelow`=TRUE,
`type`="text"),
list(
`name`="target",
`title`="Interaction",
`type`="text"),
list(
`name`="label",
`title`="Contrasts",
`visible`=FALSE,
`type`="text"),
list(
`name`="est",
`title`="Estimate",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"),
list(
`name`="ci.lower",
`type`="number",
`title`="Lower",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="ci.upper",
`type`="number",
`title`="Upper",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="std.all",
`type`="number",
`title`="\u03B2",
`visible`="(tableOptions:beta)"),
list(
`name`="z",
`title`="z",
`type`="number"),
list(
`name`="pvalue",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="main",
title="Indirect and Total Effects",
refs="lavaan",
clearWith=list(
"dep",
"modelTerms",
"contrasts",
"fixedIntercept",
"simpleScale",
"ciType"),
columns=list(
list(
`name`="type",
`title`="Type",
`type`="text",
`combineBelow`=TRUE),
list(
`name`="source",
`title`="Effect",
`type`="text"),
list(
`name`="label",
`title`="Contrasts",
`visible`=FALSE,
`type`="text"),
list(
`name`="est",
`title`="Estimate",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"),
list(
`name`="ci.lower",
`type`="number",
`title`="Lower",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="ci.upper",
`type`="number",
`title`="Upper",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="std.all",
`type`="number",
`title`="\u03B2",
`visible`="(tableOptions:beta)"),
list(
`name`="z",
`title`="z",
`type`="number"),
list(
`name`="pvalue",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Array$new(
options=options,
name="contrastCodeTables",
title="Contrast Coefficients",
visible="(showContrastCode)",
clearWith=list(
"contrasts",
"showContrastCode"),
template=jmvcore::Table$new(
options=options,
title="$key",
visible="(showContrastCode)",
columns=list(
list(
`name`="rnames",
`title`="Name",
`type`="text"),
list(
`name`="clabs",
`title`="Contrast",
`type`="text")))))}))$new(options=options))
self$add(R6::R6Class(
inherit = jmvcore::Group,
active = list(
overall = function() private$.items[["overall"]],
mediator_regressions = function() private$.items[["mediator_regressions"]],
full = function() private$.items[["full"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="regressions",
title="",
clearWith=list(
"dep",
"contrasts",
"scaling"))
self$add(R6::R6Class(
inherit = jmvcore::Group,
active = list(
anova = function() private$.items[["anova"]],
regression = function() private$.items[["regression"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="overall",
title="Total effects",
clearWith=list(
"dep",
"contrasts",
"scaling"))
self$add(jmvcore::Table$new(
options=options,
name="anova",
title="ANOVA Table",
visible="(tableOptions:regression)",
columns=list(
list(
`name`="rsquared",
`title`="R-squared",
`type`="number"),
list(
`name`="f",
`type`="number",
`title`="F"),
list(
`name`="df1",
`title`="df1",
`type`="number"),
list(
`name`="df2",
`title`="df2",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="regression",
title="Regression Table",
visible="(tableOptions:regression)",
columns=list(
list(
`name`="source",
`title`="Names",
`type`="text",
`visible`="(showRealNames)"),
list(
`name`="label",
`title`="Effect",
`type`="text"),
list(
`name`="estimate",
`title`="Estimate",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"),
list(
`name`="cilow",
`type`="number",
`title`="Lower",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="cihig",
`type`="number",
`title`="Upper",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="beta",
`type`="number",
`title`="\u03B2",
`visible`="(tableOptions:beta)"),
list(
`name`="df",
`title`="df",
`type`="number"),
list(
`name`="t",
`title`="t",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))}))$new(options=options))
self$add(jmvcore::Array$new(
options=options,
name="mediator_regressions",
title="Mediator Model",
clearWith=list(
"dep",
"contrasts",
"scaling"),
template=R6::R6Class(
inherit = jmvcore::Group,
active = list(
anova = function() private$.items[["anova"]],
regression = function() private$.items[["regression"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="undefined",
title="",
clearWith=list())
self$add(jmvcore::Table$new(
options=options,
name="anova",
title="ANOVA",
columns=list(
list(
`name`="rsquared",
`title`="R-squared",
`type`="number"),
list(
`name`="f",
`type`="number",
`title`="F"),
list(
`name`="df1",
`title`="df1",
`type`="number"),
list(
`name`="df2",
`title`="df2",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="regression",
title="Regression",
visible="(tableOptions:regression)",
columns=list(
list(
`name`="source",
`title`="Names",
`type`="text",
`visible`="(showRealNames)"),
list(
`name`="label",
`title`="Effect",
`type`="text"),
list(
`name`="estimate",
`title`="Estimate",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"),
list(
`name`="cilow",
`type`="number",
`title`="Lower",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="cihig",
`type`="number",
`title`="Upper",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="beta",
`type`="number",
`title`="\u03B2",
`visible`="(tableOptions:beta)"),
list(
`name`="df",
`title`="df",
`type`="number"),
list(
`name`="t",
`title`="t",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))}))$new(options=options)))
self$add(R6::R6Class(
inherit = jmvcore::Group,
active = list(
anova = function() private$.items[["anova"]],
regression = function() private$.items[["regression"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="full",
title="Full model effects",
clearWith=list(
"dep",
"contrasts",
"scaling"))
self$add(jmvcore::Table$new(
options=options,
name="anova",
title="ANOVA Table",
visible="(tableOptions:regression)",
columns=list(
list(
`name`="rsquared",
`title`="R-squared",
`type`="number"),
list(
`name`="f",
`type`="number",
`title`="F"),
list(
`name`="df1",
`title`="df1",
`type`="number"),
list(
`name`="df2",
`title`="df2",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="regression",
title="Regression Table",
visible="(tableOptions:regression)",
columns=list(
list(
`name`="source",
`title`="Names",
`type`="text",
`visible`="(showRealNames)"),
list(
`name`="label",
`title`="Effect",
`type`="text"),
list(
`name`="estimate",
`title`="Estimate",
`type`="number"),
list(
`name`="se",
`title`="SE",
`type`="number"),
list(
`name`="cilow",
`type`="number",
`title`="Lower",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="cihig",
`type`="number",
`title`="Upper",
`visible`="(ciType:standard || ciType:perc || ciType:norm || ciType:bca)"),
list(
`name`="beta",
`type`="number",
`title`="\u03B2",
`visible`="(tableOptions:beta)"),
list(
`name`="df",
`title`="df",
`type`="number"),
list(
`name`="t",
`title`="t",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))}))$new(options=options))}))$new(options=options))}))
jammGLMBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"jammGLMBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "jamm",
name = "jammGLM",
version = c(1,1,0),
options = options,
results = jammGLMResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
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