R/mfa.h.R
In hyunsooseol/snowCluster: Multivariate Analysis
Defines functions
mfa
Documented in
mfa
# This file is automatically generated, you probably don't want to edit this
mfaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"mfaOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
vars = NULL,
facs = NULL,
labels = NULL,
group = "2,5,3,10,9,2",
type = "n,s,s,s,s,s",
gn = "a,b,c,d,e,f",
eigen = TRUE,
colvar = "coordinates",
rowvar = "coordinates",
cg = FALSE,
ci = FALSE,
quanti = FALSE,
quanvar = "coordinates",
plot = FALSE,
plot1 = FALSE,
plot2 = FALSE,
plot3 = FALSE,
plot4 = FALSE,
plot5 = FALSE,
plot6 = FALSE,
plot7 = FALSE,
plot8 = FALSE,
angle = 0,
width = 500,
height = 500,
width1 = 500,
height1 = 500,
width2 = 500,
height2 = 500,
width3 = 500,
height3 = 500,
width4 = 500,
height4 = 500,
width5 = 500,
height5 = 500,
width6 = 500,
height6 = 500,
width7 = 500,
height7 = 500,
width8 = 500,
height8 = 500, ...) {
super$initialize(
package="snowCluster",
name="mfa",
requiresData=TRUE,
...)
private$..vars <- jmvcore::OptionVariables$new(
"vars",
vars)
private$..facs <- jmvcore::OptionVariable$new(
"facs",
facs,
suggested=list(
"nominal"),
permitted=list(
"factor"))
private$..labels <- jmvcore::OptionVariable$new(
"labels",
labels,
suggested=list(
"id"),
permitted=list(
"id",
"factor"))
private$..group <- jmvcore::OptionString$new(
"group",
group,
default="2,5,3,10,9,2")
private$..type <- jmvcore::OptionString$new(
"type",
type,
default="n,s,s,s,s,s")
private$..gn <- jmvcore::OptionString$new(
"gn",
gn,
default="a,b,c,d,e,f")
private$..eigen <- jmvcore::OptionBool$new(
"eigen",
eigen,
default=TRUE)
private$..colvar <- jmvcore::OptionList$new(
"colvar",
colvar,
options=list(
"coordinates",
"cos2",
"contribution"),
default="coordinates")
private$..rowvar <- jmvcore::OptionList$new(
"rowvar",
rowvar,
options=list(
"coordinates",
"cos2",
"contribution"),
default="coordinates")
private$..cg <- jmvcore::OptionBool$new(
"cg",
cg,
default=FALSE)
private$..ci <- jmvcore::OptionBool$new(
"ci",
ci,
default=FALSE)
private$..quanti <- jmvcore::OptionBool$new(
"quanti",
quanti,
default=FALSE)
private$..quanvar <- jmvcore::OptionList$new(
"quanvar",
quanvar,
options=list(
"coordinates",
"cos2",
"contribution"),
default="coordinates")
private$..plot <- jmvcore::OptionBool$new(
"plot",
plot,
default=FALSE)
private$..plot1 <- jmvcore::OptionBool$new(
"plot1",
plot1,
default=FALSE)
private$..plot2 <- jmvcore::OptionBool$new(
"plot2",
plot2,
default=FALSE)
private$..plot3 <- jmvcore::OptionBool$new(
"plot3",
plot3,
default=FALSE)
private$..plot4 <- jmvcore::OptionBool$new(
"plot4",
plot4,
default=FALSE)
private$..plot5 <- jmvcore::OptionBool$new(
"plot5",
plot5,
default=FALSE)
private$..plot6 <- jmvcore::OptionBool$new(
"plot6",
plot6,
default=FALSE)
private$..plot7 <- jmvcore::OptionBool$new(
"plot7",
plot7,
default=FALSE)
private$..plot8 <- jmvcore::OptionBool$new(
"plot8",
plot8,
default=FALSE)
private$..angle <- jmvcore::OptionNumber$new(
"angle",
angle,
min=0,
max=90,
default=0)
private$..width <- jmvcore::OptionInteger$new(
"width",
width,
default=500)
private$..height <- jmvcore::OptionInteger$new(
"height",
height,
default=500)
private$..width1 <- jmvcore::OptionInteger$new(
"width1",
width1,
default=500)
private$..height1 <- jmvcore::OptionInteger$new(
"height1",
height1,
default=500)
private$..width2 <- jmvcore::OptionInteger$new(
"width2",
width2,
default=500)
private$..height2 <- jmvcore::OptionInteger$new(
"height2",
height2,
default=500)
private$..width3 <- jmvcore::OptionInteger$new(
"width3",
width3,
default=500)
private$..height3 <- jmvcore::OptionInteger$new(
"height3",
height3,
default=500)
private$..width4 <- jmvcore::OptionInteger$new(
"width4",
width4,
default=500)
private$..height4 <- jmvcore::OptionInteger$new(
"height4",
height4,
default=500)
private$..width5 <- jmvcore::OptionInteger$new(
"width5",
width5,
default=500)
private$..height5 <- jmvcore::OptionInteger$new(
"height5",
height5,
default=500)
private$..width6 <- jmvcore::OptionInteger$new(
"width6",
width6,
default=500)
private$..height6 <- jmvcore::OptionInteger$new(
"height6",
height6,
default=500)
private$..width7 <- jmvcore::OptionInteger$new(
"width7",
width7,
default=500)
private$..height7 <- jmvcore::OptionInteger$new(
"height7",
height7,
default=500)
private$..width8 <- jmvcore::OptionInteger$new(
"width8",
width8,
default=500)
private$..height8 <- jmvcore::OptionInteger$new(
"height8",
height8,
default=500)
self$.addOption(private$..vars)
self$.addOption(private$..facs)
self$.addOption(private$..labels)
self$.addOption(private$..group)
self$.addOption(private$..type)
self$.addOption(private$..gn)
self$.addOption(private$..eigen)
self$.addOption(private$..colvar)
self$.addOption(private$..rowvar)
self$.addOption(private$..cg)
self$.addOption(private$..ci)
self$.addOption(private$..quanti)
self$.addOption(private$..quanvar)
self$.addOption(private$..plot)
self$.addOption(private$..plot1)
self$.addOption(private$..plot2)
self$.addOption(private$..plot3)
self$.addOption(private$..plot4)
self$.addOption(private$..plot5)
self$.addOption(private$..plot6)
self$.addOption(private$..plot7)
self$.addOption(private$..plot8)
self$.addOption(private$..angle)
self$.addOption(private$..width)
self$.addOption(private$..height)
self$.addOption(private$..width1)
self$.addOption(private$..height1)
self$.addOption(private$..width2)
self$.addOption(private$..height2)
self$.addOption(private$..width3)
self$.addOption(private$..height3)
self$.addOption(private$..width4)
self$.addOption(private$..height4)
self$.addOption(private$..width5)
self$.addOption(private$..height5)
self$.addOption(private$..width6)
self$.addOption(private$..height6)
self$.addOption(private$..width7)
self$.addOption(private$..height7)
self$.addOption(private$..width8)
self$.addOption(private$..height8)
}),
active = list(
vars = function() private$..vars$value,
facs = function() private$..facs$value,
labels = function() private$..labels$value,
group = function() private$..group$value,
type = function() private$..type$value,
gn = function() private$..gn$value,
eigen = function() private$..eigen$value,
colvar = function() private$..colvar$value,
rowvar = function() private$..rowvar$value,
cg = function() private$..cg$value,
ci = function() private$..ci$value,
quanti = function() private$..quanti$value,
quanvar = function() private$..quanvar$value,
plot = function() private$..plot$value,
plot1 = function() private$..plot1$value,
plot2 = function() private$..plot2$value,
plot3 = function() private$..plot3$value,
plot4 = function() private$..plot4$value,
plot5 = function() private$..plot5$value,
plot6 = function() private$..plot6$value,
plot7 = function() private$..plot7$value,
plot8 = function() private$..plot8$value,
angle = function() private$..angle$value,
width = function() private$..width$value,
height = function() private$..height$value,
width1 = function() private$..width1$value,
height1 = function() private$..height1$value,
width2 = function() private$..width2$value,
height2 = function() private$..height2$value,
width3 = function() private$..width3$value,
height3 = function() private$..height3$value,
width4 = function() private$..width4$value,
height4 = function() private$..height4$value,
width5 = function() private$..width5$value,
height5 = function() private$..height5$value,
width6 = function() private$..width6$value,
height6 = function() private$..height6$value,
width7 = function() private$..width7$value,
height7 = function() private$..height7$value,
width8 = function() private$..width8$value,
height8 = function() private$..height8$value),
private = list(
..vars = NA,
..facs = NA,
..labels = NA,
..group = NA,
..type = NA,
..gn = NA,
..eigen = NA,
..colvar = NA,
..rowvar = NA,
..cg = NA,
..ci = NA,
..quanti = NA,
..quanvar = NA,
..plot = NA,
..plot1 = NA,
..plot2 = NA,
..plot3 = NA,
..plot4 = NA,
..plot5 = NA,
..plot6 = NA,
..plot7 = NA,
..plot8 = NA,
..angle = NA,
..width = NA,
..height = NA,
..width1 = NA,
..height1 = NA,
..width2 = NA,
..height2 = NA,
..width3 = NA,
..height3 = NA,
..width4 = NA,
..height4 = NA,
..width5 = NA,
..height5 = NA,
..width6 = NA,
..height6 = NA,
..width7 = NA,
..height7 = NA,
..width8 = NA,
..height8 = NA)
)
mfaResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"mfaResults",
inherit = jmvcore::Group,
active = list(
instructions = function() private$.items[["instructions"]],
eigen = function() private$.items[["eigen"]],
cg = function() private$.items[["cg"]],
ci = function() private$.items[["ci"]],
quanti = function() private$.items[["quanti"]],
plot8 = function() private$.items[["plot8"]],
plot = function() private$.items[["plot"]],
plot6 = function() private$.items[["plot6"]],
plot7 = function() private$.items[["plot7"]],
plot1 = function() private$.items[["plot1"]],
plot2 = function() private$.items[["plot2"]],
plot3 = function() private$.items[["plot3"]],
plot4 = function() private$.items[["plot4"]],
plot5 = function() private$.items[["plot5"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Multiple Factor Analysis",
refs="snowCluster")
self$add(jmvcore::Html$new(
options=options,
name="instructions",
title="Instructions",
visible=TRUE))
self$add(jmvcore::Table$new(
options=options,
name="eigen",
title="Eigenvalues",
visible="(eigen)",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar"),
columns=list(
list(
`name`="comp",
`title`="Component",
`type`="text"),
list(
`name`="eigen",
`title`="Eigenvalue",
`type`="number"),
list(
`name`="varProp",
`title`="% of Variance",
`type`="number"),
list(
`name`="varCum",
`title`="Cumulative %",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="cg",
title="`Groups of variables - ${colvar}`",
visible="(cg)",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar"),
columns=list(
list(
`name`="name",
`title`="",
`type`="text",
`content`="($key)"),
list(
`name`="pc1",
`title`="1",
`type`="number",
`superTitle`="Dimension"))))
self$add(jmvcore::Table$new(
options=options,
name="ci",
title="`Individuals - ${rowvar}`",
visible="(ci)",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar"),
columns=list(
list(
`name`="name",
`title`="",
`type`="text",
`content`="($key)"),
list(
`name`="pc1",
`title`="1",
`type`="number",
`superTitle`="Dimension"))))
self$add(jmvcore::Table$new(
options=options,
name="quanti",
title="`Quantitative variables - ${quanvar}`",
visible="(quanti)",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar"),
columns=list(
list(
`name`="name",
`title`="",
`type`="text",
`content`="($key)"),
list(
`name`="pc1",
`title`="1",
`type`="number",
`superTitle`="Dimension"))))
self$add(jmvcore::Image$new(
options=options,
name="plot8",
title="Scree plot",
requiresData=TRUE,
refs="factoextra",
visible="(plot8)",
renderFun=".plot8",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar",
"width8",
"height8")))
self$add(jmvcore::Image$new(
options=options,
name="plot",
title="Variable groups",
requiresData=TRUE,
refs="factoextra",
visible="(plot)",
renderFun=".plot",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar",
"width",
"height")))
self$add(jmvcore::Image$new(
options=options,
name="plot6",
title="Contribution of groups to dimension 1",
requiresData=TRUE,
refs="factoextra",
visible="(plot6)",
renderFun=".plot6",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar",
"width6",
"height6",
"angle")))
self$add(jmvcore::Image$new(
options=options,
name="plot7",
title="Contribution of groups to dimension 2",
requiresData=TRUE,
refs="factoextra",
visible="(plot7)",
renderFun=".plot7",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar",
"width7",
"height7",
"angle")))
self$add(jmvcore::Image$new(
options=options,
name="plot1",
title="Quantitative variables by groups",
requiresData=TRUE,
refs="factoextra",
visible="(plot1)",
renderFun=".plot1",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar",
"width1",
"height1")))
self$add(jmvcore::Image$new(
options=options,
name="plot2",
title="Contribution to dimension 1",
requiresData=TRUE,
refs="factoextra",
visible="(plot2)",
renderFun=".plot2",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar",
"width2",
"height2",
"angle")))
self$add(jmvcore::Image$new(
options=options,
name="plot3",
title="Contribution to dimension 2",
requiresData=TRUE,
refs="factoextra",
visible="(plot3)",
renderFun=".plot3",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar",
"width3",
"height3",
"angle")))
self$add(jmvcore::Image$new(
options=options,
name="plot4",
title="Graph of individuals",
requiresData=TRUE,
refs="factoextra",
visible="(plot4)",
renderFun=".plot4",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar",
"width4",
"height4")))
self$add(jmvcore::Image$new(
options=options,
name="plot5",
title="Individuals by group",
requiresData=TRUE,
refs="factoextra",
visible="(plot5)",
renderFun=".plot5",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar",
"width5",
"height5")))}))
mfaBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"mfaBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "snowCluster",
name = "mfa",
version = c(1,0,0),
options = options,
results = mfaResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
#' Multiple Factor Analysis
#'
#'
#' @param data The data as a data frame.
#' @param vars .
#' @param facs .
#' @param labels .
#' @param group .
#' @param type .
#' @param gn .
#' @param eigen .
#' @param colvar .
#' @param rowvar .
#' @param cg .
#' @param ci .
#' @param quanti .
#' @param quanvar .
#' @param plot .
#' @param plot1 .
#' @param plot2 .
#' @param plot3 .
#' @param plot4 .
#' @param plot5 .
#' @param plot6 .
#' @param plot7 .
#' @param plot8 .
#' @param angle .
#' @param width .
#' @param height .
#' @param width1 .
#' @param height1 .
#' @param width2 .
#' @param height2 .
#' @param width3 .
#' @param height3 .
#' @param width4 .
#' @param height4 .
#' @param width5 .
#' @param height5 .
#' @param width6 .
#' @param height6 .
#' @param width7 .
#' @param height7 .
#' @param width8 .
#' @param height8 .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$instructions} \tab \tab \tab \tab \tab a html \cr
#' \code{results$eigen} \tab \tab \tab \tab \tab a table \cr
#' \code{results$cg} \tab \tab \tab \tab \tab a table \cr
#' \code{results$ci} \tab \tab \tab \tab \tab a table \cr
#' \code{results$quanti} \tab \tab \tab \tab \tab a table \cr
#' \code{results$plot8} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot6} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot7} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot1} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot2} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot3} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot4} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot5} \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$eigen$asDF}
#'
#' \code{as.data.frame(results$eigen)}
#'
#' @export
mfa <- function(
data,
vars,
facs,
labels,
group = "2,5,3,10,9,2",
type = "n,s,s,s,s,s",
gn = "a,b,c,d,e,f",
eigen = TRUE,
colvar = "coordinates",
rowvar = "coordinates",
cg = FALSE,
ci = FALSE,
quanti = FALSE,
quanvar = "coordinates",
plot = FALSE,
plot1 = FALSE,
plot2 = FALSE,
plot3 = FALSE,
plot4 = FALSE,
plot5 = FALSE,
plot6 = FALSE,
plot7 = FALSE,
plot8 = FALSE,
angle = 0,
width = 500,
height = 500,
width1 = 500,
height1 = 500,
width2 = 500,
height2 = 500,
width3 = 500,
height3 = 500,
width4 = 500,
height4 = 500,
width5 = 500,
height5 = 500,
width6 = 500,
height6 = 500,
width7 = 500,
height7 = 500,
width8 = 500,
height8 = 500) {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("mfa requires jmvcore to be installed (restart may be required)")
if ( ! missing(vars)) vars <- jmvcore::resolveQuo(jmvcore::enquo(vars))
if ( ! missing(facs)) facs <- jmvcore::resolveQuo(jmvcore::enquo(facs))
if ( ! missing(labels)) labels <- jmvcore::resolveQuo(jmvcore::enquo(labels))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(vars), vars, NULL),
`if`( ! missing(facs), facs, NULL),
`if`( ! missing(labels), labels, NULL))
for (v in facs) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
options <- mfaOptions$new(
vars = vars,
facs = facs,
labels = labels,
group = group,
type = type,
gn = gn,
eigen = eigen,
colvar = colvar,
rowvar = rowvar,
cg = cg,
ci = ci,
quanti = quanti,
quanvar = quanvar,
plot = plot,
plot1 = plot1,
plot2 = plot2,
plot3 = plot3,
plot4 = plot4,
plot5 = plot5,
plot6 = plot6,
plot7 = plot7,
plot8 = plot8,
angle = angle,
width = width,
height = height,
width1 = width1,
height1 = height1,
width2 = width2,
height2 = height2,
width3 = width3,
height3 = height3,
width4 = width4,
height4 = height4,
width5 = width5,
height5 = height5,
width6 = width6,
height6 = height6,
width7 = width7,
height7 = height7,
width8 = width8,
height8 = height8)
analysis <- mfaClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
hyunsooseol/snowCluster documentation built on April 5, 2025, 2:06 a.m.
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Defines functions mfa
Documented in mfa
# This file is automatically generated, you probably don't want to edit this
mfaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"mfaOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
vars = NULL,
facs = NULL,
labels = NULL,
group = "2,5,3,10,9,2",
type = "n,s,s,s,s,s",
gn = "a,b,c,d,e,f",
eigen = TRUE,
colvar = "coordinates",
rowvar = "coordinates",
cg = FALSE,
ci = FALSE,
quanti = FALSE,
quanvar = "coordinates",
plot = FALSE,
plot1 = FALSE,
plot2 = FALSE,
plot3 = FALSE,
plot4 = FALSE,
plot5 = FALSE,
plot6 = FALSE,
plot7 = FALSE,
plot8 = FALSE,
angle = 0,
width = 500,
height = 500,
width1 = 500,
height1 = 500,
width2 = 500,
height2 = 500,
width3 = 500,
height3 = 500,
width4 = 500,
height4 = 500,
width5 = 500,
height5 = 500,
width6 = 500,
height6 = 500,
width7 = 500,
height7 = 500,
width8 = 500,
height8 = 500, ...) {
super$initialize(
package="snowCluster",
name="mfa",
requiresData=TRUE,
...)
private$..vars <- jmvcore::OptionVariables$new(
"vars",
vars)
private$..facs <- jmvcore::OptionVariable$new(
"facs",
facs,
suggested=list(
"nominal"),
permitted=list(
"factor"))
private$..labels <- jmvcore::OptionVariable$new(
"labels",
labels,
suggested=list(
"id"),
permitted=list(
"id",
"factor"))
private$..group <- jmvcore::OptionString$new(
"group",
group,
default="2,5,3,10,9,2")
private$..type <- jmvcore::OptionString$new(
"type",
type,
default="n,s,s,s,s,s")
private$..gn <- jmvcore::OptionString$new(
"gn",
gn,
default="a,b,c,d,e,f")
private$..eigen <- jmvcore::OptionBool$new(
"eigen",
eigen,
default=TRUE)
private$..colvar <- jmvcore::OptionList$new(
"colvar",
colvar,
options=list(
"coordinates",
"cos2",
"contribution"),
default="coordinates")
private$..rowvar <- jmvcore::OptionList$new(
"rowvar",
rowvar,
options=list(
"coordinates",
"cos2",
"contribution"),
default="coordinates")
private$..cg <- jmvcore::OptionBool$new(
"cg",
cg,
default=FALSE)
private$..ci <- jmvcore::OptionBool$new(
"ci",
ci,
default=FALSE)
private$..quanti <- jmvcore::OptionBool$new(
"quanti",
quanti,
default=FALSE)
private$..quanvar <- jmvcore::OptionList$new(
"quanvar",
quanvar,
options=list(
"coordinates",
"cos2",
"contribution"),
default="coordinates")
private$..plot <- jmvcore::OptionBool$new(
"plot",
plot,
default=FALSE)
private$..plot1 <- jmvcore::OptionBool$new(
"plot1",
plot1,
default=FALSE)
private$..plot2 <- jmvcore::OptionBool$new(
"plot2",
plot2,
default=FALSE)
private$..plot3 <- jmvcore::OptionBool$new(
"plot3",
plot3,
default=FALSE)
private$..plot4 <- jmvcore::OptionBool$new(
"plot4",
plot4,
default=FALSE)
private$..plot5 <- jmvcore::OptionBool$new(
"plot5",
plot5,
default=FALSE)
private$..plot6 <- jmvcore::OptionBool$new(
"plot6",
plot6,
default=FALSE)
private$..plot7 <- jmvcore::OptionBool$new(
"plot7",
plot7,
default=FALSE)
private$..plot8 <- jmvcore::OptionBool$new(
"plot8",
plot8,
default=FALSE)
private$..angle <- jmvcore::OptionNumber$new(
"angle",
angle,
min=0,
max=90,
default=0)
private$..width <- jmvcore::OptionInteger$new(
"width",
width,
default=500)
private$..height <- jmvcore::OptionInteger$new(
"height",
height,
default=500)
private$..width1 <- jmvcore::OptionInteger$new(
"width1",
width1,
default=500)
private$..height1 <- jmvcore::OptionInteger$new(
"height1",
height1,
default=500)
private$..width2 <- jmvcore::OptionInteger$new(
"width2",
width2,
default=500)
private$..height2 <- jmvcore::OptionInteger$new(
"height2",
height2,
default=500)
private$..width3 <- jmvcore::OptionInteger$new(
"width3",
width3,
default=500)
private$..height3 <- jmvcore::OptionInteger$new(
"height3",
height3,
default=500)
private$..width4 <- jmvcore::OptionInteger$new(
"width4",
width4,
default=500)
private$..height4 <- jmvcore::OptionInteger$new(
"height4",
height4,
default=500)
private$..width5 <- jmvcore::OptionInteger$new(
"width5",
width5,
default=500)
private$..height5 <- jmvcore::OptionInteger$new(
"height5",
height5,
default=500)
private$..width6 <- jmvcore::OptionInteger$new(
"width6",
width6,
default=500)
private$..height6 <- jmvcore::OptionInteger$new(
"height6",
height6,
default=500)
private$..width7 <- jmvcore::OptionInteger$new(
"width7",
width7,
default=500)
private$..height7 <- jmvcore::OptionInteger$new(
"height7",
height7,
default=500)
private$..width8 <- jmvcore::OptionInteger$new(
"width8",
width8,
default=500)
private$..height8 <- jmvcore::OptionInteger$new(
"height8",
height8,
default=500)
self$.addOption(private$..vars)
self$.addOption(private$..facs)
self$.addOption(private$..labels)
self$.addOption(private$..group)
self$.addOption(private$..type)
self$.addOption(private$..gn)
self$.addOption(private$..eigen)
self$.addOption(private$..colvar)
self$.addOption(private$..rowvar)
self$.addOption(private$..cg)
self$.addOption(private$..ci)
self$.addOption(private$..quanti)
self$.addOption(private$..quanvar)
self$.addOption(private$..plot)
self$.addOption(private$..plot1)
self$.addOption(private$..plot2)
self$.addOption(private$..plot3)
self$.addOption(private$..plot4)
self$.addOption(private$..plot5)
self$.addOption(private$..plot6)
self$.addOption(private$..plot7)
self$.addOption(private$..plot8)
self$.addOption(private$..angle)
self$.addOption(private$..width)
self$.addOption(private$..height)
self$.addOption(private$..width1)
self$.addOption(private$..height1)
self$.addOption(private$..width2)
self$.addOption(private$..height2)
self$.addOption(private$..width3)
self$.addOption(private$..height3)
self$.addOption(private$..width4)
self$.addOption(private$..height4)
self$.addOption(private$..width5)
self$.addOption(private$..height5)
self$.addOption(private$..width6)
self$.addOption(private$..height6)
self$.addOption(private$..width7)
self$.addOption(private$..height7)
self$.addOption(private$..width8)
self$.addOption(private$..height8)
}),
active = list(
vars = function() private$..vars$value,
facs = function() private$..facs$value,
labels = function() private$..labels$value,
group = function() private$..group$value,
type = function() private$..type$value,
gn = function() private$..gn$value,
eigen = function() private$..eigen$value,
colvar = function() private$..colvar$value,
rowvar = function() private$..rowvar$value,
cg = function() private$..cg$value,
ci = function() private$..ci$value,
quanti = function() private$..quanti$value,
quanvar = function() private$..quanvar$value,
plot = function() private$..plot$value,
plot1 = function() private$..plot1$value,
plot2 = function() private$..plot2$value,
plot3 = function() private$..plot3$value,
plot4 = function() private$..plot4$value,
plot5 = function() private$..plot5$value,
plot6 = function() private$..plot6$value,
plot7 = function() private$..plot7$value,
plot8 = function() private$..plot8$value,
angle = function() private$..angle$value,
width = function() private$..width$value,
height = function() private$..height$value,
width1 = function() private$..width1$value,
height1 = function() private$..height1$value,
width2 = function() private$..width2$value,
height2 = function() private$..height2$value,
width3 = function() private$..width3$value,
height3 = function() private$..height3$value,
width4 = function() private$..width4$value,
height4 = function() private$..height4$value,
width5 = function() private$..width5$value,
height5 = function() private$..height5$value,
width6 = function() private$..width6$value,
height6 = function() private$..height6$value,
width7 = function() private$..width7$value,
height7 = function() private$..height7$value,
width8 = function() private$..width8$value,
height8 = function() private$..height8$value),
private = list(
..vars = NA,
..facs = NA,
..labels = NA,
..group = NA,
..type = NA,
..gn = NA,
..eigen = NA,
..colvar = NA,
..rowvar = NA,
..cg = NA,
..ci = NA,
..quanti = NA,
..quanvar = NA,
..plot = NA,
..plot1 = NA,
..plot2 = NA,
..plot3 = NA,
..plot4 = NA,
..plot5 = NA,
..plot6 = NA,
..plot7 = NA,
..plot8 = NA,
..angle = NA,
..width = NA,
..height = NA,
..width1 = NA,
..height1 = NA,
..width2 = NA,
..height2 = NA,
..width3 = NA,
..height3 = NA,
..width4 = NA,
..height4 = NA,
..width5 = NA,
..height5 = NA,
..width6 = NA,
..height6 = NA,
..width7 = NA,
..height7 = NA,
..width8 = NA,
..height8 = NA)
)
mfaResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"mfaResults",
inherit = jmvcore::Group,
active = list(
instructions = function() private$.items[["instructions"]],
eigen = function() private$.items[["eigen"]],
cg = function() private$.items[["cg"]],
ci = function() private$.items[["ci"]],
quanti = function() private$.items[["quanti"]],
plot8 = function() private$.items[["plot8"]],
plot = function() private$.items[["plot"]],
plot6 = function() private$.items[["plot6"]],
plot7 = function() private$.items[["plot7"]],
plot1 = function() private$.items[["plot1"]],
plot2 = function() private$.items[["plot2"]],
plot3 = function() private$.items[["plot3"]],
plot4 = function() private$.items[["plot4"]],
plot5 = function() private$.items[["plot5"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Multiple Factor Analysis",
refs="snowCluster")
self$add(jmvcore::Html$new(
options=options,
name="instructions",
title="Instructions",
visible=TRUE))
self$add(jmvcore::Table$new(
options=options,
name="eigen",
title="Eigenvalues",
visible="(eigen)",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar"),
columns=list(
list(
`name`="comp",
`title`="Component",
`type`="text"),
list(
`name`="eigen",
`title`="Eigenvalue",
`type`="number"),
list(
`name`="varProp",
`title`="% of Variance",
`type`="number"),
list(
`name`="varCum",
`title`="Cumulative %",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="cg",
title="`Groups of variables - ${colvar}`",
visible="(cg)",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar"),
columns=list(
list(
`name`="name",
`title`="",
`type`="text",
`content`="($key)"),
list(
`name`="pc1",
`title`="1",
`type`="number",
`superTitle`="Dimension"))))
self$add(jmvcore::Table$new(
options=options,
name="ci",
title="`Individuals - ${rowvar}`",
visible="(ci)",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar"),
columns=list(
list(
`name`="name",
`title`="",
`type`="text",
`content`="($key)"),
list(
`name`="pc1",
`title`="1",
`type`="number",
`superTitle`="Dimension"))))
self$add(jmvcore::Table$new(
options=options,
name="quanti",
title="`Quantitative variables - ${quanvar}`",
visible="(quanti)",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar"),
columns=list(
list(
`name`="name",
`title`="",
`type`="text",
`content`="($key)"),
list(
`name`="pc1",
`title`="1",
`type`="number",
`superTitle`="Dimension"))))
self$add(jmvcore::Image$new(
options=options,
name="plot8",
title="Scree plot",
requiresData=TRUE,
refs="factoextra",
visible="(plot8)",
renderFun=".plot8",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar",
"width8",
"height8")))
self$add(jmvcore::Image$new(
options=options,
name="plot",
title="Variable groups",
requiresData=TRUE,
refs="factoextra",
visible="(plot)",
renderFun=".plot",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar",
"width",
"height")))
self$add(jmvcore::Image$new(
options=options,
name="plot6",
title="Contribution of groups to dimension 1",
requiresData=TRUE,
refs="factoextra",
visible="(plot6)",
renderFun=".plot6",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar",
"width6",
"height6",
"angle")))
self$add(jmvcore::Image$new(
options=options,
name="plot7",
title="Contribution of groups to dimension 2",
requiresData=TRUE,
refs="factoextra",
visible="(plot7)",
renderFun=".plot7",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar",
"width7",
"height7",
"angle")))
self$add(jmvcore::Image$new(
options=options,
name="plot1",
title="Quantitative variables by groups",
requiresData=TRUE,
refs="factoextra",
visible="(plot1)",
renderFun=".plot1",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar",
"width1",
"height1")))
self$add(jmvcore::Image$new(
options=options,
name="plot2",
title="Contribution to dimension 1",
requiresData=TRUE,
refs="factoextra",
visible="(plot2)",
renderFun=".plot2",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar",
"width2",
"height2",
"angle")))
self$add(jmvcore::Image$new(
options=options,
name="plot3",
title="Contribution to dimension 2",
requiresData=TRUE,
refs="factoextra",
visible="(plot3)",
renderFun=".plot3",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar",
"width3",
"height3",
"angle")))
self$add(jmvcore::Image$new(
options=options,
name="plot4",
title="Graph of individuals",
requiresData=TRUE,
refs="factoextra",
visible="(plot4)",
renderFun=".plot4",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar",
"width4",
"height4")))
self$add(jmvcore::Image$new(
options=options,
name="plot5",
title="Individuals by group",
requiresData=TRUE,
refs="factoextra",
visible="(plot5)",
renderFun=".plot5",
clearWith=list(
"vars",
"groups",
"type",
"gn",
"colvar",
"rowvar",
"quanvar",
"width5",
"height5")))}))
mfaBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"mfaBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "snowCluster",
name = "mfa",
version = c(1,0,0),
options = options,
results = mfaResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
#' Multiple Factor Analysis
#'
#'
#' @param data The data as a data frame.
#' @param vars .
#' @param facs .
#' @param labels .
#' @param group .
#' @param type .
#' @param gn .
#' @param eigen .
#' @param colvar .
#' @param rowvar .
#' @param cg .
#' @param ci .
#' @param quanti .
#' @param quanvar .
#' @param plot .
#' @param plot1 .
#' @param plot2 .
#' @param plot3 .
#' @param plot4 .
#' @param plot5 .
#' @param plot6 .
#' @param plot7 .
#' @param plot8 .
#' @param angle .
#' @param width .
#' @param height .
#' @param width1 .
#' @param height1 .
#' @param width2 .
#' @param height2 .
#' @param width3 .
#' @param height3 .
#' @param width4 .
#' @param height4 .
#' @param width5 .
#' @param height5 .
#' @param width6 .
#' @param height6 .
#' @param width7 .
#' @param height7 .
#' @param width8 .
#' @param height8 .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$instructions} \tab \tab \tab \tab \tab a html \cr
#' \code{results$eigen} \tab \tab \tab \tab \tab a table \cr
#' \code{results$cg} \tab \tab \tab \tab \tab a table \cr
#' \code{results$ci} \tab \tab \tab \tab \tab a table \cr
#' \code{results$quanti} \tab \tab \tab \tab \tab a table \cr
#' \code{results$plot8} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot6} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot7} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot1} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot2} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot3} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot4} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot5} \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$eigen$asDF}
#'
#' \code{as.data.frame(results$eigen)}
#'
#' @export
mfa <- function(
data,
vars,
facs,
labels,
group = "2,5,3,10,9,2",
type = "n,s,s,s,s,s",
gn = "a,b,c,d,e,f",
eigen = TRUE,
colvar = "coordinates",
rowvar = "coordinates",
cg = FALSE,
ci = FALSE,
quanti = FALSE,
quanvar = "coordinates",
plot = FALSE,
plot1 = FALSE,
plot2 = FALSE,
plot3 = FALSE,
plot4 = FALSE,
plot5 = FALSE,
plot6 = FALSE,
plot7 = FALSE,
plot8 = FALSE,
angle = 0,
width = 500,
height = 500,
width1 = 500,
height1 = 500,
width2 = 500,
height2 = 500,
width3 = 500,
height3 = 500,
width4 = 500,
height4 = 500,
width5 = 500,
height5 = 500,
width6 = 500,
height6 = 500,
width7 = 500,
height7 = 500,
width8 = 500,
height8 = 500) {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("mfa requires jmvcore to be installed (restart may be required)")
if ( ! missing(vars)) vars <- jmvcore::resolveQuo(jmvcore::enquo(vars))
if ( ! missing(facs)) facs <- jmvcore::resolveQuo(jmvcore::enquo(facs))
if ( ! missing(labels)) labels <- jmvcore::resolveQuo(jmvcore::enquo(labels))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(vars), vars, NULL),
`if`( ! missing(facs), facs, NULL),
`if`( ! missing(labels), labels, NULL))
for (v in facs) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
options <- mfaOptions$new(
vars = vars,
facs = facs,
labels = labels,
group = group,
type = type,
gn = gn,
eigen = eigen,
colvar = colvar,
rowvar = rowvar,
cg = cg,
ci = ci,
quanti = quanti,
quanvar = quanvar,
plot = plot,
plot1 = plot1,
plot2 = plot2,
plot3 = plot3,
plot4 = plot4,
plot5 = plot5,
plot6 = plot6,
plot7 = plot7,
plot8 = plot8,
angle = angle,
width = width,
height = height,
width1 = width1,
height1 = height1,
width2 = width2,
height2 = height2,
width3 = width3,
height3 = height3,
width4 = width4,
height4 = height4,
width5 = width5,
height5 = height5,
width6 = width6,
height6 = height6,
width7 = width7,
height7 = height7,
width8 = width8,
height8 = height8)
analysis <- mfaClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
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