R/roc.h.R
In hyunsooseol/snowCluster: Multivariate Analysis
Defines functions
roc
Documented in
roc
# This file is automatically generated, you probably don't want to edit this
rocOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"rocOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
dep = NULL,
covs = NULL,
plot1 = FALSE,
width1 = 500,
height1 = 500,
plot2 = FALSE,
width2 = 500,
height2 = 500,
plot3 = FALSE,
width3 = 500,
height3 = 500,
auc = FALSE,
dif = FALSE,
overall = FALSE, ...) {
super$initialize(
package="snowCluster",
name="roc",
requiresData=TRUE,
...)
private$..dep <- jmvcore::OptionVariable$new(
"dep",
dep,
suggested=list(
"nominal"),
permitted=list(
"factor"))
private$..covs <- jmvcore::OptionVariables$new(
"covs",
covs)
private$..plot1 <- jmvcore::OptionBool$new(
"plot1",
plot1,
default=FALSE)
private$..width1 <- jmvcore::OptionInteger$new(
"width1",
width1,
default=500)
private$..height1 <- jmvcore::OptionInteger$new(
"height1",
height1,
default=500)
private$..plot2 <- jmvcore::OptionBool$new(
"plot2",
plot2,
default=FALSE)
private$..width2 <- jmvcore::OptionInteger$new(
"width2",
width2,
default=500)
private$..height2 <- jmvcore::OptionInteger$new(
"height2",
height2,
default=500)
private$..plot3 <- jmvcore::OptionBool$new(
"plot3",
plot3,
default=FALSE)
private$..width3 <- jmvcore::OptionInteger$new(
"width3",
width3,
default=500)
private$..height3 <- jmvcore::OptionInteger$new(
"height3",
height3,
default=500)
private$..auc <- jmvcore::OptionBool$new(
"auc",
auc,
default=FALSE)
private$..dif <- jmvcore::OptionBool$new(
"dif",
dif,
default=FALSE)
private$..overall <- jmvcore::OptionBool$new(
"overall",
overall,
default=FALSE)
self$.addOption(private$..dep)
self$.addOption(private$..covs)
self$.addOption(private$..plot1)
self$.addOption(private$..width1)
self$.addOption(private$..height1)
self$.addOption(private$..plot2)
self$.addOption(private$..width2)
self$.addOption(private$..height2)
self$.addOption(private$..plot3)
self$.addOption(private$..width3)
self$.addOption(private$..height3)
self$.addOption(private$..auc)
self$.addOption(private$..dif)
self$.addOption(private$..overall)
}),
active = list(
dep = function() private$..dep$value,
covs = function() private$..covs$value,
plot1 = function() private$..plot1$value,
width1 = function() private$..width1$value,
height1 = function() private$..height1$value,
plot2 = function() private$..plot2$value,
width2 = function() private$..width2$value,
height2 = function() private$..height2$value,
plot3 = function() private$..plot3$value,
width3 = function() private$..width3$value,
height3 = function() private$..height3$value,
auc = function() private$..auc$value,
dif = function() private$..dif$value,
overall = function() private$..overall$value),
private = list(
..dep = NA,
..covs = NA,
..plot1 = NA,
..width1 = NA,
..height1 = NA,
..plot2 = NA,
..width2 = NA,
..height2 = NA,
..plot3 = NA,
..width3 = NA,
..height3 = NA,
..auc = NA,
..dif = NA,
..overall = NA)
)
rocResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"rocResults",
inherit = jmvcore::Group,
active = list(
instructions = function() private$.items[["instructions"]],
text = function() private$.items[["text"]],
plot1 = function() private$.items[["plot1"]],
plot2 = function() private$.items[["plot2"]],
plot3 = function() private$.items[["plot3"]],
auc = function() private$.items[["auc"]],
dif = function() private$.items[["dif"]],
overall = function() private$.items[["overall"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="ROC Analysis",
refs="snowCluster")
self$add(jmvcore::Html$new(
options=options,
name="instructions",
title="Instructions",
visible=TRUE))
self$add(jmvcore::Preformatted$new(
options=options,
name="text",
title=""))
self$add(jmvcore::Image$new(
options=options,
name="plot1",
title="ROC Curve",
requiresData=TRUE,
visible="(plot1)",
renderFun=".plot1",
refs="multipleROC",
clearWith=list(
"covs",
"dep",
"width1",
"height1")))
self$add(jmvcore::Image$new(
options=options,
name="plot2",
title="Multiple ROC curves",
requiresData=TRUE,
visible="(plot2)",
renderFun=".plot2",
refs="multipleROC",
clearWith=list(
"covs",
"dep",
"width2",
"height2")))
self$add(jmvcore::Image$new(
options=options,
name="plot3",
title="Faceted ROC plots",
requiresData=TRUE,
visible="(plot3)",
renderFun=".plot3",
refs="multipleROC",
clearWith=list(
"covs",
"dep",
"width3",
"height3")))
self$add(jmvcore::Table$new(
options=options,
name="auc",
title="A nonparametric test for AUC",
visible="(auc)",
clearWith=list(
"dep",
"covs"),
columns=list(
list(
`name`="name",
`title`="",
`type`="text",
`content`="($key)"),
list(
`name`="auc",
`title`="AUC",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="dif",
title="Pairwise comparisons for AUC difference",
visible="(auc)",
clearWith=list(
"dep",
"covs"),
columns=list(
list(
`name`="name",
`title`="",
`type`="text",
`content`="($key)"),
list(
`name`="auc",
`title`="AUC Difference",
`type`="number"),
list(
`name`="lower",
`title`="Lower",
`type`="number",
`superTitle`="95% CI"),
list(
`name`="upper",
`title`="Upper",
`type`="number",
`superTitle`="95% CI"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="overall",
title="Overall test",
rows=1,
visible="(overall)",
clearWith=list(
"dep",
"covs"),
columns=list(
list(
`name`="name",
`title`="",
`type`="text",
`content`="Value"),
list(
`name`="Z",
`type`="number"),
list(
`name`="p",
`type`="number",
`format`="zto,pvalue"))))}))
rocBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"rocBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "snowCluster",
name = "roc",
version = c(1,0,0),
options = options,
results = rocResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
#' ROC Analysis
#'
#'
#' @param data .
#' @param dep .
#' @param covs .
#' @param plot1 .
#' @param width1 .
#' @param height1 .
#' @param plot2 .
#' @param width2 .
#' @param height2 .
#' @param plot3 .
#' @param width3 .
#' @param height3 .
#' @param auc .
#' @param dif .
#' @param overall .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$instructions} \tab \tab \tab \tab \tab a html \cr
#' \code{results$text} \tab \tab \tab \tab \tab a preformatted \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$plot3} \tab \tab \tab \tab \tab an image \cr
#' \code{results$auc} \tab \tab \tab \tab \tab a table \cr
#' \code{results$dif} \tab \tab \tab \tab \tab a table \cr
#' \code{results$overall} \tab \tab \tab \tab \tab a table \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$auc$asDF}
#'
#' \code{as.data.frame(results$auc)}
#'
#' @export
roc <- function(
data,
dep,
covs,
plot1 = FALSE,
width1 = 500,
height1 = 500,
plot2 = FALSE,
width2 = 500,
height2 = 500,
plot3 = FALSE,
width3 = 500,
height3 = 500,
auc = FALSE,
dif = FALSE,
overall = FALSE) {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("roc requires jmvcore to be installed (restart may be required)")
if ( ! missing(dep)) dep <- jmvcore::resolveQuo(jmvcore::enquo(dep))
if ( ! missing(covs)) covs <- jmvcore::resolveQuo(jmvcore::enquo(covs))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(dep), dep, NULL),
`if`( ! missing(covs), covs, NULL))
for (v in dep) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
options <- rocOptions$new(
dep = dep,
covs = covs,
plot1 = plot1,
width1 = width1,
height1 = height1,
plot2 = plot2,
width2 = width2,
height2 = height2,
plot3 = plot3,
width3 = width3,
height3 = height3,
auc = auc,
dif = dif,
overall = overall)
analysis <- rocClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
hyunsooseol/snowCluster documentation built on April 5, 2025, 2:06 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions roc
Documented in roc
# This file is automatically generated, you probably don't want to edit this
rocOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"rocOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
dep = NULL,
covs = NULL,
plot1 = FALSE,
width1 = 500,
height1 = 500,
plot2 = FALSE,
width2 = 500,
height2 = 500,
plot3 = FALSE,
width3 = 500,
height3 = 500,
auc = FALSE,
dif = FALSE,
overall = FALSE, ...) {
super$initialize(
package="snowCluster",
name="roc",
requiresData=TRUE,
...)
private$..dep <- jmvcore::OptionVariable$new(
"dep",
dep,
suggested=list(
"nominal"),
permitted=list(
"factor"))
private$..covs <- jmvcore::OptionVariables$new(
"covs",
covs)
private$..plot1 <- jmvcore::OptionBool$new(
"plot1",
plot1,
default=FALSE)
private$..width1 <- jmvcore::OptionInteger$new(
"width1",
width1,
default=500)
private$..height1 <- jmvcore::OptionInteger$new(
"height1",
height1,
default=500)
private$..plot2 <- jmvcore::OptionBool$new(
"plot2",
plot2,
default=FALSE)
private$..width2 <- jmvcore::OptionInteger$new(
"width2",
width2,
default=500)
private$..height2 <- jmvcore::OptionInteger$new(
"height2",
height2,
default=500)
private$..plot3 <- jmvcore::OptionBool$new(
"plot3",
plot3,
default=FALSE)
private$..width3 <- jmvcore::OptionInteger$new(
"width3",
width3,
default=500)
private$..height3 <- jmvcore::OptionInteger$new(
"height3",
height3,
default=500)
private$..auc <- jmvcore::OptionBool$new(
"auc",
auc,
default=FALSE)
private$..dif <- jmvcore::OptionBool$new(
"dif",
dif,
default=FALSE)
private$..overall <- jmvcore::OptionBool$new(
"overall",
overall,
default=FALSE)
self$.addOption(private$..dep)
self$.addOption(private$..covs)
self$.addOption(private$..plot1)
self$.addOption(private$..width1)
self$.addOption(private$..height1)
self$.addOption(private$..plot2)
self$.addOption(private$..width2)
self$.addOption(private$..height2)
self$.addOption(private$..plot3)
self$.addOption(private$..width3)
self$.addOption(private$..height3)
self$.addOption(private$..auc)
self$.addOption(private$..dif)
self$.addOption(private$..overall)
}),
active = list(
dep = function() private$..dep$value,
covs = function() private$..covs$value,
plot1 = function() private$..plot1$value,
width1 = function() private$..width1$value,
height1 = function() private$..height1$value,
plot2 = function() private$..plot2$value,
width2 = function() private$..width2$value,
height2 = function() private$..height2$value,
plot3 = function() private$..plot3$value,
width3 = function() private$..width3$value,
height3 = function() private$..height3$value,
auc = function() private$..auc$value,
dif = function() private$..dif$value,
overall = function() private$..overall$value),
private = list(
..dep = NA,
..covs = NA,
..plot1 = NA,
..width1 = NA,
..height1 = NA,
..plot2 = NA,
..width2 = NA,
..height2 = NA,
..plot3 = NA,
..width3 = NA,
..height3 = NA,
..auc = NA,
..dif = NA,
..overall = NA)
)
rocResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"rocResults",
inherit = jmvcore::Group,
active = list(
instructions = function() private$.items[["instructions"]],
text = function() private$.items[["text"]],
plot1 = function() private$.items[["plot1"]],
plot2 = function() private$.items[["plot2"]],
plot3 = function() private$.items[["plot3"]],
auc = function() private$.items[["auc"]],
dif = function() private$.items[["dif"]],
overall = function() private$.items[["overall"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="ROC Analysis",
refs="snowCluster")
self$add(jmvcore::Html$new(
options=options,
name="instructions",
title="Instructions",
visible=TRUE))
self$add(jmvcore::Preformatted$new(
options=options,
name="text",
title=""))
self$add(jmvcore::Image$new(
options=options,
name="plot1",
title="ROC Curve",
requiresData=TRUE,
visible="(plot1)",
renderFun=".plot1",
refs="multipleROC",
clearWith=list(
"covs",
"dep",
"width1",
"height1")))
self$add(jmvcore::Image$new(
options=options,
name="plot2",
title="Multiple ROC curves",
requiresData=TRUE,
visible="(plot2)",
renderFun=".plot2",
refs="multipleROC",
clearWith=list(
"covs",
"dep",
"width2",
"height2")))
self$add(jmvcore::Image$new(
options=options,
name="plot3",
title="Faceted ROC plots",
requiresData=TRUE,
visible="(plot3)",
renderFun=".plot3",
refs="multipleROC",
clearWith=list(
"covs",
"dep",
"width3",
"height3")))
self$add(jmvcore::Table$new(
options=options,
name="auc",
title="A nonparametric test for AUC",
visible="(auc)",
clearWith=list(
"dep",
"covs"),
columns=list(
list(
`name`="name",
`title`="",
`type`="text",
`content`="($key)"),
list(
`name`="auc",
`title`="AUC",
`type`="number"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="dif",
title="Pairwise comparisons for AUC difference",
visible="(auc)",
clearWith=list(
"dep",
"covs"),
columns=list(
list(
`name`="name",
`title`="",
`type`="text",
`content`="($key)"),
list(
`name`="auc",
`title`="AUC Difference",
`type`="number"),
list(
`name`="lower",
`title`="Lower",
`type`="number",
`superTitle`="95% CI"),
list(
`name`="upper",
`title`="Upper",
`type`="number",
`superTitle`="95% CI"),
list(
`name`="p",
`title`="p",
`type`="number",
`format`="zto,pvalue"))))
self$add(jmvcore::Table$new(
options=options,
name="overall",
title="Overall test",
rows=1,
visible="(overall)",
clearWith=list(
"dep",
"covs"),
columns=list(
list(
`name`="name",
`title`="",
`type`="text",
`content`="Value"),
list(
`name`="Z",
`type`="number"),
list(
`name`="p",
`type`="number",
`format`="zto,pvalue"))))}))
rocBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"rocBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "snowCluster",
name = "roc",
version = c(1,0,0),
options = options,
results = rocResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
#' ROC Analysis
#'
#'
#' @param data .
#' @param dep .
#' @param covs .
#' @param plot1 .
#' @param width1 .
#' @param height1 .
#' @param plot2 .
#' @param width2 .
#' @param height2 .
#' @param plot3 .
#' @param width3 .
#' @param height3 .
#' @param auc .
#' @param dif .
#' @param overall .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$instructions} \tab \tab \tab \tab \tab a html \cr
#' \code{results$text} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$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$auc} \tab \tab \tab \tab \tab a table \cr
#' \code{results$dif} \tab \tab \tab \tab \tab a table \cr
#' \code{results$overall} \tab \tab \tab \tab \tab a table \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$auc$asDF}
#'
#' \code{as.data.frame(results$auc)}
#'
#' @export
roc <- function(
data,
dep,
covs,
plot1 = FALSE,
width1 = 500,
height1 = 500,
plot2 = FALSE,
width2 = 500,
height2 = 500,
plot3 = FALSE,
width3 = 500,
height3 = 500,
auc = FALSE,
dif = FALSE,
overall = FALSE) {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("roc requires jmvcore to be installed (restart may be required)")
if ( ! missing(dep)) dep <- jmvcore::resolveQuo(jmvcore::enquo(dep))
if ( ! missing(covs)) covs <- jmvcore::resolveQuo(jmvcore::enquo(covs))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(dep), dep, NULL),
`if`( ! missing(covs), covs, NULL))
for (v in dep) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
options <- rocOptions$new(
dep = dep,
covs = covs,
plot1 = plot1,
width1 = width1,
height1 = height1,
plot2 = plot2,
width2 = width2,
height2 = height2,
plot3 = plot3,
width3 = width3,
height3 = height3,
auc = auc,
dif = dif,
overall = overall)
analysis <- rocClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
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