R/screeningcalculator.h.R
In sbalci/ClinicoPathJamoviModule: Analysis for Clinicopathological Research
Defines functions
screeningcalculator
Documented in
screeningcalculator
# This file is automatically generated, you probably don't want to edit this
screeningcalculatorOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"screeningcalculatorOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
sens = 0.9,
spec = 0.8,
prev = 0.1,
repeat2 = TRUE,
repeat3 = TRUE,
fnote = FALSE,
fagan = FALSE, ...) {
super$initialize(
package="ClinicoPath",
name="screeningcalculator",
requiresData=FALSE,
...)
private$..sens <- jmvcore::OptionNumber$new(
"sens",
sens,
default=0.9,
min=0.01,
max=0.99)
private$..spec <- jmvcore::OptionNumber$new(
"spec",
spec,
default=0.8,
min=0.01,
max=0.99)
private$..prev <- jmvcore::OptionNumber$new(
"prev",
prev,
default=0.1,
min=0.001,
max=0.999)
private$..repeat2 <- jmvcore::OptionBool$new(
"repeat2",
repeat2,
default=TRUE)
private$..repeat3 <- jmvcore::OptionBool$new(
"repeat3",
repeat3,
default=TRUE)
private$..fnote <- jmvcore::OptionBool$new(
"fnote",
fnote,
default=FALSE)
private$..fagan <- jmvcore::OptionBool$new(
"fagan",
fagan,
default=FALSE)
self$.addOption(private$..sens)
self$.addOption(private$..spec)
self$.addOption(private$..prev)
self$.addOption(private$..repeat2)
self$.addOption(private$..repeat3)
self$.addOption(private$..fnote)
self$.addOption(private$..fagan)
}),
active = list(
sens = function() private$..sens$value,
spec = function() private$..spec$value,
prev = function() private$..prev$value,
repeat2 = function() private$..repeat2$value,
repeat3 = function() private$..repeat3$value,
fnote = function() private$..fnote$value,
fagan = function() private$..fagan$value),
private = list(
..sens = NA,
..spec = NA,
..prev = NA,
..repeat2 = NA,
..repeat3 = NA,
..fnote = NA,
..fagan = NA)
)
screeningcalculatorResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"screeningcalculatorResults",
inherit = jmvcore::Group,
active = list(
explanatoryText = function() private$.items[["explanatoryText"]],
mathText = function() private$.items[["mathText"]],
singleTestTable = function() private$.items[["singleTestTable"]],
repeatTest2Table = function() private$.items[["repeatTest2Table"]],
repeatTest3Table = function() private$.items[["repeatTest3Table"]],
plot1 = function() private$.items[["plot1"]],
plot2PP = function() private$.items[["plot2PP"]],
plot2NN = function() private$.items[["plot2NN"]],
plot3PPP = function() private$.items[["plot3PPP"]],
plot3NNN = function() private$.items[["plot3NNN"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Screening Test Calculator",
refs=list(
"DiagnosticTests",
"sensspecwiki"))
self$add(jmvcore::Html$new(
options=options,
name="explanatoryText",
title="How Sequential Testing Works"))
self$add(jmvcore::Html$new(
options=options,
name="mathText",
title="Math Behind the Calculations"))
self$add(jmvcore::Table$new(
options=options,
name="singleTestTable",
title="Single Test Results",
swapRowsColumns=TRUE,
rows=1,
columns=list(
list(
`name`="tablename",
`title`="",
`type`="text"),
list(
`name`="Sensitivity",
`title`="Sensitivity",
`type`="number",
`format`="pc"),
list(
`name`="Specificity",
`title`="Specificity",
`type`="number",
`format`="pc"),
list(
`name`="Prevalence",
`title`="Prevalence",
`type`="number",
`format`="pc"),
list(
`name`="PPV",
`title`="Positive Predictive Value",
`type`="number",
`format`="pc"),
list(
`name`="NPV",
`title`="Negative Predictive Value",
`type`="number",
`format`="pc"),
list(
`name`="LRP",
`title`="Positive Likelihood Ratio",
`type`="number"),
list(
`name`="LRN",
`title`="Negative Likelihood Ratio",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="repeatTest2Table",
title="Two Consecutive Tests",
visible="(repeat2)",
rows=0,
columns=list(
list(
`name`="testResult",
`title`="Test Result Pattern",
`type`="text"),
list(
`name`="probDisease",
`title`="Probability of Disease",
`type`="number",
`format`="pc"),
list(
`name`="explanation",
`title`="Interpretation",
`type`="text"))))
self$add(jmvcore::Table$new(
options=options,
name="repeatTest3Table",
title="Three Consecutive Tests",
visible="(repeat3)",
rows=0,
columns=list(
list(
`name`="testResult",
`title`="Test Result Pattern",
`type`="text"),
list(
`name`="probDisease",
`title`="Probability of Disease",
`type`="number",
`format`="pc"),
list(
`name`="explanation",
`title`="Interpretation",
`type`="text"))))
self$add(jmvcore::Image$new(
options=options,
name="plot1",
title="Fagan Nomogram (Single Test)",
width=600,
height=450,
renderFun=".plot1",
requiresData=TRUE,
visible="(fagan)",
clearWith=list(
"sens",
"spec",
"prev",
"fagan")))
self$add(jmvcore::Image$new(
options=options,
name="plot2PP",
title="Fagan Nomogram (Second Test after Positive)",
width=600,
height=450,
renderFun=".plot2PP",
requiresData=TRUE,
visible="(fagan && repeat2)",
clearWith=list(
"sens",
"spec",
"prev",
"fagan",
"repeat2")))
self$add(jmvcore::Image$new(
options=options,
name="plot2NN",
title="Fagan Nomogram (Second Test after Negative)",
width=600,
height=450,
renderFun=".plot2NN",
requiresData=TRUE,
visible="(fagan && repeat2)",
clearWith=list(
"sens",
"spec",
"prev",
"fagan",
"repeat2")))
self$add(jmvcore::Image$new(
options=options,
name="plot3PPP",
title="Fagan Nomogram (Third Test after Two Positives)",
width=600,
height=450,
renderFun=".plot3PPP",
requiresData=TRUE,
visible="(fagan && repeat3)",
clearWith=list(
"sens",
"spec",
"prev",
"fagan",
"repeat3")))
self$add(jmvcore::Image$new(
options=options,
name="plot3NNN",
title="Fagan Nomogram (Third Test after Two Negatives)",
width=600,
height=450,
renderFun=".plot3NNN",
requiresData=TRUE,
visible="(fagan && repeat3)",
clearWith=list(
"sens",
"spec",
"prev",
"fagan",
"repeat3")))}))
screeningcalculatorBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"screeningcalculatorBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "ClinicoPath",
name = "screeningcalculator",
version = c(0,0,3),
options = options,
results = screeningcalculatorResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'na')
}))
#' Screening Test Calculator
#'
#' Function for Screening Test Probability Calculator.
#'
#' @examples
#' \donttest{
#' # example will be added
#'}
#' @param sens .
#' @param spec .
#' @param prev .
#' @param repeat2 .
#' @param repeat3 .
#' @param fnote .
#' @param fagan .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$explanatoryText} \tab \tab \tab \tab \tab a html \cr
#' \code{results$mathText} \tab \tab \tab \tab \tab a html \cr
#' \code{results$singleTestTable} \tab \tab \tab \tab \tab a table \cr
#' \code{results$repeatTest2Table} \tab \tab \tab \tab \tab a table \cr
#' \code{results$repeatTest3Table} \tab \tab \tab \tab \tab a table \cr
#' \code{results$plot1} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot2PP} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot2NN} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot3PPP} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot3NNN} \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$singleTestTable$asDF}
#'
#' \code{as.data.frame(results$singleTestTable)}
#'
#' @export
screeningcalculator <- function(
sens = 0.9,
spec = 0.8,
prev = 0.1,
repeat2 = TRUE,
repeat3 = TRUE,
fnote = FALSE,
fagan = FALSE) {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("screeningcalculator requires jmvcore to be installed (restart may be required)")
options <- screeningcalculatorOptions$new(
sens = sens,
spec = spec,
prev = prev,
repeat2 = repeat2,
repeat3 = repeat3,
fnote = fnote,
fagan = fagan)
analysis <- screeningcalculatorClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
sbalci/ClinicoPathJamoviModule documentation built on June 13, 2025, 9:34 a.m.
R Package Documentation
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Defines functions screeningcalculator
Documented in screeningcalculator
# This file is automatically generated, you probably don't want to edit this
screeningcalculatorOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"screeningcalculatorOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
sens = 0.9,
spec = 0.8,
prev = 0.1,
repeat2 = TRUE,
repeat3 = TRUE,
fnote = FALSE,
fagan = FALSE, ...) {
super$initialize(
package="ClinicoPath",
name="screeningcalculator",
requiresData=FALSE,
...)
private$..sens <- jmvcore::OptionNumber$new(
"sens",
sens,
default=0.9,
min=0.01,
max=0.99)
private$..spec <- jmvcore::OptionNumber$new(
"spec",
spec,
default=0.8,
min=0.01,
max=0.99)
private$..prev <- jmvcore::OptionNumber$new(
"prev",
prev,
default=0.1,
min=0.001,
max=0.999)
private$..repeat2 <- jmvcore::OptionBool$new(
"repeat2",
repeat2,
default=TRUE)
private$..repeat3 <- jmvcore::OptionBool$new(
"repeat3",
repeat3,
default=TRUE)
private$..fnote <- jmvcore::OptionBool$new(
"fnote",
fnote,
default=FALSE)
private$..fagan <- jmvcore::OptionBool$new(
"fagan",
fagan,
default=FALSE)
self$.addOption(private$..sens)
self$.addOption(private$..spec)
self$.addOption(private$..prev)
self$.addOption(private$..repeat2)
self$.addOption(private$..repeat3)
self$.addOption(private$..fnote)
self$.addOption(private$..fagan)
}),
active = list(
sens = function() private$..sens$value,
spec = function() private$..spec$value,
prev = function() private$..prev$value,
repeat2 = function() private$..repeat2$value,
repeat3 = function() private$..repeat3$value,
fnote = function() private$..fnote$value,
fagan = function() private$..fagan$value),
private = list(
..sens = NA,
..spec = NA,
..prev = NA,
..repeat2 = NA,
..repeat3 = NA,
..fnote = NA,
..fagan = NA)
)
screeningcalculatorResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"screeningcalculatorResults",
inherit = jmvcore::Group,
active = list(
explanatoryText = function() private$.items[["explanatoryText"]],
mathText = function() private$.items[["mathText"]],
singleTestTable = function() private$.items[["singleTestTable"]],
repeatTest2Table = function() private$.items[["repeatTest2Table"]],
repeatTest3Table = function() private$.items[["repeatTest3Table"]],
plot1 = function() private$.items[["plot1"]],
plot2PP = function() private$.items[["plot2PP"]],
plot2NN = function() private$.items[["plot2NN"]],
plot3PPP = function() private$.items[["plot3PPP"]],
plot3NNN = function() private$.items[["plot3NNN"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Screening Test Calculator",
refs=list(
"DiagnosticTests",
"sensspecwiki"))
self$add(jmvcore::Html$new(
options=options,
name="explanatoryText",
title="How Sequential Testing Works"))
self$add(jmvcore::Html$new(
options=options,
name="mathText",
title="Math Behind the Calculations"))
self$add(jmvcore::Table$new(
options=options,
name="singleTestTable",
title="Single Test Results",
swapRowsColumns=TRUE,
rows=1,
columns=list(
list(
`name`="tablename",
`title`="",
`type`="text"),
list(
`name`="Sensitivity",
`title`="Sensitivity",
`type`="number",
`format`="pc"),
list(
`name`="Specificity",
`title`="Specificity",
`type`="number",
`format`="pc"),
list(
`name`="Prevalence",
`title`="Prevalence",
`type`="number",
`format`="pc"),
list(
`name`="PPV",
`title`="Positive Predictive Value",
`type`="number",
`format`="pc"),
list(
`name`="NPV",
`title`="Negative Predictive Value",
`type`="number",
`format`="pc"),
list(
`name`="LRP",
`title`="Positive Likelihood Ratio",
`type`="number"),
list(
`name`="LRN",
`title`="Negative Likelihood Ratio",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="repeatTest2Table",
title="Two Consecutive Tests",
visible="(repeat2)",
rows=0,
columns=list(
list(
`name`="testResult",
`title`="Test Result Pattern",
`type`="text"),
list(
`name`="probDisease",
`title`="Probability of Disease",
`type`="number",
`format`="pc"),
list(
`name`="explanation",
`title`="Interpretation",
`type`="text"))))
self$add(jmvcore::Table$new(
options=options,
name="repeatTest3Table",
title="Three Consecutive Tests",
visible="(repeat3)",
rows=0,
columns=list(
list(
`name`="testResult",
`title`="Test Result Pattern",
`type`="text"),
list(
`name`="probDisease",
`title`="Probability of Disease",
`type`="number",
`format`="pc"),
list(
`name`="explanation",
`title`="Interpretation",
`type`="text"))))
self$add(jmvcore::Image$new(
options=options,
name="plot1",
title="Fagan Nomogram (Single Test)",
width=600,
height=450,
renderFun=".plot1",
requiresData=TRUE,
visible="(fagan)",
clearWith=list(
"sens",
"spec",
"prev",
"fagan")))
self$add(jmvcore::Image$new(
options=options,
name="plot2PP",
title="Fagan Nomogram (Second Test after Positive)",
width=600,
height=450,
renderFun=".plot2PP",
requiresData=TRUE,
visible="(fagan && repeat2)",
clearWith=list(
"sens",
"spec",
"prev",
"fagan",
"repeat2")))
self$add(jmvcore::Image$new(
options=options,
name="plot2NN",
title="Fagan Nomogram (Second Test after Negative)",
width=600,
height=450,
renderFun=".plot2NN",
requiresData=TRUE,
visible="(fagan && repeat2)",
clearWith=list(
"sens",
"spec",
"prev",
"fagan",
"repeat2")))
self$add(jmvcore::Image$new(
options=options,
name="plot3PPP",
title="Fagan Nomogram (Third Test after Two Positives)",
width=600,
height=450,
renderFun=".plot3PPP",
requiresData=TRUE,
visible="(fagan && repeat3)",
clearWith=list(
"sens",
"spec",
"prev",
"fagan",
"repeat3")))
self$add(jmvcore::Image$new(
options=options,
name="plot3NNN",
title="Fagan Nomogram (Third Test after Two Negatives)",
width=600,
height=450,
renderFun=".plot3NNN",
requiresData=TRUE,
visible="(fagan && repeat3)",
clearWith=list(
"sens",
"spec",
"prev",
"fagan",
"repeat3")))}))
screeningcalculatorBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"screeningcalculatorBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "ClinicoPath",
name = "screeningcalculator",
version = c(0,0,3),
options = options,
results = screeningcalculatorResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'na')
}))
#' Screening Test Calculator
#'
#' Function for Screening Test Probability Calculator.
#'
#' @examples
#' \donttest{
#' # example will be added
#'}
#' @param sens .
#' @param spec .
#' @param prev .
#' @param repeat2 .
#' @param repeat3 .
#' @param fnote .
#' @param fagan .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$explanatoryText} \tab \tab \tab \tab \tab a html \cr
#' \code{results$mathText} \tab \tab \tab \tab \tab a html \cr
#' \code{results$singleTestTable} \tab \tab \tab \tab \tab a table \cr
#' \code{results$repeatTest2Table} \tab \tab \tab \tab \tab a table \cr
#' \code{results$repeatTest3Table} \tab \tab \tab \tab \tab a table \cr
#' \code{results$plot1} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot2PP} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot2NN} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot3PPP} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot3NNN} \tab \tab \tab \tab \tab an image \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$singleTestTable$asDF}
#'
#' \code{as.data.frame(results$singleTestTable)}
#'
#' @export
screeningcalculator <- function(
sens = 0.9,
spec = 0.8,
prev = 0.1,
repeat2 = TRUE,
repeat3 = TRUE,
fnote = FALSE,
fagan = FALSE) {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("screeningcalculator requires jmvcore to be installed (restart may be required)")
options <- screeningcalculatorOptions$new(
sens = sens,
spec = spec,
prev = prev,
repeat2 = repeat2,
repeat3 = repeat3,
fnote = fnote,
fagan = fagan)
analysis <- screeningcalculatorClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
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