R/sequentialtests.h.R
In sbalci/ClinicoPathJamoviModule: Analysis for Clinicopathological Research
Defines functions
sequentialtests
Documented in
sequentialtests
# This file is automatically generated, you probably don't want to edit this
sequentialtestsOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"sequentialtestsOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
test1_name = "Screening Test",
test1_sens = 0.95,
test1_spec = 0.7,
test2_name = "Confirmatory Test",
test2_sens = 0.8,
test2_spec = 0.98,
strategy = "serial_positive",
prevalence = 0.1,
show_explanation = TRUE,
show_formulas = FALSE,
show_nomogram = FALSE, ...) {
super$initialize(
package="ClinicoPath",
name="sequentialtests",
requiresData=FALSE,
...)
private$..test1_name <- jmvcore::OptionString$new(
"test1_name",
test1_name,
default="Screening Test")
private$..test1_sens <- jmvcore::OptionNumber$new(
"test1_sens",
test1_sens,
default=0.95,
min=0.01,
max=0.99)
private$..test1_spec <- jmvcore::OptionNumber$new(
"test1_spec",
test1_spec,
default=0.7,
min=0.01,
max=0.99)
private$..test2_name <- jmvcore::OptionString$new(
"test2_name",
test2_name,
default="Confirmatory Test")
private$..test2_sens <- jmvcore::OptionNumber$new(
"test2_sens",
test2_sens,
default=0.8,
min=0.01,
max=0.99)
private$..test2_spec <- jmvcore::OptionNumber$new(
"test2_spec",
test2_spec,
default=0.98,
min=0.01,
max=0.99)
private$..strategy <- jmvcore::OptionList$new(
"strategy",
strategy,
options=list(
"serial_positive",
"serial_negative",
"parallel"),
default="serial_positive")
private$..prevalence <- jmvcore::OptionNumber$new(
"prevalence",
prevalence,
default=0.1,
min=0.001,
max=0.999)
private$..show_explanation <- jmvcore::OptionBool$new(
"show_explanation",
show_explanation,
default=TRUE)
private$..show_formulas <- jmvcore::OptionBool$new(
"show_formulas",
show_formulas,
default=FALSE)
private$..show_nomogram <- jmvcore::OptionBool$new(
"show_nomogram",
show_nomogram,
default=FALSE)
self$.addOption(private$..test1_name)
self$.addOption(private$..test1_sens)
self$.addOption(private$..test1_spec)
self$.addOption(private$..test2_name)
self$.addOption(private$..test2_sens)
self$.addOption(private$..test2_spec)
self$.addOption(private$..strategy)
self$.addOption(private$..prevalence)
self$.addOption(private$..show_explanation)
self$.addOption(private$..show_formulas)
self$.addOption(private$..show_nomogram)
}),
active = list(
test1_name = function() private$..test1_name$value,
test1_sens = function() private$..test1_sens$value,
test1_spec = function() private$..test1_spec$value,
test2_name = function() private$..test2_name$value,
test2_sens = function() private$..test2_sens$value,
test2_spec = function() private$..test2_spec$value,
strategy = function() private$..strategy$value,
prevalence = function() private$..prevalence$value,
show_explanation = function() private$..show_explanation$value,
show_formulas = function() private$..show_formulas$value,
show_nomogram = function() private$..show_nomogram$value),
private = list(
..test1_name = NA,
..test1_sens = NA,
..test1_spec = NA,
..test2_name = NA,
..test2_sens = NA,
..test2_spec = NA,
..strategy = NA,
..prevalence = NA,
..show_explanation = NA,
..show_formulas = NA,
..show_nomogram = NA)
)
sequentialtestsResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"sequentialtestsResults",
inherit = jmvcore::Group,
active = list(
summary_table = function() private$.items[["summary_table"]],
individual_tests_table = function() private$.items[["individual_tests_table"]],
population_flow_table = function() private$.items[["population_flow_table"]],
explanation_text = function() private$.items[["explanation_text"]],
formulas_text = function() private$.items[["formulas_text"]],
plot_nomogram = function() private$.items[["plot_nomogram"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Sequential Testing Analysis",
refs=list(
"DiagnosticTests",
"Fagan",
"Fagan2",
"sensspecwiki",
"ClinicoPathJamoviModule"))
self$add(jmvcore::Table$new(
options=options,
name="summary_table",
title="Summary of Testing Strategy",
rows=1,
columns=list(
list(
`name`="strategy_name",
`title`="Testing Strategy",
`type`="text"),
list(
`name`="prevalence",
`title`="Disease Prevalence",
`type`="number",
`format`="pc"),
list(
`name`="first_test",
`title`="First Test",
`type`="text"),
list(
`name`="second_test",
`title`="Second Test",
`type`="text"),
list(
`name`="combined_sens",
`title`="Combined Sensitivity",
`type`="number",
`format`="pc"),
list(
`name`="combined_spec",
`title`="Combined Specificity",
`type`="number",
`format`="pc"),
list(
`name`="combined_ppv",
`title`="Combined PPV",
`type`="number",
`format`="pc"),
list(
`name`="combined_npv",
`title`="Combined NPV",
`type`="number",
`format`="pc"))))
self$add(jmvcore::Table$new(
options=options,
name="individual_tests_table",
title="Individual Test Performance",
rows=0,
columns=list(
list(
`name`="test_name",
`title`="Test",
`type`="text"),
list(
`name`="sensitivity",
`title`="Sensitivity",
`type`="number",
`format`="pc"),
list(
`name`="specificity",
`title`="Specificity",
`type`="number",
`format`="pc"),
list(
`name`="ppv",
`title`="PPV",
`type`="number",
`format`="pc"),
list(
`name`="npv",
`title`="NPV",
`type`="number",
`format`="pc"),
list(
`name`="plr",
`title`="Positive LR",
`type`="number"),
list(
`name`="nlr",
`title`="Negative LR",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="population_flow_table",
title="Population Flow Analysis",
rows=0,
columns=list(
list(
`name`="stage",
`title`="Testing Stage",
`type`="text"),
list(
`name`="total_n",
`title`="Total Subjects",
`type`="number"),
list(
`name`="disease_pos",
`title`="Disease Positive",
`type`="number"),
list(
`name`="disease_neg",
`title`="Disease Negative",
`type`="number"),
list(
`name`="test_pos",
`title`="Test Positive",
`type`="number"),
list(
`name`="test_neg",
`title`="Test Negative",
`type`="number"),
list(
`name`="true_pos",
`title`="True Positives",
`type`="number"),
list(
`name`="false_pos",
`title`="False Positives",
`type`="number"),
list(
`name`="false_neg",
`title`="False Negatives",
`type`="number"),
list(
`name`="true_neg",
`title`="True Negatives",
`type`="number"))))
self$add(jmvcore::Html$new(
options=options,
name="explanation_text",
title="Explanation",
visible="(show_explanation)"))
self$add(jmvcore::Html$new(
options=options,
name="formulas_text",
title="Formulas Used",
visible="(show_formulas)"))
self$add(jmvcore::Image$new(
options=options,
name="plot_nomogram",
title="Sequential Testing Nomogram",
width=900,
height=600,
renderFun=".plot_nomogram",
visible="(show_nomogram)"))}))
sequentialtestsBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"sequentialtestsBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "ClinicoPath",
name = "sequentialtests",
version = c(0,0,3),
options = options,
results = sequentialtestsResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'na')
}))
#' Sequential Testing Analysis
#'
#' Function for Sequential Testing Analysis. Analyzes how diagnostic accuracy
#' changes when applying two tests in sequence (screening followed by
#' confirmation).
#'
#'
#' @examples
#' \donttest{
#' # example will be added
#'}
#' @param test1_name .
#' @param test1_sens .
#' @param test1_spec .
#' @param test2_name .
#' @param test2_sens .
#' @param test2_spec .
#' @param strategy .
#' @param prevalence .
#' @param show_explanation .
#' @param show_formulas .
#' @param show_nomogram .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$summary_table} \tab \tab \tab \tab \tab a table \cr
#' \code{results$individual_tests_table} \tab \tab \tab \tab \tab a table \cr
#' \code{results$population_flow_table} \tab \tab \tab \tab \tab a table \cr
#' \code{results$explanation_text} \tab \tab \tab \tab \tab a html \cr
#' \code{results$formulas_text} \tab \tab \tab \tab \tab a html \cr
#' \code{results$plot_nomogram} \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$summary_table$asDF}
#'
#' \code{as.data.frame(results$summary_table)}
#'
#' @export
sequentialtests <- function(
test1_name = "Screening Test",
test1_sens = 0.95,
test1_spec = 0.7,
test2_name = "Confirmatory Test",
test2_sens = 0.8,
test2_spec = 0.98,
strategy = "serial_positive",
prevalence = 0.1,
show_explanation = TRUE,
show_formulas = FALSE,
show_nomogram = FALSE) {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("sequentialtests requires jmvcore to be installed (restart may be required)")
options <- sequentialtestsOptions$new(
test1_name = test1_name,
test1_sens = test1_sens,
test1_spec = test1_spec,
test2_name = test2_name,
test2_sens = test2_sens,
test2_spec = test2_spec,
strategy = strategy,
prevalence = prevalence,
show_explanation = show_explanation,
show_formulas = show_formulas,
show_nomogram = show_nomogram)
analysis <- sequentialtestsClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
sbalci/ClinicoPathJamoviModule documentation built on June 13, 2025, 9:34 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions sequentialtests
Documented in sequentialtests
# This file is automatically generated, you probably don't want to edit this
sequentialtestsOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"sequentialtestsOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
test1_name = "Screening Test",
test1_sens = 0.95,
test1_spec = 0.7,
test2_name = "Confirmatory Test",
test2_sens = 0.8,
test2_spec = 0.98,
strategy = "serial_positive",
prevalence = 0.1,
show_explanation = TRUE,
show_formulas = FALSE,
show_nomogram = FALSE, ...) {
super$initialize(
package="ClinicoPath",
name="sequentialtests",
requiresData=FALSE,
...)
private$..test1_name <- jmvcore::OptionString$new(
"test1_name",
test1_name,
default="Screening Test")
private$..test1_sens <- jmvcore::OptionNumber$new(
"test1_sens",
test1_sens,
default=0.95,
min=0.01,
max=0.99)
private$..test1_spec <- jmvcore::OptionNumber$new(
"test1_spec",
test1_spec,
default=0.7,
min=0.01,
max=0.99)
private$..test2_name <- jmvcore::OptionString$new(
"test2_name",
test2_name,
default="Confirmatory Test")
private$..test2_sens <- jmvcore::OptionNumber$new(
"test2_sens",
test2_sens,
default=0.8,
min=0.01,
max=0.99)
private$..test2_spec <- jmvcore::OptionNumber$new(
"test2_spec",
test2_spec,
default=0.98,
min=0.01,
max=0.99)
private$..strategy <- jmvcore::OptionList$new(
"strategy",
strategy,
options=list(
"serial_positive",
"serial_negative",
"parallel"),
default="serial_positive")
private$..prevalence <- jmvcore::OptionNumber$new(
"prevalence",
prevalence,
default=0.1,
min=0.001,
max=0.999)
private$..show_explanation <- jmvcore::OptionBool$new(
"show_explanation",
show_explanation,
default=TRUE)
private$..show_formulas <- jmvcore::OptionBool$new(
"show_formulas",
show_formulas,
default=FALSE)
private$..show_nomogram <- jmvcore::OptionBool$new(
"show_nomogram",
show_nomogram,
default=FALSE)
self$.addOption(private$..test1_name)
self$.addOption(private$..test1_sens)
self$.addOption(private$..test1_spec)
self$.addOption(private$..test2_name)
self$.addOption(private$..test2_sens)
self$.addOption(private$..test2_spec)
self$.addOption(private$..strategy)
self$.addOption(private$..prevalence)
self$.addOption(private$..show_explanation)
self$.addOption(private$..show_formulas)
self$.addOption(private$..show_nomogram)
}),
active = list(
test1_name = function() private$..test1_name$value,
test1_sens = function() private$..test1_sens$value,
test1_spec = function() private$..test1_spec$value,
test2_name = function() private$..test2_name$value,
test2_sens = function() private$..test2_sens$value,
test2_spec = function() private$..test2_spec$value,
strategy = function() private$..strategy$value,
prevalence = function() private$..prevalence$value,
show_explanation = function() private$..show_explanation$value,
show_formulas = function() private$..show_formulas$value,
show_nomogram = function() private$..show_nomogram$value),
private = list(
..test1_name = NA,
..test1_sens = NA,
..test1_spec = NA,
..test2_name = NA,
..test2_sens = NA,
..test2_spec = NA,
..strategy = NA,
..prevalence = NA,
..show_explanation = NA,
..show_formulas = NA,
..show_nomogram = NA)
)
sequentialtestsResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"sequentialtestsResults",
inherit = jmvcore::Group,
active = list(
summary_table = function() private$.items[["summary_table"]],
individual_tests_table = function() private$.items[["individual_tests_table"]],
population_flow_table = function() private$.items[["population_flow_table"]],
explanation_text = function() private$.items[["explanation_text"]],
formulas_text = function() private$.items[["formulas_text"]],
plot_nomogram = function() private$.items[["plot_nomogram"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Sequential Testing Analysis",
refs=list(
"DiagnosticTests",
"Fagan",
"Fagan2",
"sensspecwiki",
"ClinicoPathJamoviModule"))
self$add(jmvcore::Table$new(
options=options,
name="summary_table",
title="Summary of Testing Strategy",
rows=1,
columns=list(
list(
`name`="strategy_name",
`title`="Testing Strategy",
`type`="text"),
list(
`name`="prevalence",
`title`="Disease Prevalence",
`type`="number",
`format`="pc"),
list(
`name`="first_test",
`title`="First Test",
`type`="text"),
list(
`name`="second_test",
`title`="Second Test",
`type`="text"),
list(
`name`="combined_sens",
`title`="Combined Sensitivity",
`type`="number",
`format`="pc"),
list(
`name`="combined_spec",
`title`="Combined Specificity",
`type`="number",
`format`="pc"),
list(
`name`="combined_ppv",
`title`="Combined PPV",
`type`="number",
`format`="pc"),
list(
`name`="combined_npv",
`title`="Combined NPV",
`type`="number",
`format`="pc"))))
self$add(jmvcore::Table$new(
options=options,
name="individual_tests_table",
title="Individual Test Performance",
rows=0,
columns=list(
list(
`name`="test_name",
`title`="Test",
`type`="text"),
list(
`name`="sensitivity",
`title`="Sensitivity",
`type`="number",
`format`="pc"),
list(
`name`="specificity",
`title`="Specificity",
`type`="number",
`format`="pc"),
list(
`name`="ppv",
`title`="PPV",
`type`="number",
`format`="pc"),
list(
`name`="npv",
`title`="NPV",
`type`="number",
`format`="pc"),
list(
`name`="plr",
`title`="Positive LR",
`type`="number"),
list(
`name`="nlr",
`title`="Negative LR",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="population_flow_table",
title="Population Flow Analysis",
rows=0,
columns=list(
list(
`name`="stage",
`title`="Testing Stage",
`type`="text"),
list(
`name`="total_n",
`title`="Total Subjects",
`type`="number"),
list(
`name`="disease_pos",
`title`="Disease Positive",
`type`="number"),
list(
`name`="disease_neg",
`title`="Disease Negative",
`type`="number"),
list(
`name`="test_pos",
`title`="Test Positive",
`type`="number"),
list(
`name`="test_neg",
`title`="Test Negative",
`type`="number"),
list(
`name`="true_pos",
`title`="True Positives",
`type`="number"),
list(
`name`="false_pos",
`title`="False Positives",
`type`="number"),
list(
`name`="false_neg",
`title`="False Negatives",
`type`="number"),
list(
`name`="true_neg",
`title`="True Negatives",
`type`="number"))))
self$add(jmvcore::Html$new(
options=options,
name="explanation_text",
title="Explanation",
visible="(show_explanation)"))
self$add(jmvcore::Html$new(
options=options,
name="formulas_text",
title="Formulas Used",
visible="(show_formulas)"))
self$add(jmvcore::Image$new(
options=options,
name="plot_nomogram",
title="Sequential Testing Nomogram",
width=900,
height=600,
renderFun=".plot_nomogram",
visible="(show_nomogram)"))}))
sequentialtestsBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"sequentialtestsBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "ClinicoPath",
name = "sequentialtests",
version = c(0,0,3),
options = options,
results = sequentialtestsResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'na')
}))
#' Sequential Testing Analysis
#'
#' Function for Sequential Testing Analysis. Analyzes how diagnostic accuracy
#' changes when applying two tests in sequence (screening followed by
#' confirmation).
#'
#'
#' @examples
#' \donttest{
#' # example will be added
#'}
#' @param test1_name .
#' @param test1_sens .
#' @param test1_spec .
#' @param test2_name .
#' @param test2_sens .
#' @param test2_spec .
#' @param strategy .
#' @param prevalence .
#' @param show_explanation .
#' @param show_formulas .
#' @param show_nomogram .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$summary_table} \tab \tab \tab \tab \tab a table \cr
#' \code{results$individual_tests_table} \tab \tab \tab \tab \tab a table \cr
#' \code{results$population_flow_table} \tab \tab \tab \tab \tab a table \cr
#' \code{results$explanation_text} \tab \tab \tab \tab \tab a html \cr
#' \code{results$formulas_text} \tab \tab \tab \tab \tab a html \cr
#' \code{results$plot_nomogram} \tab \tab \tab \tab \tab an image \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$summary_table$asDF}
#'
#' \code{as.data.frame(results$summary_table)}
#'
#' @export
sequentialtests <- function(
test1_name = "Screening Test",
test1_sens = 0.95,
test1_spec = 0.7,
test2_name = "Confirmatory Test",
test2_sens = 0.8,
test2_spec = 0.98,
strategy = "serial_positive",
prevalence = 0.1,
show_explanation = TRUE,
show_formulas = FALSE,
show_nomogram = FALSE) {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("sequentialtests requires jmvcore to be installed (restart may be required)")
options <- sequentialtestsOptions$new(
test1_name = test1_name,
test1_sens = test1_sens,
test1_spec = test1_spec,
test2_name = test2_name,
test2_sens = test2_sens,
test2_spec = test2_spec,
strategy = strategy,
prevalence = prevalence,
show_explanation = show_explanation,
show_formulas = show_formulas,
show_nomogram = show_nomogram)
analysis <- sequentialtestsClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
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