R/cotest.h.R
In sbalci/ClinicoPathJamoviModule: Analysis for Clinicopathological Research
Defines functions
cotest
Documented in
cotest
# This file is automatically generated, you probably don't want to edit this
cotestOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"cotestOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
test1_sens = 0.8,
test1_spec = 0.9,
test2_sens = 0.75,
test2_spec = 0.95,
indep = TRUE,
cond_dep_pos = 0.05,
cond_dep_neg = 0.05,
prevalence = 0.1,
fnote = FALSE,
fagan = FALSE, ...) {
super$initialize(
package="ClinicoPath",
name="cotest",
requiresData=FALSE,
...)
private$..test1_sens <- jmvcore::OptionNumber$new(
"test1_sens",
test1_sens,
default=0.8,
min=0.01,
max=0.99)
private$..test1_spec <- jmvcore::OptionNumber$new(
"test1_spec",
test1_spec,
default=0.9,
min=0.01,
max=0.99)
private$..test2_sens <- jmvcore::OptionNumber$new(
"test2_sens",
test2_sens,
default=0.75,
min=0.01,
max=0.99)
private$..test2_spec <- jmvcore::OptionNumber$new(
"test2_spec",
test2_spec,
default=0.95,
min=0.01,
max=0.99)
private$..indep <- jmvcore::OptionBool$new(
"indep",
indep,
default=TRUE)
private$..cond_dep_pos <- jmvcore::OptionNumber$new(
"cond_dep_pos",
cond_dep_pos,
default=0.05,
min=0,
max=1)
private$..cond_dep_neg <- jmvcore::OptionNumber$new(
"cond_dep_neg",
cond_dep_neg,
default=0.05,
min=0,
max=1)
private$..prevalence <- jmvcore::OptionNumber$new(
"prevalence",
prevalence,
default=0.1,
min=0.001,
max=0.999)
private$..fnote <- jmvcore::OptionBool$new(
"fnote",
fnote,
default=FALSE)
private$..fagan <- jmvcore::OptionBool$new(
"fagan",
fagan,
default=FALSE)
self$.addOption(private$..test1_sens)
self$.addOption(private$..test1_spec)
self$.addOption(private$..test2_sens)
self$.addOption(private$..test2_spec)
self$.addOption(private$..indep)
self$.addOption(private$..cond_dep_pos)
self$.addOption(private$..cond_dep_neg)
self$.addOption(private$..prevalence)
self$.addOption(private$..fnote)
self$.addOption(private$..fagan)
}),
active = list(
test1_sens = function() private$..test1_sens$value,
test1_spec = function() private$..test1_spec$value,
test2_sens = function() private$..test2_sens$value,
test2_spec = function() private$..test2_spec$value,
indep = function() private$..indep$value,
cond_dep_pos = function() private$..cond_dep_pos$value,
cond_dep_neg = function() private$..cond_dep_neg$value,
prevalence = function() private$..prevalence$value,
fnote = function() private$..fnote$value,
fagan = function() private$..fagan$value),
private = list(
..test1_sens = NA,
..test1_spec = NA,
..test2_sens = NA,
..test2_spec = NA,
..indep = NA,
..cond_dep_pos = NA,
..cond_dep_neg = NA,
..prevalence = NA,
..fnote = NA,
..fagan = NA)
)
cotestResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"cotestResults",
inherit = jmvcore::Group,
active = list(
testParamsTable = function() private$.items[["testParamsTable"]],
cotestResultsTable = function() private$.items[["cotestResultsTable"]],
dependenceInfo = function() private$.items[["dependenceInfo"]],
dependenceExplanation = function() private$.items[["dependenceExplanation"]],
explanation = function() private$.items[["explanation"]],
plot1 = function() private$.items[["plot1"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Co-Testing Analysis",
refs=list(
"DiagnosticTests",
"MultipleDiagnosticTests"))
self$add(jmvcore::Table$new(
options=options,
name="testParamsTable",
title="Test Parameters",
rows=0,
columns=list(
list(
`name`="test",
`title`="Test",
`type`="text"),
list(
`name`="sens",
`title`="Sensitivity",
`type`="number",
`format`="pc"),
list(
`name`="spec",
`title`="Specificity",
`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="cotestResultsTable",
title="Co-Testing Results",
rows=0,
columns=list(
list(
`name`="scenario",
`title`="Scenario",
`type`="text"),
list(
`name`="postProb",
`title`="Post-test Probability",
`type`="number",
`format`="pc"),
list(
`name`="relativeProbability",
`title`="Relative to Prevalence",
`type`="number"),
list(
`name`="orValue",
`title`="Odds Ratio",
`type`="number"))))
self$add(jmvcore::Html$new(
options=options,
name="dependenceInfo",
title="Test Dependence Information",
visible="(!indep)"))
self$add(jmvcore::Html$new(
options=options,
name="dependenceExplanation",
title="Understanding Test Dependence"))
self$add(jmvcore::Html$new(
options=options,
name="explanation",
title="Explanation"))
self$add(jmvcore::Image$new(
options=options,
name="plot1",
title="Fagan nomogram",
width=600,
height=450,
renderFun=".plot1",
requiresData=TRUE,
visible="(fagan)",
clearWith=list(
"test1_sens",
"test1_spec",
"test2_sens",
"test2_spec",
"prevalence",
"fagan")))}))
cotestBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"cotestBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "ClinicoPath",
name = "cotest",
version = c(0,0,3),
options = options,
results = cotestResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'na')
}))
#' Co-Testing Analysis
#'
#' Function for analyzing combined results of two concurrent diagnostic tests.
#' Calculates post-test probabilities based on various scenarios (either test
#' positive, both positive, both negative).
#'
#'
#' @examples
#' \donttest{
#' # example will be added
#'}
#' @param test1_sens Sensitivity (true positive rate) of Test 1.
#' @param test1_spec Specificity (true negative rate) of Test 1.
#' @param test2_sens Sensitivity (true positive rate) of Test 2.
#' @param test2_spec Specificity (true negative rate) of Test 2.
#' @param indep Assume tests are conditionally independent (default is true).
#' @param cond_dep_pos Conditional dependence between tests for subjects with
#' disease. Value between 0 (independence) and 1 (complete dependence).
#' @param cond_dep_neg Conditional dependence between tests for subjects
#' without disease. Value between 0 (independence) and 1 (complete
#' dependence).
#' @param prevalence Prior probability (disease prevalence in the population).
#' Requires a value between 0.001 and 0.999.
#' @param fnote .
#' @param fagan .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$testParamsTable} \tab \tab \tab \tab \tab a table \cr
#' \code{results$cotestResultsTable} \tab \tab \tab \tab \tab a table \cr
#' \code{results$dependenceInfo} \tab \tab \tab \tab \tab a html \cr
#' \code{results$dependenceExplanation} \tab \tab \tab \tab \tab a html \cr
#' \code{results$explanation} \tab \tab \tab \tab \tab a html \cr
#' \code{results$plot1} \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$testParamsTable$asDF}
#'
#' \code{as.data.frame(results$testParamsTable)}
#'
#' @export
cotest <- function(
test1_sens = 0.8,
test1_spec = 0.9,
test2_sens = 0.75,
test2_spec = 0.95,
indep = TRUE,
cond_dep_pos = 0.05,
cond_dep_neg = 0.05,
prevalence = 0.1,
fnote = FALSE,
fagan = FALSE) {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("cotest requires jmvcore to be installed (restart may be required)")
options <- cotestOptions$new(
test1_sens = test1_sens,
test1_spec = test1_spec,
test2_sens = test2_sens,
test2_spec = test2_spec,
indep = indep,
cond_dep_pos = cond_dep_pos,
cond_dep_neg = cond_dep_neg,
prevalence = prevalence,
fnote = fnote,
fagan = fagan)
analysis <- cotestClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
sbalci/ClinicoPathJamoviModule documentation built on June 13, 2025, 9:34 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions cotest
Documented in cotest
# This file is automatically generated, you probably don't want to edit this
cotestOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"cotestOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
test1_sens = 0.8,
test1_spec = 0.9,
test2_sens = 0.75,
test2_spec = 0.95,
indep = TRUE,
cond_dep_pos = 0.05,
cond_dep_neg = 0.05,
prevalence = 0.1,
fnote = FALSE,
fagan = FALSE, ...) {
super$initialize(
package="ClinicoPath",
name="cotest",
requiresData=FALSE,
...)
private$..test1_sens <- jmvcore::OptionNumber$new(
"test1_sens",
test1_sens,
default=0.8,
min=0.01,
max=0.99)
private$..test1_spec <- jmvcore::OptionNumber$new(
"test1_spec",
test1_spec,
default=0.9,
min=0.01,
max=0.99)
private$..test2_sens <- jmvcore::OptionNumber$new(
"test2_sens",
test2_sens,
default=0.75,
min=0.01,
max=0.99)
private$..test2_spec <- jmvcore::OptionNumber$new(
"test2_spec",
test2_spec,
default=0.95,
min=0.01,
max=0.99)
private$..indep <- jmvcore::OptionBool$new(
"indep",
indep,
default=TRUE)
private$..cond_dep_pos <- jmvcore::OptionNumber$new(
"cond_dep_pos",
cond_dep_pos,
default=0.05,
min=0,
max=1)
private$..cond_dep_neg <- jmvcore::OptionNumber$new(
"cond_dep_neg",
cond_dep_neg,
default=0.05,
min=0,
max=1)
private$..prevalence <- jmvcore::OptionNumber$new(
"prevalence",
prevalence,
default=0.1,
min=0.001,
max=0.999)
private$..fnote <- jmvcore::OptionBool$new(
"fnote",
fnote,
default=FALSE)
private$..fagan <- jmvcore::OptionBool$new(
"fagan",
fagan,
default=FALSE)
self$.addOption(private$..test1_sens)
self$.addOption(private$..test1_spec)
self$.addOption(private$..test2_sens)
self$.addOption(private$..test2_spec)
self$.addOption(private$..indep)
self$.addOption(private$..cond_dep_pos)
self$.addOption(private$..cond_dep_neg)
self$.addOption(private$..prevalence)
self$.addOption(private$..fnote)
self$.addOption(private$..fagan)
}),
active = list(
test1_sens = function() private$..test1_sens$value,
test1_spec = function() private$..test1_spec$value,
test2_sens = function() private$..test2_sens$value,
test2_spec = function() private$..test2_spec$value,
indep = function() private$..indep$value,
cond_dep_pos = function() private$..cond_dep_pos$value,
cond_dep_neg = function() private$..cond_dep_neg$value,
prevalence = function() private$..prevalence$value,
fnote = function() private$..fnote$value,
fagan = function() private$..fagan$value),
private = list(
..test1_sens = NA,
..test1_spec = NA,
..test2_sens = NA,
..test2_spec = NA,
..indep = NA,
..cond_dep_pos = NA,
..cond_dep_neg = NA,
..prevalence = NA,
..fnote = NA,
..fagan = NA)
)
cotestResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"cotestResults",
inherit = jmvcore::Group,
active = list(
testParamsTable = function() private$.items[["testParamsTable"]],
cotestResultsTable = function() private$.items[["cotestResultsTable"]],
dependenceInfo = function() private$.items[["dependenceInfo"]],
dependenceExplanation = function() private$.items[["dependenceExplanation"]],
explanation = function() private$.items[["explanation"]],
plot1 = function() private$.items[["plot1"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Co-Testing Analysis",
refs=list(
"DiagnosticTests",
"MultipleDiagnosticTests"))
self$add(jmvcore::Table$new(
options=options,
name="testParamsTable",
title="Test Parameters",
rows=0,
columns=list(
list(
`name`="test",
`title`="Test",
`type`="text"),
list(
`name`="sens",
`title`="Sensitivity",
`type`="number",
`format`="pc"),
list(
`name`="spec",
`title`="Specificity",
`type`="number",
`format`="pc"),
list(
`name`="plr",
`title`="Positive LR",
`type`="number"),
list(
`name`="nlr",
`title`="Negative LR",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="cotestResultsTable",
title="Co-Testing Results",
rows=0,
columns=list(
list(
`name`="scenario",
`title`="Scenario",
`type`="text"),
list(
`name`="postProb",
`title`="Post-test Probability",
`type`="number",
`format`="pc"),
list(
`name`="relativeProbability",
`title`="Relative to Prevalence",
`type`="number"),
list(
`name`="orValue",
`title`="Odds Ratio",
`type`="number"))))
self$add(jmvcore::Html$new(
options=options,
name="dependenceInfo",
title="Test Dependence Information",
visible="(!indep)"))
self$add(jmvcore::Html$new(
options=options,
name="dependenceExplanation",
title="Understanding Test Dependence"))
self$add(jmvcore::Html$new(
options=options,
name="explanation",
title="Explanation"))
self$add(jmvcore::Image$new(
options=options,
name="plot1",
title="Fagan nomogram",
width=600,
height=450,
renderFun=".plot1",
requiresData=TRUE,
visible="(fagan)",
clearWith=list(
"test1_sens",
"test1_spec",
"test2_sens",
"test2_spec",
"prevalence",
"fagan")))}))
cotestBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"cotestBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "ClinicoPath",
name = "cotest",
version = c(0,0,3),
options = options,
results = cotestResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'na')
}))
#' Co-Testing Analysis
#'
#' Function for analyzing combined results of two concurrent diagnostic tests.
#' Calculates post-test probabilities based on various scenarios (either test
#' positive, both positive, both negative).
#'
#'
#' @examples
#' \donttest{
#' # example will be added
#'}
#' @param test1_sens Sensitivity (true positive rate) of Test 1.
#' @param test1_spec Specificity (true negative rate) of Test 1.
#' @param test2_sens Sensitivity (true positive rate) of Test 2.
#' @param test2_spec Specificity (true negative rate) of Test 2.
#' @param indep Assume tests are conditionally independent (default is true).
#' @param cond_dep_pos Conditional dependence between tests for subjects with
#' disease. Value between 0 (independence) and 1 (complete dependence).
#' @param cond_dep_neg Conditional dependence between tests for subjects
#' without disease. Value between 0 (independence) and 1 (complete
#' dependence).
#' @param prevalence Prior probability (disease prevalence in the population).
#' Requires a value between 0.001 and 0.999.
#' @param fnote .
#' @param fagan .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$testParamsTable} \tab \tab \tab \tab \tab a table \cr
#' \code{results$cotestResultsTable} \tab \tab \tab \tab \tab a table \cr
#' \code{results$dependenceInfo} \tab \tab \tab \tab \tab a html \cr
#' \code{results$dependenceExplanation} \tab \tab \tab \tab \tab a html \cr
#' \code{results$explanation} \tab \tab \tab \tab \tab a html \cr
#' \code{results$plot1} \tab \tab \tab \tab \tab an image \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$testParamsTable$asDF}
#'
#' \code{as.data.frame(results$testParamsTable)}
#'
#' @export
cotest <- function(
test1_sens = 0.8,
test1_spec = 0.9,
test2_sens = 0.75,
test2_spec = 0.95,
indep = TRUE,
cond_dep_pos = 0.05,
cond_dep_neg = 0.05,
prevalence = 0.1,
fnote = FALSE,
fagan = FALSE) {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("cotest requires jmvcore to be installed (restart may be required)")
options <- cotestOptions$new(
test1_sens = test1_sens,
test1_spec = test1_spec,
test2_sens = test2_sens,
test2_spec = test2_spec,
indep = indep,
cond_dep_pos = cond_dep_pos,
cond_dep_neg = cond_dep_neg,
prevalence = prevalence,
fnote = fnote,
fagan = fagan)
analysis <- cotestClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
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