R/outcomeorganizer.h.R
In sbalci/ClinicoPathJamoviModule: Analysis for Clinicopathological Research
Defines functions
outcomeorganizer
Documented in
outcomeorganizer
# This file is automatically generated, you probably don't want to edit this
outcomeorganizerOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"outcomeorganizerOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
outcome = NULL,
outcomeLevel = NULL,
recurrence = NULL,
recurrenceLevel = NULL,
patientID = NULL,
analysistype = "os",
multievent = FALSE,
dod = NULL,
dooc = NULL,
awd = NULL,
awod = NULL,
useHierarchy = FALSE,
eventPriority = 1,
intervalCensoring = FALSE,
intervalStart = NULL,
intervalEnd = NULL,
adminCensoring = FALSE,
adminDate = NULL,
outputTable = TRUE,
diagnostics = FALSE,
visualization = FALSE, ...) {
super$initialize(
package="ClinicoPath",
name="outcomeorganizer",
requiresData=TRUE,
...)
private$..outcome <- jmvcore::OptionVariable$new(
"outcome",
outcome,
suggested=list(
"ordinal",
"nominal",
"continuous"),
permitted=list(
"factor",
"numeric"))
private$..outcomeLevel <- jmvcore::OptionLevel$new(
"outcomeLevel",
outcomeLevel,
variable="(outcome)")
private$..recurrence <- jmvcore::OptionVariable$new(
"recurrence",
recurrence,
suggested=list(
"ordinal",
"nominal"),
permitted=list(
"factor"))
private$..recurrenceLevel <- jmvcore::OptionLevel$new(
"recurrenceLevel",
recurrenceLevel,
variable="(recurrence)")
private$..patientID <- jmvcore::OptionVariable$new(
"patientID",
patientID)
private$..analysistype <- jmvcore::OptionList$new(
"analysistype",
analysistype,
options=list(
"os",
"cause",
"compete",
"rfs",
"pfs",
"dfs",
"ttp",
"multistate"),
default="os")
private$..multievent <- jmvcore::OptionBool$new(
"multievent",
multievent,
default=FALSE)
private$..dod <- jmvcore::OptionLevel$new(
"dod",
dod,
variable="(outcome)",
allowNone=TRUE)
private$..dooc <- jmvcore::OptionLevel$new(
"dooc",
dooc,
variable="(outcome)",
allowNone=TRUE)
private$..awd <- jmvcore::OptionLevel$new(
"awd",
awd,
variable="(outcome)",
allowNone=TRUE)
private$..awod <- jmvcore::OptionLevel$new(
"awod",
awod,
variable="(outcome)",
allowNone=TRUE)
private$..useHierarchy <- jmvcore::OptionBool$new(
"useHierarchy",
useHierarchy,
default=FALSE)
private$..eventPriority <- jmvcore::OptionInteger$new(
"eventPriority",
eventPriority,
default=1)
private$..intervalCensoring <- jmvcore::OptionBool$new(
"intervalCensoring",
intervalCensoring,
default=FALSE)
private$..intervalStart <- jmvcore::OptionVariable$new(
"intervalStart",
intervalStart)
private$..intervalEnd <- jmvcore::OptionVariable$new(
"intervalEnd",
intervalEnd)
private$..adminCensoring <- jmvcore::OptionBool$new(
"adminCensoring",
adminCensoring,
default=FALSE)
private$..adminDate <- jmvcore::OptionVariable$new(
"adminDate",
adminDate)
private$..outputTable <- jmvcore::OptionBool$new(
"outputTable",
outputTable,
default=TRUE)
private$..diagnostics <- jmvcore::OptionBool$new(
"diagnostics",
diagnostics,
default=FALSE)
private$..visualization <- jmvcore::OptionBool$new(
"visualization",
visualization,
default=FALSE)
private$..addOutcome <- jmvcore::OptionOutput$new(
"addOutcome")
self$.addOption(private$..outcome)
self$.addOption(private$..outcomeLevel)
self$.addOption(private$..recurrence)
self$.addOption(private$..recurrenceLevel)
self$.addOption(private$..patientID)
self$.addOption(private$..analysistype)
self$.addOption(private$..multievent)
self$.addOption(private$..dod)
self$.addOption(private$..dooc)
self$.addOption(private$..awd)
self$.addOption(private$..awod)
self$.addOption(private$..useHierarchy)
self$.addOption(private$..eventPriority)
self$.addOption(private$..intervalCensoring)
self$.addOption(private$..intervalStart)
self$.addOption(private$..intervalEnd)
self$.addOption(private$..adminCensoring)
self$.addOption(private$..adminDate)
self$.addOption(private$..outputTable)
self$.addOption(private$..diagnostics)
self$.addOption(private$..visualization)
self$.addOption(private$..addOutcome)
}),
active = list(
outcome = function() private$..outcome$value,
outcomeLevel = function() private$..outcomeLevel$value,
recurrence = function() private$..recurrence$value,
recurrenceLevel = function() private$..recurrenceLevel$value,
patientID = function() private$..patientID$value,
analysistype = function() private$..analysistype$value,
multievent = function() private$..multievent$value,
dod = function() private$..dod$value,
dooc = function() private$..dooc$value,
awd = function() private$..awd$value,
awod = function() private$..awod$value,
useHierarchy = function() private$..useHierarchy$value,
eventPriority = function() private$..eventPriority$value,
intervalCensoring = function() private$..intervalCensoring$value,
intervalStart = function() private$..intervalStart$value,
intervalEnd = function() private$..intervalEnd$value,
adminCensoring = function() private$..adminCensoring$value,
adminDate = function() private$..adminDate$value,
outputTable = function() private$..outputTable$value,
diagnostics = function() private$..diagnostics$value,
visualization = function() private$..visualization$value,
addOutcome = function() private$..addOutcome$value),
private = list(
..outcome = NA,
..outcomeLevel = NA,
..recurrence = NA,
..recurrenceLevel = NA,
..patientID = NA,
..analysistype = NA,
..multievent = NA,
..dod = NA,
..dooc = NA,
..awd = NA,
..awod = NA,
..useHierarchy = NA,
..eventPriority = NA,
..intervalCensoring = NA,
..intervalStart = NA,
..intervalEnd = NA,
..adminCensoring = NA,
..adminDate = NA,
..outputTable = NA,
..diagnostics = NA,
..visualization = NA,
..addOutcome = NA)
)
outcomeorganizerResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"outcomeorganizerResults",
inherit = jmvcore::Group,
active = list(
todo = function() private$.items[["todo"]],
summary = function() private$.items[["summary"]],
outputTable = function() private$.items[["outputTable"]],
diagnosticsTable = function() private$.items[["diagnosticsTable"]],
outcomeViz = function() private$.items[["outcomeViz"]],
addOutcome = function() private$.items[["addOutcome"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Enhanced Outcome Organizer for Survival Analysis",
refs=list(
"survival",
"survminer",
"finalfit",
"cmprsk",
"mstate",
"survivaltutorial",
"ClinicoPathJamoviModule"))
self$add(jmvcore::Html$new(
options=options,
name="todo",
title="To Do",
clearWith=list(
"outcome",
"outcomeLevel",
"multievent",
"analysistype",
"dod",
"dooc",
"awd",
"awod",
"recurrence",
"recurrenceLevel")))
self$add(jmvcore::Html$new(
options=options,
name="summary",
title="Summary of Outcome Recoding",
clearWith=list(
"outcome",
"outcomeLevel",
"multievent",
"analysistype",
"dod",
"dooc",
"awd",
"awod",
"recurrence",
"recurrenceLevel",
"useHierarchy",
"eventPriority",
"intervalCensoring",
"adminCensoring")))
self$add(jmvcore::Table$new(
options=options,
name="outputTable",
title="Recoded Outcome Summary",
visible="(outputTable)",
rows=0,
columns=list(
list(
`name`="outcome",
`title`="Value",
`type`="text"),
list(
`name`="label",
`title`="Meaning",
`type`="text"),
list(
`name`="count",
`title`="Count",
`type`="integer"),
list(
`name`="percentage",
`title`="Percentage",
`type`="number")),
clearWith=list(
"outcome",
"outcomeLevel",
"multievent",
"analysistype",
"dod",
"dooc",
"awd",
"awod",
"recurrence",
"recurrenceLevel",
"useHierarchy",
"eventPriority")))
self$add(jmvcore::Table$new(
options=options,
name="diagnosticsTable",
title="Diagnostic Information",
visible="(diagnostics)",
rows=0,
columns=list(
list(
`name`="check",
`title`="Check",
`type`="text"),
list(
`name`="result",
`title`="Result",
`type`="text")),
clearWith=list(
"outcome",
"outcomeLevel",
"multievent",
"analysistype",
"dod",
"dooc",
"awd",
"awod",
"recurrence",
"recurrenceLevel",
"useHierarchy",
"eventPriority",
"intervalCensoring",
"adminCensoring")))
self$add(jmvcore::Image$new(
options=options,
name="outcomeViz",
title="Outcome Distribution",
width=500,
height=400,
renderFun=".plotOutcome",
visible="(visualization)",
clearWith=list(
"outcome",
"outcomeLevel",
"multievent",
"analysistype",
"dod",
"dooc",
"awd",
"awod")))
self$add(jmvcore::Output$new(
options=options,
name="addOutcome",
title="Add Recoded Outcome to Data",
varTitle="`Recoded Outcome for {analysistype} Survival Analysis`",
varDescription="Outcome variable recoded for survival analysis based on selected analysis type",
measureType="nominal",
clearWith=list(
"outcome",
"outcomeLevel",
"multievent",
"analysistype",
"dod",
"dooc",
"awd",
"awod",
"recurrence",
"recurrenceLevel",
"useHierarchy",
"eventPriority",
"intervalCensoring",
"adminCensoring")))}))
outcomeorganizerBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"outcomeorganizerBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "ClinicoPath",
name = "outcomeorganizer",
version = c(0,0,3),
options = options,
results = outcomeorganizerResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'none')
}))
#' Enhanced Outcome Organizer for Survival Analysis
#'
#' Advanced tool for preparing outcome variables for various types of survival
#' analysis including overall survival, cause-specific, competing risks,
#' progression-free survival, and multistate models.
#'
#' @examples
#' \donttest{
#' # Example usage will be added
#'}
#' @param data The data as a data frame.
#' @param outcome The primary outcome variable to be recoded for survival
#' analysis (e.g., vital status).
#' @param outcomeLevel The level of the outcome variable that represents the
#' event of interest (e.g., "Death", "Relapse").
#' @param recurrence Variable indicating disease recurrence or progression
#' (for RFS/PFS/DFS analyses).
#' @param recurrenceLevel The level indicating recurrence or progression has
#' occurred.
#' @param patientID Patient identifier for handling multiple records or
#' applying event hierarchies.
#' @param analysistype The type of survival analysis to prepare the outcome
#' for.
#' @param multievent If true, allows for multiple event types (e.g., death
#' from disease vs death from other causes).
#' @param dod The level representing death from the disease of interest.
#' @param dooc The level representing death from causes other than the disease
#' of interest.
#' @param awd The level representing patients who are alive but have the
#' disease.
#' @param awod The level representing patients who are alive and disease-free.
#' @param useHierarchy If true, applies a hierarchy when multiple events occur
#' for the same patient.
#' @param eventPriority The event code (e.g., 1, 2) that takes precedence when
#' multiple events occur.
#' @param intervalCensoring If true, prepares data for interval-censored
#' analysis where exact event times are unknown.
#' @param intervalStart Variable containing the start of the interval when the
#' event might have occurred.
#' @param intervalEnd Variable containing the end of the interval when the
#' event might have occurred.
#' @param adminCensoring If true, applies administrative censoring at a
#' specified date.
#' @param adminDate Variable containing the administrative censoring date.
#' @param outputTable If true, displays a table showing the frequency of each
#' recoded outcome value.
#' @param diagnostics If true, displays diagnostic information about the
#' recoding process.
#' @param visualization If true, displays a visualization of the distribution
#' of recoded outcomes.
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$todo} \tab \tab \tab \tab \tab a html \cr
#' \code{results$summary} \tab \tab \tab \tab \tab a html \cr
#' \code{results$outputTable} \tab \tab \tab \tab \tab a table \cr
#' \code{results$diagnosticsTable} \tab \tab \tab \tab \tab a table \cr
#' \code{results$outcomeViz} \tab \tab \tab \tab \tab an image \cr
#' \code{results$addOutcome} \tab \tab \tab \tab \tab an output \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$outputTable$asDF}
#'
#' \code{as.data.frame(results$outputTable)}
#'
#' @export
outcomeorganizer <- function(
data,
outcome,
outcomeLevel,
recurrence,
recurrenceLevel,
patientID,
analysistype = "os",
multievent = FALSE,
dod,
dooc,
awd,
awod,
useHierarchy = FALSE,
eventPriority = 1,
intervalCensoring = FALSE,
intervalStart,
intervalEnd,
adminCensoring = FALSE,
adminDate,
outputTable = TRUE,
diagnostics = FALSE,
visualization = FALSE) {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("outcomeorganizer requires jmvcore to be installed (restart may be required)")
if ( ! missing(outcome)) outcome <- jmvcore::resolveQuo(jmvcore::enquo(outcome))
if ( ! missing(recurrence)) recurrence <- jmvcore::resolveQuo(jmvcore::enquo(recurrence))
if ( ! missing(patientID)) patientID <- jmvcore::resolveQuo(jmvcore::enquo(patientID))
if ( ! missing(intervalStart)) intervalStart <- jmvcore::resolveQuo(jmvcore::enquo(intervalStart))
if ( ! missing(intervalEnd)) intervalEnd <- jmvcore::resolveQuo(jmvcore::enquo(intervalEnd))
if ( ! missing(adminDate)) adminDate <- jmvcore::resolveQuo(jmvcore::enquo(adminDate))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(outcome), outcome, NULL),
`if`( ! missing(recurrence), recurrence, NULL),
`if`( ! missing(patientID), patientID, NULL),
`if`( ! missing(intervalStart), intervalStart, NULL),
`if`( ! missing(intervalEnd), intervalEnd, NULL),
`if`( ! missing(adminDate), adminDate, NULL))
for (v in recurrence) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
options <- outcomeorganizerOptions$new(
outcome = outcome,
outcomeLevel = outcomeLevel,
recurrence = recurrence,
recurrenceLevel = recurrenceLevel,
patientID = patientID,
analysistype = analysistype,
multievent = multievent,
dod = dod,
dooc = dooc,
awd = awd,
awod = awod,
useHierarchy = useHierarchy,
eventPriority = eventPriority,
intervalCensoring = intervalCensoring,
intervalStart = intervalStart,
intervalEnd = intervalEnd,
adminCensoring = adminCensoring,
adminDate = adminDate,
outputTable = outputTable,
diagnostics = diagnostics,
visualization = visualization)
analysis <- outcomeorganizerClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
sbalci/ClinicoPathJamoviModule documentation built on June 13, 2025, 9:34 a.m.
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Defines functions outcomeorganizer
Documented in outcomeorganizer
# This file is automatically generated, you probably don't want to edit this
outcomeorganizerOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"outcomeorganizerOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
outcome = NULL,
outcomeLevel = NULL,
recurrence = NULL,
recurrenceLevel = NULL,
patientID = NULL,
analysistype = "os",
multievent = FALSE,
dod = NULL,
dooc = NULL,
awd = NULL,
awod = NULL,
useHierarchy = FALSE,
eventPriority = 1,
intervalCensoring = FALSE,
intervalStart = NULL,
intervalEnd = NULL,
adminCensoring = FALSE,
adminDate = NULL,
outputTable = TRUE,
diagnostics = FALSE,
visualization = FALSE, ...) {
super$initialize(
package="ClinicoPath",
name="outcomeorganizer",
requiresData=TRUE,
...)
private$..outcome <- jmvcore::OptionVariable$new(
"outcome",
outcome,
suggested=list(
"ordinal",
"nominal",
"continuous"),
permitted=list(
"factor",
"numeric"))
private$..outcomeLevel <- jmvcore::OptionLevel$new(
"outcomeLevel",
outcomeLevel,
variable="(outcome)")
private$..recurrence <- jmvcore::OptionVariable$new(
"recurrence",
recurrence,
suggested=list(
"ordinal",
"nominal"),
permitted=list(
"factor"))
private$..recurrenceLevel <- jmvcore::OptionLevel$new(
"recurrenceLevel",
recurrenceLevel,
variable="(recurrence)")
private$..patientID <- jmvcore::OptionVariable$new(
"patientID",
patientID)
private$..analysistype <- jmvcore::OptionList$new(
"analysistype",
analysistype,
options=list(
"os",
"cause",
"compete",
"rfs",
"pfs",
"dfs",
"ttp",
"multistate"),
default="os")
private$..multievent <- jmvcore::OptionBool$new(
"multievent",
multievent,
default=FALSE)
private$..dod <- jmvcore::OptionLevel$new(
"dod",
dod,
variable="(outcome)",
allowNone=TRUE)
private$..dooc <- jmvcore::OptionLevel$new(
"dooc",
dooc,
variable="(outcome)",
allowNone=TRUE)
private$..awd <- jmvcore::OptionLevel$new(
"awd",
awd,
variable="(outcome)",
allowNone=TRUE)
private$..awod <- jmvcore::OptionLevel$new(
"awod",
awod,
variable="(outcome)",
allowNone=TRUE)
private$..useHierarchy <- jmvcore::OptionBool$new(
"useHierarchy",
useHierarchy,
default=FALSE)
private$..eventPriority <- jmvcore::OptionInteger$new(
"eventPriority",
eventPriority,
default=1)
private$..intervalCensoring <- jmvcore::OptionBool$new(
"intervalCensoring",
intervalCensoring,
default=FALSE)
private$..intervalStart <- jmvcore::OptionVariable$new(
"intervalStart",
intervalStart)
private$..intervalEnd <- jmvcore::OptionVariable$new(
"intervalEnd",
intervalEnd)
private$..adminCensoring <- jmvcore::OptionBool$new(
"adminCensoring",
adminCensoring,
default=FALSE)
private$..adminDate <- jmvcore::OptionVariable$new(
"adminDate",
adminDate)
private$..outputTable <- jmvcore::OptionBool$new(
"outputTable",
outputTable,
default=TRUE)
private$..diagnostics <- jmvcore::OptionBool$new(
"diagnostics",
diagnostics,
default=FALSE)
private$..visualization <- jmvcore::OptionBool$new(
"visualization",
visualization,
default=FALSE)
private$..addOutcome <- jmvcore::OptionOutput$new(
"addOutcome")
self$.addOption(private$..outcome)
self$.addOption(private$..outcomeLevel)
self$.addOption(private$..recurrence)
self$.addOption(private$..recurrenceLevel)
self$.addOption(private$..patientID)
self$.addOption(private$..analysistype)
self$.addOption(private$..multievent)
self$.addOption(private$..dod)
self$.addOption(private$..dooc)
self$.addOption(private$..awd)
self$.addOption(private$..awod)
self$.addOption(private$..useHierarchy)
self$.addOption(private$..eventPriority)
self$.addOption(private$..intervalCensoring)
self$.addOption(private$..intervalStart)
self$.addOption(private$..intervalEnd)
self$.addOption(private$..adminCensoring)
self$.addOption(private$..adminDate)
self$.addOption(private$..outputTable)
self$.addOption(private$..diagnostics)
self$.addOption(private$..visualization)
self$.addOption(private$..addOutcome)
}),
active = list(
outcome = function() private$..outcome$value,
outcomeLevel = function() private$..outcomeLevel$value,
recurrence = function() private$..recurrence$value,
recurrenceLevel = function() private$..recurrenceLevel$value,
patientID = function() private$..patientID$value,
analysistype = function() private$..analysistype$value,
multievent = function() private$..multievent$value,
dod = function() private$..dod$value,
dooc = function() private$..dooc$value,
awd = function() private$..awd$value,
awod = function() private$..awod$value,
useHierarchy = function() private$..useHierarchy$value,
eventPriority = function() private$..eventPriority$value,
intervalCensoring = function() private$..intervalCensoring$value,
intervalStart = function() private$..intervalStart$value,
intervalEnd = function() private$..intervalEnd$value,
adminCensoring = function() private$..adminCensoring$value,
adminDate = function() private$..adminDate$value,
outputTable = function() private$..outputTable$value,
diagnostics = function() private$..diagnostics$value,
visualization = function() private$..visualization$value,
addOutcome = function() private$..addOutcome$value),
private = list(
..outcome = NA,
..outcomeLevel = NA,
..recurrence = NA,
..recurrenceLevel = NA,
..patientID = NA,
..analysistype = NA,
..multievent = NA,
..dod = NA,
..dooc = NA,
..awd = NA,
..awod = NA,
..useHierarchy = NA,
..eventPriority = NA,
..intervalCensoring = NA,
..intervalStart = NA,
..intervalEnd = NA,
..adminCensoring = NA,
..adminDate = NA,
..outputTable = NA,
..diagnostics = NA,
..visualization = NA,
..addOutcome = NA)
)
outcomeorganizerResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"outcomeorganizerResults",
inherit = jmvcore::Group,
active = list(
todo = function() private$.items[["todo"]],
summary = function() private$.items[["summary"]],
outputTable = function() private$.items[["outputTable"]],
diagnosticsTable = function() private$.items[["diagnosticsTable"]],
outcomeViz = function() private$.items[["outcomeViz"]],
addOutcome = function() private$.items[["addOutcome"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Enhanced Outcome Organizer for Survival Analysis",
refs=list(
"survival",
"survminer",
"finalfit",
"cmprsk",
"mstate",
"survivaltutorial",
"ClinicoPathJamoviModule"))
self$add(jmvcore::Html$new(
options=options,
name="todo",
title="To Do",
clearWith=list(
"outcome",
"outcomeLevel",
"multievent",
"analysistype",
"dod",
"dooc",
"awd",
"awod",
"recurrence",
"recurrenceLevel")))
self$add(jmvcore::Html$new(
options=options,
name="summary",
title="Summary of Outcome Recoding",
clearWith=list(
"outcome",
"outcomeLevel",
"multievent",
"analysistype",
"dod",
"dooc",
"awd",
"awod",
"recurrence",
"recurrenceLevel",
"useHierarchy",
"eventPriority",
"intervalCensoring",
"adminCensoring")))
self$add(jmvcore::Table$new(
options=options,
name="outputTable",
title="Recoded Outcome Summary",
visible="(outputTable)",
rows=0,
columns=list(
list(
`name`="outcome",
`title`="Value",
`type`="text"),
list(
`name`="label",
`title`="Meaning",
`type`="text"),
list(
`name`="count",
`title`="Count",
`type`="integer"),
list(
`name`="percentage",
`title`="Percentage",
`type`="number")),
clearWith=list(
"outcome",
"outcomeLevel",
"multievent",
"analysistype",
"dod",
"dooc",
"awd",
"awod",
"recurrence",
"recurrenceLevel",
"useHierarchy",
"eventPriority")))
self$add(jmvcore::Table$new(
options=options,
name="diagnosticsTable",
title="Diagnostic Information",
visible="(diagnostics)",
rows=0,
columns=list(
list(
`name`="check",
`title`="Check",
`type`="text"),
list(
`name`="result",
`title`="Result",
`type`="text")),
clearWith=list(
"outcome",
"outcomeLevel",
"multievent",
"analysistype",
"dod",
"dooc",
"awd",
"awod",
"recurrence",
"recurrenceLevel",
"useHierarchy",
"eventPriority",
"intervalCensoring",
"adminCensoring")))
self$add(jmvcore::Image$new(
options=options,
name="outcomeViz",
title="Outcome Distribution",
width=500,
height=400,
renderFun=".plotOutcome",
visible="(visualization)",
clearWith=list(
"outcome",
"outcomeLevel",
"multievent",
"analysistype",
"dod",
"dooc",
"awd",
"awod")))
self$add(jmvcore::Output$new(
options=options,
name="addOutcome",
title="Add Recoded Outcome to Data",
varTitle="`Recoded Outcome for {analysistype} Survival Analysis`",
varDescription="Outcome variable recoded for survival analysis based on selected analysis type",
measureType="nominal",
clearWith=list(
"outcome",
"outcomeLevel",
"multievent",
"analysistype",
"dod",
"dooc",
"awd",
"awod",
"recurrence",
"recurrenceLevel",
"useHierarchy",
"eventPriority",
"intervalCensoring",
"adminCensoring")))}))
outcomeorganizerBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"outcomeorganizerBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "ClinicoPath",
name = "outcomeorganizer",
version = c(0,0,3),
options = options,
results = outcomeorganizerResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'none')
}))
#' Enhanced Outcome Organizer for Survival Analysis
#'
#' Advanced tool for preparing outcome variables for various types of survival
#' analysis including overall survival, cause-specific, competing risks,
#' progression-free survival, and multistate models.
#'
#' @examples
#' \donttest{
#' # Example usage will be added
#'}
#' @param data The data as a data frame.
#' @param outcome The primary outcome variable to be recoded for survival
#' analysis (e.g., vital status).
#' @param outcomeLevel The level of the outcome variable that represents the
#' event of interest (e.g., "Death", "Relapse").
#' @param recurrence Variable indicating disease recurrence or progression
#' (for RFS/PFS/DFS analyses).
#' @param recurrenceLevel The level indicating recurrence or progression has
#' occurred.
#' @param patientID Patient identifier for handling multiple records or
#' applying event hierarchies.
#' @param analysistype The type of survival analysis to prepare the outcome
#' for.
#' @param multievent If true, allows for multiple event types (e.g., death
#' from disease vs death from other causes).
#' @param dod The level representing death from the disease of interest.
#' @param dooc The level representing death from causes other than the disease
#' of interest.
#' @param awd The level representing patients who are alive but have the
#' disease.
#' @param awod The level representing patients who are alive and disease-free.
#' @param useHierarchy If true, applies a hierarchy when multiple events occur
#' for the same patient.
#' @param eventPriority The event code (e.g., 1, 2) that takes precedence when
#' multiple events occur.
#' @param intervalCensoring If true, prepares data for interval-censored
#' analysis where exact event times are unknown.
#' @param intervalStart Variable containing the start of the interval when the
#' event might have occurred.
#' @param intervalEnd Variable containing the end of the interval when the
#' event might have occurred.
#' @param adminCensoring If true, applies administrative censoring at a
#' specified date.
#' @param adminDate Variable containing the administrative censoring date.
#' @param outputTable If true, displays a table showing the frequency of each
#' recoded outcome value.
#' @param diagnostics If true, displays diagnostic information about the
#' recoding process.
#' @param visualization If true, displays a visualization of the distribution
#' of recoded outcomes.
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$todo} \tab \tab \tab \tab \tab a html \cr
#' \code{results$summary} \tab \tab \tab \tab \tab a html \cr
#' \code{results$outputTable} \tab \tab \tab \tab \tab a table \cr
#' \code{results$diagnosticsTable} \tab \tab \tab \tab \tab a table \cr
#' \code{results$outcomeViz} \tab \tab \tab \tab \tab an image \cr
#' \code{results$addOutcome} \tab \tab \tab \tab \tab an output \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$outputTable$asDF}
#'
#' \code{as.data.frame(results$outputTable)}
#'
#' @export
outcomeorganizer <- function(
data,
outcome,
outcomeLevel,
recurrence,
recurrenceLevel,
patientID,
analysistype = "os",
multievent = FALSE,
dod,
dooc,
awd,
awod,
useHierarchy = FALSE,
eventPriority = 1,
intervalCensoring = FALSE,
intervalStart,
intervalEnd,
adminCensoring = FALSE,
adminDate,
outputTable = TRUE,
diagnostics = FALSE,
visualization = FALSE) {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("outcomeorganizer requires jmvcore to be installed (restart may be required)")
if ( ! missing(outcome)) outcome <- jmvcore::resolveQuo(jmvcore::enquo(outcome))
if ( ! missing(recurrence)) recurrence <- jmvcore::resolveQuo(jmvcore::enquo(recurrence))
if ( ! missing(patientID)) patientID <- jmvcore::resolveQuo(jmvcore::enquo(patientID))
if ( ! missing(intervalStart)) intervalStart <- jmvcore::resolveQuo(jmvcore::enquo(intervalStart))
if ( ! missing(intervalEnd)) intervalEnd <- jmvcore::resolveQuo(jmvcore::enquo(intervalEnd))
if ( ! missing(adminDate)) adminDate <- jmvcore::resolveQuo(jmvcore::enquo(adminDate))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(outcome), outcome, NULL),
`if`( ! missing(recurrence), recurrence, NULL),
`if`( ! missing(patientID), patientID, NULL),
`if`( ! missing(intervalStart), intervalStart, NULL),
`if`( ! missing(intervalEnd), intervalEnd, NULL),
`if`( ! missing(adminDate), adminDate, NULL))
for (v in recurrence) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
options <- outcomeorganizerOptions$new(
outcome = outcome,
outcomeLevel = outcomeLevel,
recurrence = recurrence,
recurrenceLevel = recurrenceLevel,
patientID = patientID,
analysistype = analysistype,
multievent = multievent,
dod = dod,
dooc = dooc,
awd = awd,
awod = awod,
useHierarchy = useHierarchy,
eventPriority = eventPriority,
intervalCensoring = intervalCensoring,
intervalStart = intervalStart,
intervalEnd = intervalEnd,
adminCensoring = adminCensoring,
adminDate = adminDate,
outputTable = outputTable,
diagnostics = diagnostics,
visualization = visualization)
analysis <- outcomeorganizerClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
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