outcomeorganizer: Enhanced Outcome Organizer for Survival Analysis

In sbalci/ClinicoPathJamoviModule: Analysis for Clinicopathological Research

Enhanced Outcome Organizer for Survival Analysis

Description

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.

Usage

outcomeorganizer(
  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
)

Arguments

data	The data as a data frame.
outcome	The primary outcome variable to be recoded for survival analysis (e.g., vital status).
outcomeLevel	The level of the outcome variable that represents the event of interest (e.g., "Death", "Relapse").
recurrence	Variable indicating disease recurrence or progression (for RFS/PFS/DFS analyses).
recurrenceLevel	The level indicating recurrence or progression has occurred.
patientID	Patient identifier for handling multiple records or applying event hierarchies.
analysistype	The type of survival analysis to prepare the outcome for.
multievent	If true, allows for multiple event types (e.g., death from disease vs death from other causes).
dod	The level representing death from the disease of interest.
dooc	The level representing death from causes other than the disease of interest.
awd	The level representing patients who are alive but have the disease.
awod	The level representing patients who are alive and disease-free.
useHierarchy	If true, applies a hierarchy when multiple events occur for the same patient.
eventPriority	The event code (e.g., 1, 2) that takes precedence when multiple events occur.
intervalCensoring	If true, prepares data for interval-censored analysis where exact event times are unknown.
intervalStart	Variable containing the start of the interval when the event might have occurred.
intervalEnd	Variable containing the end of the interval when the event might have occurred.
adminCensoring	If true, applies administrative censoring at a specified date.
adminDate	Variable containing the administrative censoring date.
outputTable	If true, displays a table showing the frequency of each recoded outcome value.
diagnostics	If true, displays diagnostic information about the recoding process.
visualization	If true, displays a visualization of the distribution of recoded outcomes.

Value

A results object containing:

results$todo					a html
results$summary					a html
results$outputTable					a table
results$diagnosticsTable					a table
results$outcomeViz					an image
results$addOutcome					an output

Tables can be converted to data frames with asDF or as.data.frame. For example:

results$outputTable$asDF

as.data.frame(results$outputTable)

Examples

# Example usage will be added

sbalci/ClinicoPathJamoviModule documentation built on June 13, 2025, 9:34 a.m.