Fine-Gray subdistribution hazard regression for competing risks data. Models the cumulative incidence function (CIF) while accounting for competing events. Provides sub-hazard ratios (sHR) for covariate effects.
Usage
finegray(
data,
survivalTime,
status,
eventOfInterest,
censorLevel,
covariates,
groupVar,
showCoefficientTable = TRUE,
exponentiate = TRUE,
confLevel = 0.95,
showGrayTest = TRUE,
showModelFit = TRUE,
showCIFPlot = TRUE,
cifPlotBy = "group",
cifPlotTimes = "",
showRiskTable = TRUE,
colorScheme = "default",
cifConfInt = FALSE,
cifConfLevel = 0.95,
predictAt = "",
predictCovariatePattern = "mean",
customCovariateValues = "",
showInterpretation = TRUE
)Arguments
- data
The data as a data frame.
- survivalTime
Time to event or censoring. Must be numeric and positive.
- status
Event status with multiple levels: 0 or first level = censored, 1 or second level = event of interest, 2+ = competing events.
- eventOfInterest
Which level of status represents the event of interest. Other non-censored levels are treated as competing events.
- censorLevel
Which level of status represents censoring.
- covariates
Predictor variables for the regression model. Can include continuous and categorical variables.
- groupVar
Optional grouping variable for cumulative incidence plots.
- showCoefficientTable
Display table of sub-hazard ratios with confidence intervals.
- exponentiate
Report exponentiated coefficients as sub-hazard ratios (sHR). If false, reports log sub-hazard ratios.
- confLevel
Confidence level for confidence intervals.
- showGrayTest
Perform Gray's test for comparing cumulative incidence functions between groups (requires grouping variable).
- showModelFit
Display model fit statistics (pseudo-R², AIC, BIC).
- showCIFPlot
Display cumulative incidence function plot.
- cifPlotBy
How to display the CIF plot.
- cifPlotTimes
Comma-separated time points for CIF plot risk table. If empty, automatically determined.
- showRiskTable
Display numbers at risk below CIF plot.
- colorScheme
Color palette for plots.
- cifConfInt
Display confidence bands around CIF curves.
- cifConfLevel
Confidence level for CIF confidence bands.
- predictAt
Comma-separated time points for predictions. Calculates predicted CIF at these times for covariate patterns.
- predictCovariatePattern
Covariate pattern for predictions.
- customCovariateValues
Custom covariate values for predictions (comma-separated). Format: "age=65,stage=III,treatment=chemo"
- showInterpretation
Display interpretation guidance for Fine-Gray results.
Value
A results object containing:
results$instructions | a html | ||||
results$procedureNotes | a html | ||||
results$modelInfo | a table | ||||
results$shrTable | a table | ||||
results$grayTestTable | a table | ||||
results$modelFitTable | a table | ||||
results$comparisonTable | a table | ||||
results$predictionTable | a table | ||||
results$cifPlot | an image | ||||
results$stackedCIFPlot | an image | ||||
results$kmvscifPlot | Demonstrates bias in using 1-KM for competing risks | ||||
results$causeSpecificPlot | an image | ||||
results$diagnosticPlots | an image | ||||
results$influenceTable | a table | ||||
results$interpretation | a html |
Tables can be converted to data frames with asDF or as.data.frame. For example:
results$modelInfo$asDF
as.data.frame(results$modelInfo)