Comprehensive testing of the proportional hazards assumption in Cox regression models using multiple statistical approaches. This analysis provides systematic validation of the fundamental assumption underlying Cox proportional hazards models through statistical tests, graphical diagnostics, and time-dependent coefficient analysis for robust model assessment and assumption verification.
Usage
pheval(
data,
elapsedtime,
outcome,
covariates,
outcomeLevel = "1",
test_schoenfeld = TRUE,
test_scaled_schoenfeld = TRUE,
test_global = TRUE,
test_correlation = FALSE,
test_logrank = FALSE,
test_supremum = FALSE,
time_transform = "identity",
confidence_level = 0.95,
rho_parameter = 0,
global_test_method = "chisquare",
stratify_variable,
show_individual_tests = TRUE,
show_global_tests = TRUE,
show_residual_plots = TRUE,
show_diagnostic_plots = TRUE,
show_time_varying_plots = TRUE,
show_model_summary = TRUE,
show_recommendations = TRUE,
showSummaries = FALSE,
showExplanations = FALSE
)Arguments
- data
the data as a data frame
- elapsedtime
Survival time or follow-up duration variable
- outcome
Event indicator variable (0/1, FALSE/TRUE, or factor)
- covariates
Covariate variables for proportional hazards testing
- outcomeLevel
Level of outcome variable indicating event occurrence
- test_schoenfeld
Perform Schoenfeld residuals test
- test_scaled_schoenfeld
Perform scaled Schoenfeld residuals test
- test_global
Perform global proportional hazards test
- test_correlation
Perform correlation test with time
- test_logrank
Perform log-rank trend test
- test_supremum
Perform supremum test
- time_transform
Transformation function for time in testing
- confidence_level
Confidence level for test statistics and intervals
- rho_parameter
Rho parameter for weighted residuals (0=unweighted)
- global_test_method
Method for global proportional hazards test
- stratify_variable
Optional variable for stratified analysis
- show_individual_tests
Display individual covariate test results
- show_global_tests
Display global proportional hazards tests
- show_residual_plots
Display Schoenfeld residual plots
- show_diagnostic_plots
Display comprehensive diagnostic plots
- show_time_varying_plots
Display plots of potential time-varying effects
- show_model_summary
Display fitted Cox model summary
- show_recommendations
Display interpretation recommendations
- showSummaries
Generate natural language summaries of the analysis results
- showExplanations
Show detailed explanations of the methodology and interpretation
Value
A results object containing:
results$todo | a html | ||||
results$modelSummary | a html | ||||
results$individualTests | a table | ||||
results$globalTests | a table | ||||
results$residualAnalysis | a table | ||||
results$stratifiedResults | a table | ||||
results$powerAnalysis | a table | ||||
results$residualPlots | an image | ||||
results$diagnosticPlots | an image | ||||
results$timeVaryingPlots | an image | ||||
results$globalTestPlots | an image | ||||
results$stratifiedPlots | an image | ||||
results$recommendations | a html | ||||
results$analysisSummary | a html | ||||
results$methodExplanation | a html |
Tables can be converted to data frames with asDF or as.data.frame. For example:
results$individualTests$asDF
as.data.frame(results$individualTests)