Specialized progression-free survival (PFS) analysis designed for oncology research. Provides comprehensive analysis of time-to-progression endpoints with competing risks considerations, landmark analysis, and treatment effect estimation. Includes analysis of progression patterns, censoring mechanisms, and clinical interpretation specific to cancer clinical trials and observational studies.
Usage
progressionsurvival(
data,
time_var,
progression_var,
death_var,
treatment_var,
stratification_vars,
patient_id,
baseline_vars,
analysis_type = "standard_pfs",
progression_definition = "recist",
censoring_mechanism = "administrative",
survival_method = "kaplan_meier",
comparison_test = "logrank",
regression_model = "cox_ph",
landmark_times = "6,12,18,24",
rmst_tau = 24,
confidence_level = 0.95,
alpha_spending = "obrien_fleming",
kaplan_meier_curves = TRUE,
cumulative_incidence = FALSE,
landmark_analysis_plot = FALSE,
progression_patterns = FALSE,
treatment_effect_estimation = TRUE,
subgroup_analysis = FALSE,
biomarker_interaction = FALSE,
sensitivity_analysis = FALSE,
interim_monitoring = FALSE,
progression_velocity = FALSE,
clinical_significance = TRUE,
regulatory_endpoints = FALSE,
health_economic_outcomes = FALSE,
plot_theme = "publication",
risk_tables = TRUE,
median_survival_lines = TRUE,
confidence_bands = TRUE,
generate_report = FALSE,
regulatory_tables = FALSE,
consort_diagram = FALSE
)Arguments
- data
the data as a data frame
- time_var
Time to progression or censoring (PFS time)
- progression_var
Progression indicator (1=progression, 0=censored)
- death_var
Death indicator (1=death, 0=alive) for competing risks analysis
- treatment_var
Treatment or intervention variable
- stratification_vars
Variables for stratified analysis (e.g., stage, histology, biomarkers)
- patient_id
Patient identifier for longitudinal data
- baseline_vars
Baseline covariates for adjusted analysis
- analysis_type
Type of progression-free survival analysis
- progression_definition
Definition of disease progression used
- censoring_mechanism
Primary censoring mechanism in the data
- survival_method
Method for survival function estimation
- comparison_test
Statistical test for group comparisons
- regression_model
Regression model for treatment effect estimation
- landmark_times
Landmark time points in months (comma-separated)
- rmst_tau
Restriction time for RMST analysis (months)
- confidence_level
Confidence level for intervals
- alpha_spending
Alpha spending function for interim analyses
- kaplan_meier_curves
Generate Kaplan-Meier survival curves
- cumulative_incidence
Calculate cumulative incidence functions (competing risks)
- landmark_analysis_plot
Generate landmark analysis visualizations
- progression_patterns
Analyze patterns and timing of disease progression
- treatment_effect_estimation
Estimate treatment effects with confidence intervals
- subgroup_analysis
Perform pre-specified subgroup analyses
- biomarker_interaction
Test for biomarker-treatment interactions
- sensitivity_analysis
Perform sensitivity analyses for assumptions
- interim_monitoring
Analysis for interim monitoring and early stopping
- progression_velocity
Analyze velocity and acceleration of disease progression
- clinical_significance
Assess clinical significance of findings
- regulatory_endpoints
Analysis aligned with regulatory requirements (FDA/EMA)
- health_economic_outcomes
Calculate health economic outcome measures
- plot_theme
Visual theme for plots
- risk_tables
Include risk tables below survival curves
- median_survival_lines
Add median survival reference lines
- confidence_bands
Show confidence bands on survival curves
- generate_report
Generate comprehensive clinical analysis report
- regulatory_tables
Generate regulatory submission-ready tables
- consort_diagram
Generate CONSORT-style patient flow diagram
Value
A results object containing:
results$instructions | a html | ||||
results$pfs_summary | a table | ||||
results$survival_estimates | a table | ||||
results$treatment_effects | a table | ||||
results$competing_risks_analysis | a table | ||||
results$landmark_results | a table | ||||
results$subgroup_analysis_table | a table | ||||
results$progression_patterns | a table | ||||
results$sensitivity_analysis_table | a table | ||||
results$biomarker_interaction_table | a table | ||||
results$interim_monitoring_table | a table | ||||
results$clinical_significance_table | a table | ||||
results$km_plot | an image | ||||
results$cif_plot | an image | ||||
results$landmark_plot | an image | ||||
results$forest_plot | an image | ||||
results$progression_pattern_plot | an image | ||||
results$consort_flow | an image | ||||
results$clinical_interpretation | a html | ||||
results$regulatory_summary | a html |
Tables can be converted to data frames with asDF or as.data.frame. For example:
results$pfs_summary$asDF
as.data.frame(results$pfs_summary)