Building Cox Models

Functions for building penalized Cox models.

hdcox.aenet()

Adaptive Elastic-Net Model Selection for High-Dimensional Cox Models

hdcox.alasso()

Adaptive Lasso Model Selection for High-Dimensional Cox Models

hdcox.enet()

Elastic-Net Model Selection for High-Dimensional Cox Models

hdcox.flasso()

Fused Lasso Model Selection for High-Dimensional Cox Models

hdcox.lasso()

Lasso Model Selection for High-Dimensional Cox Models

hdcox.mcp()

MCP Model Selection for High-Dimensional Cox Models

hdcox.mnet()

Mnet Model Selection for High-Dimensional Cox Models

hdcox.scad()

SCAD Model Selection for High-Dimensional Cox Models

hdcox.snet()

Snet Model Selection for High-Dimensional Cox Models

print(<hdcox.model>)

Print High-Dimensional Cox Model Objects

predict(<hdcox.model>)

Make Predictions from High-Dimensional Cox Models

hdnom.varinfo()

Extract Information of Selected Variables from High-Dimensional Cox Models

Nomogram Visualization

Functions for nomogram visualization of the penalized Cox models

hdnom.nomogram()

Nomograms for High-Dimensional Cox Models

plot(<hdnom.nomogram>)

Plot Nomogram Objects Generated by hdnom.nomogram

print(<hdnom.nomogram>)

Print Nomograms Objects Generated by hdnom.nomogram

Model Validation

Functions for model validation using bootstrap, k-fold cross-validation, and repeated k-fold cross-validation. Model performance is assessed by time-dependent AUC (tAUC).

hdnom.validate()

Validate High-Dimensional Cox Models with Time-Dependent AUC

hdnom.external.validate()

Externally Validate High-Dimensional Cox Models with Time-Dependent AUC

print(<hdnom.validate>)

Print Validation Results

print(<hdnom.external.validate>)

Print External Validation Results

summary(<hdnom.validate>)

Summary of Validation Results

summary(<hdnom.external.validate>)

Summary of External Validation Results

plot(<hdnom.validate>)

Plot Optimism-Corrected Time-Dependent Discrimination Curves for Validation

plot(<hdnom.external.validate>)

Plot Time-Dependent Discrimination Curves for External Validation

Model Calibration

Functions for model calibration using direct fitting, bootstrap resampling, k-fold cross-validation, and repeated cross-validation.

hdnom.calibrate()

Calibrate High-Dimensional Cox Models

hdnom.external.calibrate()

Externally Calibrate High-Dimensional Cox Models

print(<hdnom.calibrate>)

Print Calibration Results

print(<hdnom.external.calibrate>)

Print External Calibration Results

summary(<hdnom.calibrate>)

Summary of Calibration Results

summary(<hdnom.external.calibrate>)

Summary of External Calibration Results

plot(<hdnom.calibrate>)

Plot Calibration Results

plot(<hdnom.external.calibrate>)

Plot External Calibration Results

hdnom.kmplot()

Kaplan-Meier Plot with Number at Risk Table for Internal Calibration and External Calibration Results

hdnom.logrank()

Log-Rank Test for Internal Calibration and External Calibration Results

Model Comparison

Functions for model comparison in terms of validation and calibration performance.

hdnom.compare.validate()

Compare High-Dimensional Cox Models by Model Validation

hdnom.compare.calibrate()

Compare High-Dimensional Cox Models by Model Calibration

print(<hdnom.compare.validate>)

Print Model Comparison by Validation Results

print(<hdnom.compare.calibrate>)

Print Model Comparison by Calibration Results

summary(<hdnom.compare.validate>)

Summary of Model Comparison by Validation Results

summary(<hdnom.compare.calibrate>)

Summary of Model Comparison by Calibration Results

plot(<hdnom.compare.validate>)

Plot Model Comparison by Validation Results

plot(<hdnom.compare.calibrate>)

Plot Model Comparison by Calibration Results

Miscellaneous

Miscellaneous functions for supporting survival analysis, such as baseline hazard estimation and survival curve prediction.

glmnet.basesurv()

Breslow Baseline Hazard Estimator for glmnet Objects

glmnet.survcurve()

Survival Curve Prediction for glmnet Objects

penalized.basesurv()

Breslow Baseline Hazard Estimator for "penalized" Objects

penalized.survcurve()

Survival Curve Prediction for "penalized" Objects

ncvreg.basesurv()

Breslow Baseline Hazard Estimator for ncvreg Objects

ncvreg.survcurve()

Survival Curve Prediction for ncvreg Objects

hdnom-package

Benchmarking and Visualization Toolkit for Penalized Cox Models

Datasets

Example datasets

smart

Imputed SMART Study Data

smarto

Original SMART Study Data