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

Print High-Dimensional Cox Model Objects

predict

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

Plot Nomogram Objects Generated by hdnom.nomogram

print

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

Print Validation Results

print

Print External Validation Results

summary

Summary of Validation Results

summary

Summary of External Validation Results

plot

Plot Optimism-Corrected Time-Dependent Discrimination Curves for Validation

plot

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

Print Calibration Results

print

Print External Calibration Results

summary

Summary of Calibration Results

summary

Summary of External Calibration Results

plot

Plot Calibration Results

plot

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

Print Model Comparison by Validation Results

print

Print Model Comparison by Calibration Results

summary

Summary of Model Comparison by Validation Results

summary

Summary of Model Comparison by Calibration Results

plot

Plot Model Comparison by Validation Results

plot

Plot Model Comparison by Calibration Results

Datasets

Example datasets

data

Imputed SMART Study Data

data

Original SMART Study Data