Benchmarking and Visualization Toolkit for Penalized Cox Models

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Documentation for package ‘hdnom’ version 6.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

as_nomogram	Construct nomogram ojects for high-dimensional Cox models
calibrate	Calibrate high-dimensional Cox models
calibrate_external	Externally calibrate high-dimensional Cox models
compare_by_calibrate	Compare high-dimensional Cox models by model calibration
compare_by_validate	Compare high-dimensional Cox models by model validation
fit_aenet	Model selection for high-dimensional Cox models with adaptive elastic-net penalty
fit_alasso	Model selection for high-dimensional Cox models with adaptive lasso penalty
fit_enet	Model selection for high-dimensional Cox models with elastic-net penalty
fit_flasso	Model selection for high-dimensional Cox models with fused lasso penalty
fit_lasso	Model selection for high-dimensional Cox models with lasso penalty
fit_mcp	Model selection for high-dimensional Cox models with MCP penalty
fit_mnet	Model selection for high-dimensional Cox models with Mnet penalty
fit_scad	Model selection for high-dimensional Cox models with SCAD penalty
fit_snet	Model selection for high-dimensional Cox models with Snet penalty
glmnet_basesurv	Breslow baseline hazard estimator for glmnet objects
glmnet_survcurve	Survival curve prediction for glmnet objects
infer_variable_type	Extract information of selected variables from high-dimensional Cox models
kmplot	Kaplan-Meier plot with number at risk table for internal calibration and external calibration results
logrank_test	Log-rank test for internal calibration and external calibration results
ncvreg_basesurv	Breslow baseline hazard estimator for ncvreg objects
ncvreg_survcurve	Survival curve prediction for ncvreg objects
penalized_basesurv	Breslow baseline hazard estimator for penfit objects
penalized_survcurve	Survival curve prediction for penfit objects
plot.hdnom.calibrate	Plot calibration results
plot.hdnom.calibrate.external	Plot external calibration results
plot.hdnom.compare.calibrate	Plot model comparison by calibration results
plot.hdnom.compare.validate	Plot model comparison by validation results
plot.hdnom.nomogram	Plot nomogram objects
plot.hdnom.validate	Plot optimism-corrected time-dependent discrimination curves for validation
plot.hdnom.validate.external	Plot time-dependent discrimination curves for external validation
predict.hdnom.model	Make predictions from high-dimensional Cox models
print.hdnom.calibrate	Print calibration results
print.hdnom.calibrate.external	Print external calibration results
print.hdnom.compare.calibrate	Print model comparison by calibration results
print.hdnom.compare.validate	Print model comparison by validation results
print.hdnom.model	Print high-dimensional Cox model objects
print.hdnom.nomogram	Print nomograms objects
print.hdnom.validate	Print validation results
print.hdnom.validate.external	Print external validation results
smart	Imputed SMART study data
smarto	Original SMART study data
summary.hdnom.calibrate	Summary of calibration results
summary.hdnom.calibrate.external	Summary of external calibration results
summary.hdnom.compare.calibrate	Summary of model comparison by calibration results
summary.hdnom.compare.validate	Summary of model comparison by validation results
summary.hdnom.validate	Summary of validation results
summary.hdnom.validate.external	Summary of external validation results
theme_hdnom	Plot theme (ggplot2) for hdnom
validate	Validate high-dimensional Cox models with time-dependent AUC
validate_external	Externally validate high-dimensional Cox models with time-dependent AUC