Benchmarking and Visualization Toolkit for Penalized Cox Models

as_nomogram | Nomograms for high-dimensional Cox models |

calibrate | Calibrate high-dimensional Cox models |

calibrate_external | Externally calibrate high-dimensional Cox models |

calibrate_external_surv_prob_true | Compute Kaplan-Meier estimated survival probabilities for... |

calibrate_surv_prob_true | Compute Kaplan-Meier estimated survival probabilities for... |

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... |

fit_alasso | Model selection for high-dimensional Cox models with adaptive... |

fit_enet | Model selection for high-dimensional Cox models with... |

fit_flasso | Model selection for high-dimensional Cox models with fused... |

fit_lasso | Model selection for high-dimensional Cox models with lasso... |

fit_mcp | Model selection for high-dimensional Cox models with MCP... |

fit_mnet | Model selection for high-dimensional Cox models with Mnet... |

fit_scad | Model selection for high-dimensional Cox models with SCAD... |

fit_snet | Model selection for high-dimensional Cox models with Snet... |

glmnet_basesurv | Breslow baseline hazard estimator for glmnet objects |

glmnet_calibrate_external_surv_prob_pred | Compute glmnet predicted survival probabilities for external... |

glmnet_calibrate_surv_prob_pred | Compute glmnet predicted survival probabilities for... |

glmnet_survcurve | Survival curve prediction for glmnet objects |

glmnet_tune_alpha | Automatic alpha tuning function by k-fold cross-validation |

glmnet_validate_external_tauc | Compute external validation measures for glmnet objects |

glmnet_validate_tauc | Compute validation measures for glmnet objects |

hdnom-package | hdnom: Benchmarking and Visualization Toolkit for Penalized... |

infer_variable_type | Extract information of selected variables from... |

kmplot | Kaplan-Meier plot with number at risk table for internal... |

kmplot_raw | Kaplan-Meier Plot with Number at Risk Table |

logrank_test | Log-rank test for internal calibration and external... |

ncvreg_basesurv | Breslow baseline hazard estimator for ncvreg objects |

ncvreg_calibrate_external_surv_prob_pred | Compute ncvreg predicted survival probabilities for external... |

ncvreg_calibrate_surv_prob_pred | Compute ncvreg predicted survival probabilities for... |

ncvreg_survcurve | Survival curve prediction for ncvreg objects |

ncvreg_tune_gamma | Automatic MCP/SCAD gamma tuning function by k-fold... |

ncvreg_tune_gamma_alpha | Automatic Mnet/Snet gamma and alpha tuning function by k-fold... |

ncvreg_validate_external_tauc | Compute external validation measures for ncvreg model objects |

ncvreg_validate_tauc | Compute validation measures for ncvreg model objects |

palette_aaas | Color Palette for AAAS Journals |

palette_jco | Color Palette for Journal of Clinical Oncology (JCO) |

palette_lancet | Color Palette for Lancet Journals |

palette_npg | Color Palette for NPG Journals |

penalized_basesurv | Breslow baseline hazard estimator for penfit objects |

penalized_calibrate_external_surv_prob_pred | Compute penfit predicted survival probabilities for external... |

penalized_calibrate_surv_prob_pred | Compute penfit predicted survival probabilities for... |

penalized_survcurve | Survival curve prediction for penfit objects |

penalized_tune_lambda | Automatic lambda tuning function for fused lasso by k-fold... |

penalized_validate_external_tauc | Compute external validation measures for penfit model objects |

penalized_validate_tauc | Compute validation measures for penfit model 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... |

plot.hdnom.validate.external | Plot time-dependent discrimination curves for external... |

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 |

validate | Validate high-dimensional Cox models with time-dependent AUC |

validate_external | Externally validate high-dimensional Cox models with... |

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