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hdnom

hdnom creates nomogram visualizations for penalized Cox regression models, with the support of reproducible survival model building, validation, calibration, and comparison for high-dimensional data.

Installation

To download and install hdnom from CRAN:

install.packages("hdnom")

Or try the development version on GitHub:

# install.packages("devtools")
devtools::install_github("nanxstats/hdnom")

Browse the vignettes to start.

Gallery

Nomogram Visualization / Kaplan-Meier Plot with Number at Risk Table

Model Validation / Model Calibration

Model Comparison by Validation / Calibration

Links

Contribute

To contribute to this project, please take a look at the Contributing Guidelines first. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

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Version

Install

install.packages('hdnom')

Monthly Downloads

552

Version

6.0.0

License

GPL-3 | file LICENSE

Issues

1

Pull Requests

0

Stars

46

Forks

11

Maintainer

Nan Xiao

Last Published

June 23rd, 2019

Functions in hdnom (6.0.0)

ncvreg_calibrate_external_surv_prob_pred

Compute ncvreg predicted survival probabilities for external calibration
palette_jco

Color Palette for Journal of Clinical Oncology (JCO)
ncvreg_basesurv

Breslow baseline hazard estimator for ncvreg objects
palette_aaas

Color Palette for AAAS Journals
ncvreg_calibrate_surv_prob_pred

Compute ncvreg predicted survival probabilities for calibration
summary.hdnom.compare.validate

Summary of model comparison by validation results
plot.hdnom.validate

Plot optimism-corrected time-dependent discrimination curves for validation
plot.hdnom.validate.external

Plot time-dependent discrimination curves for external validation
ncvreg_survcurve

Survival curve prediction for ncvreg objects
summary.hdnom.validate

Summary of validation results
plot.hdnom.calibrate.external

Plot external calibration results
plot.hdnom.compare.calibrate

Plot model comparison by calibration results
print.hdnom.calibrate

Print calibration results
predict.hdnom.model

Make predictions from high-dimensional Cox models
calibrate_surv_prob_true

Compute Kaplan-Meier estimated survival probabilities for calibration
fit_enet

Model selection for high-dimensional Cox models with elastic-net penalty
fit_alasso

Model selection for high-dimensional Cox models with adaptive lasso penalty
infer_variable_type

Extract information of selected variables from high-dimensional Cox models
glmnet_basesurv

Breslow baseline hazard estimator for glmnet objects
glmnet_calibrate_external_surv_prob_pred

Compute glmnet predicted survival probabilities for external calibration
kmplot

Kaplan-Meier plot with number at risk table for internal calibration and external calibration results
palette_lancet

Color Palette for Lancet Journals
fit_aenet

Model selection for high-dimensional Cox models with adaptive elastic-net penalty
compare_by_validate

Compare high-dimensional Cox models by model validation
as_nomogram

Construct nomogram ojects for high-dimensional Cox models
calibrate

Calibrate high-dimensional Cox models
print.hdnom.calibrate.external

Print external calibration results
penalized_calibrate_surv_prob_pred

Compute penfit predicted survival probabilities for calibration
palette_npg

Color Palette for NPG Journals
fit_mnet

Model selection for high-dimensional Cox models with Mnet penalty
penalized_survcurve

Survival curve prediction for penfit objects
fit_mcp

Model selection for high-dimensional Cox models with MCP penalty
compare_by_calibrate

Compare high-dimensional Cox models by model calibration
logrank_test

Log-rank test for internal calibration and external calibration results
kmplot_raw

Kaplan-Meier Plot with Number at Risk Table
fit_scad

Model selection for high-dimensional Cox models with SCAD penalty
penalized_calibrate_external_surv_prob_pred

Compute penfit predicted survival probabilities for external calibration
penalized_basesurv

Breslow baseline hazard estimator for penfit objects
fit_flasso

Model selection for high-dimensional Cox models with fused lasso penalty
print.hdnom.compare.calibrate

Print model comparison by calibration results
summary.hdnom.compare.calibrate

Summary of model comparison by calibration results
summary.hdnom.calibrate.external

Summary of external calibration results
smart

Imputed SMART study data
fit_lasso

Model selection for high-dimensional Cox models with lasso penalty
print.hdnom.validate.external

Print external validation results
validate

Validate high-dimensional Cox models with time-dependent AUC
glmnet_validate_tauc

Compute validation measures for glmnet objects
fit_snet

Model selection for high-dimensional Cox models with Snet penalty
hdnom-package

hdnom: Benchmarking and Visualization Toolkit for Penalized Cox Models
ncvreg_validate_external_tauc

Compute external validation measures for ncvreg model objects
glmnet_validate_external_tauc

Compute external validation measures for glmnet objects
glmnet_tune_alpha

Automatic alpha tuning function by k-fold cross-validation
penalized_tune_lambda

Automatic lambda tuning function for fused lasso by k-fold cross-validation
ncvreg_validate_tauc

Compute validation measures for ncvreg model objects
validate_external

Externally validate high-dimensional Cox models with time-dependent AUC
ncvreg_tune_gamma

Automatic MCP/SCAD gamma tuning function by k-fold cross-validation
ncvreg_tune_gamma_alpha

Automatic Mnet/Snet gamma and alpha tuning function by k-fold cross-validation
plot.hdnom.calibrate

Plot calibration results
penalized_validate_tauc

Compute validation measures for penfit model objects
penalized_validate_external_tauc

Compute external validation measures for penfit model objects
plot.hdnom.nomogram

Plot nomogram objects
smarto

Original SMART study data
plot.hdnom.compare.validate

Plot model comparison by validation results
print.hdnom.model

Print high-dimensional Cox model objects
print.hdnom.compare.validate

Print model comparison by validation results
print.hdnom.nomogram

Print nomograms objects
summary.hdnom.validate.external

Summary of external validation results
summary.hdnom.calibrate

Summary of calibration results
theme_hdnom

Plot theme (ggplot2) for hdnom
print.hdnom.validate

Print validation results
calibrate_external

Externally calibrate high-dimensional Cox models
calibrate_external_surv_prob_true

Compute Kaplan-Meier estimated survival probabilities for external calibration
glmnet_calibrate_surv_prob_pred

Compute glmnet predicted survival probabilities for calibration
glmnet_survcurve

Survival curve prediction for glmnet objects