hdnom: Benchmarking and Visualization Toolkit for Penalized Cox Models

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

AuthorNan Xiao [aut, cre], Qingsong Xu [aut], Miaozhu Li [aut]
Date of publication2017-01-08 12:02:12
MaintainerNan Xiao <me@nanx.me>
LicenseGPL-3 | file LICENSE
Version4.6
http://hdnom.org
https://github.com/road2stat/hdnom, http://hdnom.io

View on CRAN

Man pages

glmnet.basesurv: Breslow Baseline Hazard Estimator for glmnet Objects

glmnet.calibrate.internal.pred: Compute glmnet Predicted Survival Probabilities for...

glmnet.external.calibrate.internal.pred: Compute glmnet Predicted Survival Probabilities for External...

glmnet.external.validate.internal: Compute External Validation Measures for glmnet Objects

glmnet.survcurve: Survival Curve Prediction for glmnet Objects

glmnet.tune.alpha: Automatic alpha tuning function by k-fold cross-validation

glmnet.validate.internal: Compute Validation Measures for glmnet Objects

hdcox.aenet: Adaptive Elastic-Net Model Selection for High-Dimensional Cox...

hdcox.alasso: Adaptive Lasso Model Selection for High-Dimensional Cox...

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

hdnom.calibrate: Calibrate High-Dimensional Cox Models

hdnom.calibrate.internal.true: Compute Kaplan-Meier Estimated Survival Probabilities for...

hdnom.compare.calibrate: Compare High-Dimensional Cox Models by Model Calibration

hdnom.compare.validate: Compare High-Dimensional Cox Models by Model Validation

hdnom.external.calibrate: Externally Calibrate High-Dimensional Cox Models

hdnom.external.calibrate.internal.true: Compute Kaplan-Meier Estimated Survival Probabilities for...

hdnom.external.validate: Externally Validate High-Dimensional Cox Models with...

hdnom.kmplot: Kaplan-Meier Plot with Number at Risk Table for Internal...

hdnom.logrank: Log-Rank Test for Internal Calibration and External...

hdnom.nomogram: Nomograms for High-Dimensional Cox Models

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

hdnom.validate: Validate High-Dimensional Cox Models with Time-Dependent AUC

hdnom.varinfo: Extract Information of Selected Variables from...

kmplot: Kaplan-Meier Plot with Number at Risk Table

ncvreg.basesurv: Breslow Baseline Hazard Estimator for ncvreg Objects

ncvreg.calibrate.internal.pred: Compute ncvreg Predicted Survival Probabilities for...

ncvreg.external.calibrate.internal.pred: Compute ncvreg Predicted Survival Probabilities for External...

ncvreg.external.validate.internal: Compute External Validation Measures for ncvreg Model Objects

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.internal: 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 "penalized" Objects

penalized.calibrate.internal.pred: Compute "penalized" Predicted Survival Probabilities for...

penalized.external.calibrate.internal.pred: Compute "penalized" Predicted Survival Probabilities for...

penalized.external.validate.internal: Compute External Validation Measures for "penalized" Model...

penalized.survcurve: Survival Curve Prediction for "penalized" Objects

penalized.tune.lambda: Automatic lambda tuning function for fused lasso by k-fold...

penalized.validate.internal: Compute Validation Measures for "penalized" Model Objects

plot.hdnom.calibrate: Plot Calibration Results

plot.hdnom.compare.calibrate: Plot Model Comparison by Calibration Results

plot.hdnom.compare.validate: Plot Model Comparison by Validation Results

plot.hdnom.external.calibrate: Plot External Calibration Results

plot.hdnom.external.validate: Plot Time-Dependent Discrimination Curves for External...

plot.hdnom.nomogram: Plot Nomogram Objects Generated by hdnom.nomogram

plot.hdnom.validate: Plot Optimism-Corrected Time-Dependent Discrimination Curves...

predict.hdcox.model: Make Predictions from High-Dimensional Cox Models

print.hdcox.model: Print High-Dimensional Cox Model Objects

print.hdnom.calibrate: Print Calibration Results

print.hdnom.compare.calibrate: Print Model Comparison by Calibration Results

print.hdnom.compare.validate: Print Model Comparison by Validation Results

print.hdnom.external.calibrate: Print External Calibration Results

print.hdnom.external.validate: Print External Validation Results

print.hdnom.nomogram: Print Nomograms Objects Generated by hdnom.nomogram

print.hdnom.validate: Print Validation Results

smart: Imputed SMART Study Data

smarto: Original SMART Study Data

summary.hdnom.calibrate: Summary of 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.external.calibrate: Summary of External Calibration Results

summary.hdnom.external.validate: Summary of External Validation Results

summary.hdnom.validate: Summary of Validation Results

Files in this package

hdnom
hdnom/TODO
hdnom/inst
hdnom/inst/CITATION
hdnom/inst/doc
hdnom/inst/doc/hdnom.R
hdnom/inst/doc/hdnom.html
hdnom/inst/doc/hdnom.Rmd
hdnom/NAMESPACE
hdnom/NEWS.md
hdnom/data
hdnom/data/smarto.rda
hdnom/data/smart.rda
hdnom/R
hdnom/R/03-hdnom-validate.R hdnom/R/05-hdnom-external-validate.R hdnom/R/08-hdnom-logrank.R hdnom/R/11-hdnom-color-palette.R hdnom/R/07-hdnom-kmplot.R hdnom/R/02-hdnom-nomogram.R hdnom/R/04-hdnom-calibrate.R hdnom/R/hdnom-package.R hdnom/R/10-hdnom-compare-calibrate.R hdnom/R/hdnom-datalist.R hdnom/R/06-hdnom-external-calibrate.R hdnom/R/09-hdnom-compare-validate.R hdnom/R/01-hdnom-models.R
hdnom/vignettes
hdnom/vignettes/header.html
hdnom/vignettes/fit.rds
hdnom/vignettes/hdnom.bib
hdnom/vignettes/hdnom.Rmd
hdnom/vignettes/hdnom.css
hdnom/README.md
hdnom/MD5
hdnom/build
hdnom/build/vignette.rds
hdnom/DESCRIPTION
hdnom/man
hdnom/man/summary.hdnom.compare.calibrate.Rd hdnom/man/print.hdnom.nomogram.Rd hdnom/man/hdnom.calibrate.Rd hdnom/man/ncvreg.basesurv.Rd hdnom/man/print.hdnom.calibrate.Rd hdnom/man/print.hdnom.validate.Rd hdnom/man/ncvreg.validate.internal.Rd hdnom/man/hdnom.compare.validate.Rd hdnom/man/glmnet.survcurve.Rd hdnom/man/print.hdnom.external.calibrate.Rd hdnom/man/penalized.basesurv.Rd hdnom/man/hdnom.logrank.Rd hdnom/man/penalized.calibrate.internal.pred.Rd hdnom/man/hdcox.scad.Rd hdnom/man/plot.hdnom.validate.Rd hdnom/man/hdnom-package.Rd hdnom/man/hdcox.enet.Rd hdnom/man/print.hdnom.compare.validate.Rd hdnom/man/glmnet.external.calibrate.internal.pred.Rd hdnom/man/hdnom.validate.Rd hdnom/man/glmnet.basesurv.Rd hdnom/man/smart.Rd hdnom/man/hdnom.varinfo.Rd hdnom/man/penalized.validate.internal.Rd hdnom/man/glmnet.calibrate.internal.pred.Rd hdnom/man/print.hdcox.model.Rd hdnom/man/glmnet.validate.internal.Rd hdnom/man/hdcox.snet.Rd hdnom/man/penalized.tune.lambda.Rd hdnom/man/smarto.Rd hdnom/man/penalized.external.validate.internal.Rd hdnom/man/plot.hdnom.calibrate.Rd hdnom/man/summary.hdnom.validate.Rd hdnom/man/ncvreg.external.validate.internal.Rd hdnom/man/hdcox.lasso.Rd hdnom/man/hdnom.external.validate.Rd hdnom/man/glmnet.tune.alpha.Rd hdnom/man/plot.hdnom.nomogram.Rd hdnom/man/summary.hdnom.compare.validate.Rd hdnom/man/penalized.survcurve.Rd hdnom/man/print.hdnom.external.validate.Rd hdnom/man/palette.npg.Rd hdnom/man/predict.hdcox.model.Rd hdnom/man/ncvreg.tune.gamma.Rd hdnom/man/print.hdnom.compare.calibrate.Rd hdnom/man/hdcox.aenet.Rd hdnom/man/plot.hdnom.external.validate.Rd hdnom/man/plot.hdnom.compare.validate.Rd hdnom/man/ncvreg.external.calibrate.internal.pred.Rd hdnom/man/kmplot.Rd hdnom/man/ncvreg.calibrate.internal.pred.Rd hdnom/man/hdcox.flasso.Rd hdnom/man/summary.hdnom.external.calibrate.Rd hdnom/man/palette.jco.Rd hdnom/man/summary.hdnom.calibrate.Rd hdnom/man/palette.aaas.Rd hdnom/man/hdcox.mnet.Rd hdnom/man/ncvreg.tune.gamma.alpha.Rd hdnom/man/glmnet.external.validate.internal.Rd hdnom/man/ncvreg.survcurve.Rd hdnom/man/hdcox.mcp.Rd hdnom/man/hdnom.compare.calibrate.Rd hdnom/man/hdnom.external.calibrate.Rd hdnom/man/penalized.external.calibrate.internal.pred.Rd hdnom/man/summary.hdnom.external.validate.Rd hdnom/man/plot.hdnom.compare.calibrate.Rd hdnom/man/hdnom.calibrate.internal.true.Rd hdnom/man/palette.lancet.Rd hdnom/man/hdnom.external.calibrate.internal.true.Rd hdnom/man/hdcox.alasso.Rd hdnom/man/hdnom.kmplot.Rd hdnom/man/hdnom.nomogram.Rd hdnom/man/plot.hdnom.external.calibrate.Rd
hdnom/LICENSE

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