hdnom: Benchmarking and Visualization Toolkit for Penalized Cox Models
Version 4.8

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 publication2017-03-25 10:58:23 UTC
MaintainerNan Xiao <me@nanx.me>
LicenseGPL-3 | file LICENSE
Version4.8
URL https://hdnom.org https://github.com/road2stat/hdnom http://hdnom.io
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("hdnom")

Getting started

Package overview
README.md
An Introduction to hdnom

Popular man pages

glmnet.basesurv: Breslow Baseline Hazard Estimator for glmnet Objects
glmnet.external.calibrate.internal.pred: Compute glmnet Predicted Survival Probabilities for External...
glmnet.survcurve: Survival Curve Prediction for glmnet Objects
glmnet.tune.alpha: Automatic alpha tuning function by k-fold cross-validation
hdcox.aenet: Adaptive Elastic-Net Model Selection for High-Dimensional Cox...
hdnom.validate: Validate High-Dimensional Cox Models with Time-Dependent AUC
palette.jco: Color Palette for Journal of Clinical Oncology (JCO)
See all...

All man pages Function index File listing

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

Functions

glmnet.basesurv Man page Source code
glmnet.calibrate.internal.pred Man page Source code
glmnet.external.calibrate.internal.pred Man page Source code
glmnet.external.validate.internal Man page Source code
glmnet.survcurve Man page Source code
glmnet.tune.alpha Man page Source code
glmnet.validate.internal Man page Source code
hdcox.aenet Man page Source code
hdcox.alasso Man page Source code
hdcox.enet Man page Source code
hdcox.flasso Man page Source code
hdcox.lasso Man page Source code
hdcox.mcp Man page Source code
hdcox.mnet Man page Source code
hdcox.scad Man page Source code
hdcox.snet Man page Source code
hdnom-package Man page
hdnom.calibrate Man page Source code
hdnom.calibrate.internal.true Man page Source code
hdnom.compare.calibrate Man page Source code
hdnom.compare.validate Man page Source code
hdnom.external.calibrate Man page Source code
hdnom.external.calibrate.internal.true Man page Source code
hdnom.external.validate Man page Source code
hdnom.kmplot Man page Source code
hdnom.logrank Man page Source code
hdnom.nomogram Man page Source code
hdnom.validate Man page Source code
hdnom.varinfo Man page Source code
kmplot Man page Source code
ncvreg.basesurv Man page Source code
ncvreg.calibrate.internal.pred Man page Source code
ncvreg.external.calibrate.internal.pred Man page Source code
ncvreg.external.validate.internal Man page Source code
ncvreg.survcurve Man page Source code
ncvreg.tune.gamma Man page Source code
ncvreg.tune.gamma.alpha Man page Source code
ncvreg.validate.internal Man page Source code
palette.aaas Man page Source code
palette.jco Man page Source code
palette.lancet Man page Source code
palette.npg Man page Source code
penalized.basesurv Man page Source code
penalized.calibrate.internal.pred Man page Source code
penalized.external.calibrate.internal.pred Man page Source code
penalized.external.validate.internal Man page Source code
penalized.survcurve Man page Source code
penalized.tune.lambda Man page Source code
penalized.validate.internal Man page Source code
plot.hdnom.calibrate Man page Source code
plot.hdnom.compare.calibrate Man page Source code
plot.hdnom.compare.validate Man page Source code
plot.hdnom.external.calibrate Man page Source code
plot.hdnom.external.validate Man page Source code
plot.hdnom.nomogram Man page Source code
plot.hdnom.validate Man page Source code
predict.hdcox.model Man page Source code
print.hdcox.model Man page Source code
print.hdnom.calibrate Man page Source code
print.hdnom.compare.calibrate Man page Source code
print.hdnom.compare.validate Man page Source code
print.hdnom.external.calibrate Man page Source code
print.hdnom.external.validate Man page Source code
print.hdnom.nomogram Man page Source code
print.hdnom.validate Man page Source code
smart Man page
smarto Man page
summary.hdnom.calibrate Man page Source code
summary.hdnom.compare.calibrate Man page Source code
summary.hdnom.compare.validate Man page Source code
summary.hdnom.external.calibrate Man page Source code
summary.hdnom.external.validate Man page Source code
summary.hdnom.validate Man page Source code

Files

TODO
inst
inst/CITATION
inst/doc
inst/doc/hdnom.R
inst/doc/hdnom.html
inst/doc/hdnom.Rmd
NAMESPACE
NEWS.md
data
data/smarto.rda
data/smart.rda
R
R/03-hdnom-validate.R
R/05-hdnom-external-validate.R
R/08-hdnom-logrank.R
R/11-hdnom-color-palette.R
R/07-hdnom-kmplot.R
R/02-hdnom-nomogram.R
R/04-hdnom-calibrate.R
R/hdnom-package.R
R/10-hdnom-compare-calibrate.R
R/hdnom-datalist.R
R/06-hdnom-external-calibrate.R
R/09-hdnom-compare-validate.R
R/01-hdnom-models.R
vignettes
vignettes/header.html
vignettes/fit.rds
vignettes/hdnom.bib
vignettes/hdnom.Rmd
vignettes/hdnom.css
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/summary.hdnom.compare.calibrate.Rd
man/print.hdnom.nomogram.Rd
man/hdnom.calibrate.Rd
man/ncvreg.basesurv.Rd
man/print.hdnom.calibrate.Rd
man/print.hdnom.validate.Rd
man/ncvreg.validate.internal.Rd
man/hdnom.compare.validate.Rd
man/glmnet.survcurve.Rd
man/print.hdnom.external.calibrate.Rd
man/penalized.basesurv.Rd
man/hdnom.logrank.Rd
man/penalized.calibrate.internal.pred.Rd
man/hdcox.scad.Rd
man/plot.hdnom.validate.Rd
man/hdnom-package.Rd
man/hdcox.enet.Rd
man/print.hdnom.compare.validate.Rd
man/glmnet.external.calibrate.internal.pred.Rd
man/hdnom.validate.Rd
man/glmnet.basesurv.Rd
man/smart.Rd
man/hdnom.varinfo.Rd
man/penalized.validate.internal.Rd
man/glmnet.calibrate.internal.pred.Rd
man/print.hdcox.model.Rd
man/glmnet.validate.internal.Rd
man/hdcox.snet.Rd
man/penalized.tune.lambda.Rd
man/smarto.Rd
man/penalized.external.validate.internal.Rd
man/plot.hdnom.calibrate.Rd
man/summary.hdnom.validate.Rd
man/ncvreg.external.validate.internal.Rd
man/hdcox.lasso.Rd
man/hdnom.external.validate.Rd
man/glmnet.tune.alpha.Rd
man/plot.hdnom.nomogram.Rd
man/summary.hdnom.compare.validate.Rd
man/penalized.survcurve.Rd
man/print.hdnom.external.validate.Rd
man/palette.npg.Rd
man/predict.hdcox.model.Rd
man/ncvreg.tune.gamma.Rd
man/print.hdnom.compare.calibrate.Rd
man/hdcox.aenet.Rd
man/plot.hdnom.external.validate.Rd
man/plot.hdnom.compare.validate.Rd
man/ncvreg.external.calibrate.internal.pred.Rd
man/kmplot.Rd
man/ncvreg.calibrate.internal.pred.Rd
man/hdcox.flasso.Rd
man/summary.hdnom.external.calibrate.Rd
man/palette.jco.Rd
man/summary.hdnom.calibrate.Rd
man/palette.aaas.Rd
man/hdcox.mnet.Rd
man/ncvreg.tune.gamma.alpha.Rd
man/glmnet.external.validate.internal.Rd
man/ncvreg.survcurve.Rd
man/hdcox.mcp.Rd
man/hdnom.compare.calibrate.Rd
man/hdnom.external.calibrate.Rd
man/penalized.external.calibrate.internal.pred.Rd
man/summary.hdnom.external.validate.Rd
man/plot.hdnom.compare.calibrate.Rd
man/hdnom.calibrate.internal.true.Rd
man/palette.lancet.Rd
man/hdnom.external.calibrate.internal.true.Rd
man/hdcox.alasso.Rd
man/hdnom.kmplot.Rd
man/hdnom.nomogram.Rd
man/plot.hdnom.external.calibrate.Rd
LICENSE
hdnom documentation built on May 19, 2017, 11:42 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.