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 publication2017-03-25 10:58:23 UTC
MaintainerNan Xiao <me@nanx.me>
LicenseGPL-3 | file LICENSE
Version4.8
https://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

Functions

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

Files

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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