hdnom: Nomograms for High-Dimensional Cox Models

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Build nomograms for high-dimensional Cox models, with support for reproducible model validation, calibration, and comparison.

Author
Miaozhu Li <miaozhu.li@duke.edu>, Nan Xiao <me@nanx.me>
Date of publication
2016-10-22 12:17:34
Maintainer
Nan Xiao <me@nanx.me>
License
GPL
Version
4.2
URLs

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
Nomograms for High-Dimensional Data with Penalized Cox Models
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.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/1.hdnom.models.R
hdnom/R/2.hdnom.nomogram.R
hdnom/R/11.hdnom.color.palette.R
hdnom/R/8.hdnom.logrank.R
hdnom/R/7.hdnom.kmplot.R
hdnom/R/4.hdnom.calibrate.R
hdnom/R/hdnom-package.R
hdnom/R/3.hdnom.validate.R
hdnom/R/hdnom-datalist.R
hdnom/R/5.hdnom.external.validate.R
hdnom/R/9.hdnom.compare.validate.R
hdnom/R/10.hdnom.compare.calibrate.R
hdnom/R/6.hdnom.external.calibrate.R
hdnom/vignettes
hdnom/vignettes/header.html
hdnom/vignettes/hdnom.bib
hdnom/vignettes/aenetfit.rds
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/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