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pROC

AnR package to display andanalyze ROC curves.

For more information, see:

1. Xavier Robin, Natacha Turck, Alexandre Hainard,et al.(2011) “pROC: an open-source package for R and S+ to analyze and compareROC curves”.BMC Bioinformatics,7, 77. DOI:10.1186/1471-2105-12-77
2. The official webpage
3. The CRANpage
4. My blog
5. TheFAQ

Stable

The latest stable version is best installed from the CRAN:

install.packages("pROC")

Getting started

If you don’t want to read the manual first, try the following:

Loading

library(pROC)data(aSAH)

Basic ROC / AUC analysis

roc(aSAH$outcome, aSAH$s100b)roc(outcome~ s100b, aSAH)

Smoothing

roc(outcome~ s100b, aSAH,smooth=TRUE)

more options, CI and plotting

roc1<-roc(aSAH$outcome,            aSAH$s100b,percent=TRUE,# arguments for aucpartial.auc=c(100,90),partial.auc.correct=TRUE,partial.auc.focus="sens",# arguments for cici=TRUE,boot.n=100,ci.alpha=0.9,stratified=FALSE,# arguments for plotplot=TRUE,auc.polygon=TRUE,max.auc.polygon=TRUE,grid=TRUE,print.auc=TRUE,show.thres=TRUE)# Add to an existing plot. Beware of 'percent' specification!    roc2<-roc(aSAH$outcome, aSAH$wfns,plot=TRUE,add=TRUE,percent=roc1$percent)

Coordinates of the curve

coords(roc1,"best",ret=c("threshold","specificity","1-npv"))coords(roc2,"local maximas",ret=c("threshold","sens","spec","ppv","npv"))

Confidence intervals

# Of the AUCci(roc2)# Of the curvesens.ci<-ci.se(roc1,specificities=seq(0,100,5))plot(sens.ci,type="shape",col="lightblue")plot(sens.ci,type="bars")# need to re-add roc2 over the shapeplot(roc2,add=TRUE)# CI of thresholdsplot(ci.thresholds(roc2))

Comparisons

# Test on the whole AUCroc.test(roc1, roc2,reuse.auc=FALSE)# Test on a portion of the whole AUCroc.test(roc1, roc2,reuse.auc=FALSE,partial.auc=c(100,90),partial.auc.focus="se",partial.auc.correct=TRUE)# With modified bootstrap parametersroc.test(roc1, roc2,reuse.auc=FALSE,partial.auc=c(100,90),partial.auc.correct=TRUE,boot.n=1000,boot.stratified=FALSE)

Sample size

# Two ROC curvespower.roc.test(roc1, roc2,reuse.auc=FALSE)power.roc.test(roc1, roc2,power=0.9,reuse.auc=FALSE)# One ROC curvepower.roc.test(auc=0.8,ncases=41,ncontrols=72)power.roc.test(auc=0.8,power=0.9)power.roc.test(auc=0.8,ncases=41,ncontrols=72,sig.level=0.01)power.roc.test(ncases=41,ncontrols=72,power=0.9)

Getting Help

• Type?pROC on the R command line
• Make sure you’vereadthe FAQ
• Search forquestionstagged with pROC-R-package on Stack Overflow

If you still can’t find an answer, you can:

• Ask aquestion on Stack Overflow with the pROC-r-package tag
• Bug reports shouldbe submitted to the GitHub issue tracker

Development

Installing the developmentversion

Download the source code from git, unzip it if necessary, and thentypeR CMD INSTALL pROC. Alternatively, you can use thedevtools package byHadley Wickham to automate the process(make sure you followthe fullinstructions to get started):

if (!requireNamespace("devtools"))install.packages("devtools")devtools::install_github("xrobin/pROC@develop")

Check

To run all automated tests and R checks, including slow tests:

cd .. # Run from parent directoryVERSION=$(grep Version pROC/DESCRIPTION | sed "s/.\+ //")R CMD build pROCRUN_SLOW_TESTS=true R CMD check pROC_$VERSION.tar.gz

Or from an R command prompt with devtools:

devtools::check()

Tests

To run automated tests only from an R command prompt:

run_slow_tests <- TRUE  # Optional, include slow testsdevtools::test()

vdiffr

Thevdiffr package isused for visual tests of plots.

To run all the test cases (incl. slow ones) from the commandline:

run_slow_tests<-TRUEdevtools::test()# Must run the new teststestthat::snapshot_review()

To run the checks upon R CMD check, set environment variableNOT_CRAN=1:

NOT_CRAN=1 RUN_SLOW_TESTS=true R CMD check pROC_$VERSION.tar.gz

AppVeyor Build Cache

By default, AppVeyor stores a build cache containing installeddependencies. Sometimes you want to clean the cache, for instance if aGraphics API versionmismatch occurs on R-devel, indicatingthatggplot2 was built with a previous version of R. Forthis you need the AppVeyorAPI key to make aDELETE request:

export APPVEYOR_TOKEN="<your-api-token>"curl-H"Authorization: Bearer $APPVEYOR_TOKEN"-H"Content-Type: application/json"-X DELETE https://ci.appveyor.com/api/projects/xrobin/pROC/buildcache

Release steps

1. UpdateVersion andDate inDESCRIPTION
2. Update version and date inNEWS
3. Get new version to release:VERSION=$(grep Version pROC/DESCRIPTION | sed "s/.\+ //") && echo $VERSION
4. Build & check package:R CMD build pROC && R CMD check --as-cran pROC_$VERSION.tar.gz
5. Check with slow tests:NOT_CRAN=1 RUN_SLOW_TESTS=true R CMD check pROC_$VERSION.tar.gz
6. Check with R-devel:rhub::check_for_cran()
7. Check reverse dependencies:revdepcheck::revdep_check(num_workers=8, timeout = as.difftime(60, units = "mins"))
8. Merge into master:git checkout master && git merge develop
9. Create a tag on master:git tag v$VERSION && git push --tags
10. Submit toCRAN