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An R package to display and analyze ROC curves.
For more information, see:
- Xavier Robin, Natacha Turck, Alexandre Hainard, et al. (2011) "pROC: an open-source package for R and S+ to analyze and compare ROC curves". BMC Bioinformatics, 7, 77. DOI: 10.1186/1471-2105-12-77
- The official web page
- The CRAN page
- My blog
- The FAQ
The latest stable version is best installed from the CRAN:
install.packages("pROC")
If you don't want to read the manual first, try the following:
library(pROC) data(aSAH)
roc(aSAH$outcome, aSAH$s100b) roc(outcome ~ s100b, aSAH)
roc(outcome ~ s100b, aSAH, smooth=TRUE)
roc1 <- roc(aSAH$outcome, aSAH$s100b, percent=TRUE, # arguments for auc partial.auc=c(100, 90), partial.auc.correct=TRUE, partial.auc.focus="sens", # arguments for ci ci=TRUE, boot.n=100, ci.alpha=0.9, stratified=FALSE, # arguments for plot plot=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$percent)
coords(roc1, "best", ret=c("threshold", "specificity", "1-npv")) coords(roc2, "local maximas", ret=c("threshold", "sens", "spec", "ppv", "npv"))
# Of the AUC ci(roc2) # Of the curve sens.ci <- ci.se(roc1, specificities=seq(0, 100, 5)) plot(sens.ci, type="shape", col="lightblue") plot(sens.ci, type="bars") # need to re-add roc2 over the shape plot(roc2, add=TRUE) # CI of thresholds plot(ci.thresholds(roc2))
# Test on the whole AUC roc.test(roc1, roc2, reuse.auc=FALSE) # Test on a portion of the whole AUC roc.test(roc1, roc2, reuse.auc=FALSE, partial.auc=c(100, 90), partial.auc.focus="se", partial.auc.correct=TRUE) # With modified bootstrap parameters roc.test(roc1, roc2, reuse.auc=FALSE, partial.auc=c(100, 90), partial.auc.correct=TRUE, boot.n=1000, boot.stratified=FALSE)
# Two ROC curves power.roc.test(roc1, roc2, reuse.auc=FALSE) power.roc.test(roc1, roc2, power=0.9, reuse.auc=FALSE) # One ROC curve power.roc.test(auc=0.8, ncases=41, ncontrols=72) power.roc.test(auc=0.8, power=0.9) power.roc.test(auc=0.8, ncases=41, ncontrols=72, sig.level=0.01) power.roc.test(ncases=41, ncontrols=72, power=0.9)
- Type
?pROCon the R command line - Make sure you've read the FAQ
- Search for questions tagged with pROC-R-package on Stack Overflow
If you still can't find an answer, you can:
- Ask a question on Stack Overflow with the pROC-r-package tag
- Bug reports should be submitted to the GitHub issue tracker
Download the source code from git, unzip it if necessary, and then type R CMD INSTALL pROC. Alternatively, you can use the devtools package by Hadley Wickham to automate the process (make sure you follow the full instructions to get started):
if (! requireNamespace("devtools")) install.packages("devtools") devtools::install_github("xrobin/pROC@develop")
To run all automated tests and R checks, including slow tests:
cd .. # Run from parent directory
VERSION=$(grep Version pROC/DESCRIPTION | sed "s/.\+ //")
R CMD build pROC
RUN_SLOW_TESTS=true R CMD check pROC_$VERSION.tar.gz
Or from an R command prompt with devtools:
devtools::check()
To run automated tests only from an R command prompt:
run_slow_tests <- TRUE # Optional, include slow tests
devtools::test()
The vdiffr package is used for visual tests of plots.
To run all the test cases (incl. slow ones) from the command line:
run_slow_tests <- TRUE devtools::test() # Must run the new tests testthat::snapshot_review()
To run the checks upon R CMD check, set environment variable NOT_CRAN=1:
NOT_CRAN=1 RUN_SLOW_TESTS=true R CMD check pROC_$VERSION.tar.gz
By default, AppVeyor stores a build cache containing installed dependencies.
Sometimes you want to clean the cache, for instance if a
Graphics API versionmismatch occurs on R-devel, indicating that ggplot2 was
built with a previous version of R. For this you need the AppVeyor
API key to make a DELETE request:
export APPVEYOR_TOKEN="<your-api-token>" curl -H "Authorization: Bearer $APPVEYOR_TOKEN" -H "Content-Type: application/json" -X DELETE https://ci.appveyor.com/api/projects/xrobin/pROC/buildcache
- Update
VersionandDateinDESCRIPTION - Update version and date in
NEWS - Get new version to release:
VERSION=$(grep Version pROC/DESCRIPTION | sed "s/.\+ //") && echo $VERSION - Build & check package:
R CMD build pROC && R CMD check --as-cran pROC_$VERSION.tar.gz - Check with slow tests:
NOT_CRAN=1 RUN_SLOW_TESTS=true R CMD check pROC_$VERSION.tar.gz - Check with R-devel:
rhub::check_for_cran() - Check reverse dependencies:
revdepcheck::revdep_check(num_workers=8, timeout = as.difftime(60, units = "mins")) - Merge into master:
git checkout master && git merge develop - Create a tag on master:
git tag v$VERSION && git push --tags - Submit to CRAN