pROC v1.16.1

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Display and Analyze ROC Curves

Tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). (Partial) area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.

pROC

An R package to display and analyze ROC curves.

1. 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
2. The official web page on ExPaSy
3. The CRAN page
4. My blog
5. The FAQ

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:

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 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,
R CMD build pROC
RUN_SLOW_TESTS=true R CMD check pROC_$VERSION.tar.gz  vdiffr The vdiffr package is used for visual tests of plots. To run all the test cases (incl. slow ones) from the command line: run_slow_tests <- TRUE vdiffr::manage_cases()  To run the checks upon R CMD check, set environment variable NOT_CRAN=1: NOT_CRAN=1 RUN_SLOW_TESTS=true R CMD check pROC_$VERSION.tar.gz


Release steps

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

Functions in pROC

 Name Description aSAH Subarachnoid hemorrhage data are.paired Are two ROC curves paired? ci.thresholds Compute the confidence interval of thresholds coords Coordinates of a ROC curve ggroc.roc Plot a ROC curve with ggplot2 groupGeneric pROC Group Generic Functions has.partial.auc Does the ROC curve have a partial AUC? lines.roc Add a ROC line to a ROC plot multiclass.roc Multi-class AUC pROC-package pROC coords_transpose Transposing the output of coords cov.roc Covariance of two paired ROC curves plot.ci Plot confidence intervals plot.roc Plot a ROC curve power.roc.test Sample size and power computation for ROC curves smooth Smooth a ROC curve print Print a ROC curve object roc Build a ROC curve roc.test Compare the AUC of two ROC curves var.roc Variance of a ROC curve ci.sp Compute the confidence interval of specificities at given sensitivities ci.coords Compute the confidence interval of arbitrary coordinates ci Compute the confidence interval of a ROC curve ci.auc Compute the confidence interval of the AUC ci.se Compute the confidence interval of sensitivities at given specificities auc Compute the area under the ROC curve No Results!

Details

 Type Package Date 2020-01-13 Encoding UTF-8 LinkingTo Rcpp License GPL (>= 3) URL http://expasy.org/tools/pROC/ BugReports https://github.com/xrobin/pROC/issues LazyData yes NeedsCompilation yes Packaged 2020-01-13 19:34:51 UTC; xavier Repository CRAN Date/Publication 2020-01-14 10:00:02 UTC
 suggests doParallel , ggplot2 , logcondens , MASS , microbenchmark , tcltk , testthat , vdiffr imports methods , plyr , Rcpp (>= 0.11.1) depends R (>= 2.14) Contributors Stefan Siegert, Natacha Turck, Alexandre Hainard, Natalia Tiberti, Jean-Charles Sanchez, Frdrique Lisacek, Markus Mller, Matthias Doering