# pROC 1.6 released

Two years after the last major release 1.5, pROC 1.6 is finally available. It comes with several major enhancements:

- Power ROC tests
- Confidence intervals for arbitrary coordinates
- Speed enhancements
- Dropped S+ support
- Other changes

## Power ROC tests

This is probably the main feature of this version: power tests for ROC curves. It is now possible to compute sample size, power, significance level or minimum AUC with pROC.

library(pROC) data(aSAH) roc1 <- roc(aSAH$outcome, aSAH$ndka) roc2 <- roc(aSAH$outcome, aSAH$wfns) power.roc.test(roc1, roc2, power=0.9)

It is implemented with the methods proposed by Obuchowski and colleagues^{1, 2}, with the added possibility to use bootstrap or the DeLong^{3} method to compute variance and covariances. For more details and examples, see `?power.roc.test`

.

As a side effect, a new `method="obuchowski"`

has been implemented in the `cov`

and `var`

functions. More details in `?var.roc`

and `?cov.roc`

.

## Confidence intervals for arbitrary coordinates

It is now possible to compute confidence intervals of arbitrary coordinates, with a syntax much similar to that of the `coords`

function.

library(pROC) data(aSAH) ci.coords(aSAH$outcome, aSAH$s100b, x="best") # Or for much more information: rets <- c("threshold", "specificity", "sensitivity", "accuracy", "tn", "tp", "fn", "fp", "npv", "ppv", "1-specificity", "1-sensitivity", "1-accuracy", "1-npv", "1-ppv") ci.coords(aSAH$outcome, aSAH$wfns, x=0.9, input = "sensitivity", ret=rets)

## Speed enhancements

- A faster implemententation of the DeLong test was kindly contributed by Kazuki Yoshida. It is used in
`roc.test`

,`ci`

,`var`

and`cov`

. - Two new algorithms have been introduced to speed-up ROC analysis, and specifically the computation of sensitivity and specificity. The same code as before is used by default (
`algorithm=1`

), that goes in O(T*N) (N = number of data points and T = number of thresholds of the curve), is well tested and safe. If speed is an issue for you, you may want to consider the following alternatives:`algorithm=2`

is a pure-R algorithm that goes in O(N) instead of O(T*N). It is typically faster when the number of thresholds of the ROC curve is above 1000, but slower otherwise.`algorithm=3`

is a a C++ implementation of the standard algorithm of pROC, with a 3-5x speedup. It is typically the fastest for ROC curves with less than 3000-5000 thresholds.- The special values
`0`

means the fastest algorithm for the specific dataset will be determined with the microbenchmark package, while`4`

is a debug feature that tests all 3 algorithms and ensures they produce the same results.

NOTE: because of this change, `roc`

objects created with an earlier version will have to be re-created before they can be used in any bootstrap operation.

## Dropped S+ support

S+ support was dropped, due to diverging code bases and apparent drop of support of S+ by TIBCO. A version 1.5.9 will be released in the next few days on ExPaSy with an initial work on ROC tests. It will work only on 32bits versions of S+ 8.2 for Windows.

## Other changes

`coords`

(and`ci.coords`

) now accepts a new`ret`

value`"1-accuracy"`

`are.paired`

now also checks for identical`levels`

- Fixed a warning generated in the examples
- Fixed several bugs related with
`smooth.roc`

curves - Additional input data sanity checks
- Now requires R >= 2.13 (in fact, since 1.5.1, thanks Emmanuel Curis for the report)
- Progress bars now defaults to text on Macs where 'tcltk' seems broken (thanks Gerard Smits for the report)

As usual, you will find the new version on ExPASy (please give a few days for the update to be propagated there) and on the CRAN. To update, type `update.packages()`

or `install.packages("pROC")`

if you want to update pROC only.

- 1. Nancy A. Obuchowski, Donna K. McClish (1997). “Sample size determination for diagnostic accurary studies involving binormal ROC curve indices”. Statistics in Medicine, 16, 1529–1542. DOI: 10.1002/(SICI)1097-0258(19970715)16:13<1529::AID-SIM565>3.0.CO;2-H.
- 2. Nancy A. Obuchowski, Micharl L. Lieber, Frank H. Wians Jr. (2004). “ROC Curves in Clinical Chemistry: Uses, Misuses, and Possible Solutions”. Clinical Chemistry, 50, 1118–1125. DOI: 10.1373/clinchem.2004.031823.
- 3. Elisabeth R. DeLong, David M. DeLong and Daniel L. Clarke-Pearson (1988) “Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach”.
*Biometrics***44**, 837–845.

Xavier Robin

Publié le jeudi 26 décembre 2013 à 18:10 CET

Lien permanent : /blog/2013/12/26/proc-1.6-released

Tags :
pROC

Commentaires : 0

## Commentaires

Aucun commentaire