NEWS
pROC 1.18.5 (2023-11-01)
- Fixed formula input when given as variable and combined with 'with' (issue #111)
- Fixed formula containing variables with spaces (issue #120)
- Fixed broken grouping when 'colour' argument was given in 'ggroc' (issue #121)
pROC 1.18.4 (2023-07-05)
- Fix regression in 1.18.3 in 'legacy.axes' in 'ggroc'
pROC 1.18.3
- Fix warning about 'aes_string' in 'ggroc'
- Improvements in tests (thanks to Michael Chirico, pr #114, #115)
- Fix upcoming CRAN warning about numeric version comparisons
pROC 1.18.2 (2023-05-13)
- Fix CRAN submission NOTE (issue #112)
pROC 1.18.1
- Fix 'print'ing some curves built from a formula (issue #101)
- Fix tests following upstream updates in density() (https://bugs.r-project.org/show_bug.cgi?id=18337)
- Improvements in documentation
pROC 1.18.0 (2021-09-03)
- Add CI of the estimate for 'roc.test' (DeLong, paired only for now) (code contributed by Zane Billings) (pr #95)
- Fix documentation and alternative hypothesis for Venkatraman test (issue #92)
pROC 1.17.0.1 (2021-01-13)
- Fix CRAN incoming checks as requested by CRAN
pROC 1.17.0
- Accept more values in 'input' of coords (issue #67)
- Accept 'kappa' for the 'power.roc.test' of two ROC curves (issue #82)
- The 'input' argument to 'coords' for 'smooth.roc' curves no longer has a default
- The 'x' argument to 'coords' for 'smooth.roc' can now be set to 'all' (also the default)
- Fix bootstrap roc.test and cov with 'smooth.roc' curves
- The 'ggroc' function can now plot 'smooth.roc' curves (issue #86)
- Remove warnings with 'warnPartialMatchDollar' option (issue #87)
- Make tests depending on vdiffr conditional (issue #88)
pROC 1.16.2 (2020-03-19)
- Skip test depending on Rcpp version
pROC 1.16.1 (2020-01-14)
- Skip timing-dependent test failing occasionally on CRAN
pROC 1.16.0 (2020-01-12)
- BACKWARD INCOMPATIBLE CHANGE: 'transpose' argument to 'coords' switched to FALSE by default (issue #54)
- BACKWARD INCOMPATIBLE CHANGE: 'ci.coords' return value is now of list type and easier to use
- Fix one-sided DeLong test for curves with 'direction=">"' (issue #64)
- Fix an error in 'ci.coords' due to expected NA values in some coords (like "precision") (issue #65)
- Ordrered predictors are converted to numeric in a more robust way (issue #63)
- Cleaned up 'power.roc.test' code (issue #50)
- Fix pairing with 'roc.formula' and warn if 'na.action' is not set to "na.pass" or "na.fail" (issue #68)
- Fix 'ci.coords' not working with 'smooth.roc' curves
pROC 1.15.3 (2019-07-21)
- Fix: previous version accidentally set transpose = FALSE, should only be for next major release
pROC 1.15.2
- Fix -Inf threshold in coords for curves with 'direction = ">"' (issue #60)
- Restore lazy loading of the data and fix an 'R CMD check' warning "Variables with usage in documentation object 'aSAH' not in code"
pROC 1.15.1
- Fix erroneous error in 'ci.coords' with 'ret="threshold"' (issue #57)
- Fix vdiffr unit tests with ggplot2 3.2.0 (issue #53)
- Keep list order in 'ggroc' (issue #58)
pROC 1.15.0 (2019-06-01)
- 'roc' now prints messages when autodetecting 'levels' and 'direction' by default. Turn off with 'quiet = TRUE' or set these values explicitly
- Speedup with 'algorithm = 2' (issue #44) and in 'coords' (issue #52)
- New 'algorithm = 6' (used by default) uses 'algorithm = 2' for numeric data, and 'algorithm = 3' for ordered vectors
- New 'roc.data.frame' method and 'roc_' function for use in pipelines
- 'coords' can now returns 'youden' and 'closest.topleft' values (issue #48)
- New 'transpose' argument for 'coords', TRUE by default (issue #54)
- Use text instead of Tcl/Tk progress bar by default (issue #51)
- Fix 'method = "density"' smoothing when called directly from 'roc' (issue #49)
- Renamed 'roc' argument 'n' to 'smooth.n'
- Fixed 'are.paired' ignoring smoothing arguments of 'roc2' with 'return.paired.rocs'
- New 'ret' option "all" in 'coords' (issue #47)
- 'drop' in 'coords' now drops the dimension of 'ret' too (#issue 43)
pROC 1.14.0 (2019-03-12)
- The 'multiclass.roc' function now accepts multivariate decision values (code contributed by Matthias Döring)
- 'ggroc' supports multiple aesthetics (issue #42)
- Make 'ggplot2' dependency optional
- CSuggested packages can be installed interactively when required
- Passing both 'cases' and 'controls' or 'response' and 'predictor' arguments is now an error
- Many small bug fixes
pROC 1.13.0 (2018-09-24)
- 'roc' now returns 'NaN' when predictor contains infinite values (issue #30)
- Better handling of near-ties near +-Infinity and 0
- 'ggroc' supports aes="group" to allow curves with identical aesthetics
pROC 1.12.1 (2018-05-06)
- Fix a regression causing the allocation of a very large vector (issue #29)
pROC 1.12.0 (2018-05-05)
- Fix bug that crashed DeLong calculations when predictor had near-ties close to the floating point precision limit that were rounded back to a predictor value (issue #25)
- Fix bug that crashed 'ci.auc' and 'var' if 'direction' was ">" and 'percent=TRUE' (issue #25)
- Fix bug causing 'ci' to return 'NaN' values with 'method="delong"' when cases or controls had a single observation (issue #27)
- Fix 'power.roc.curve' failed with curves having 'percent=TRUE'
- Fix 'ci(..., of="coords")' returned the 'ci' function instead of the CI
- C++ code now check for user interrupts regularly with Rcpp::checkUserInterrupt()
- Better error message for 'ci.coords' attempting to return 'threshold'
- New algorithm = 5 (used by default) chooses the algorithm based on the number of thresholds to avoid worst case with algorithm = 3
pROC 1.11.0 (2018-03-25)
- Added argument 'legacy.axes' to 'ggroc'
- Fix NOTE about 'apparent S3 methods exported but not registered' in 'R CMD check'
pROC 1.10.0 (2017-06-10)
- Basic ggplot2 support (one and multiple ROC curves)
- Implement 'precision' and 'recall' for 'coords'
- Fix: properly handle NAs in cases when passing cases/controls to 'roc' (thanks Thomas König for the report)
- Fix various minor bugs detected with new unit tests
1.9.1 (2017-02-05)
- Fix: 'subset' and 'na.action' arguments now handled properly in 'roc.formula' (thanks Terry Therneau for the report)
- Added policies to handle the case where a ROC curve has multiple "best" threshold in 'ci' (thanks Nicola Toschi for the report)
- Support 'xlim' and 'ylim' gracefully in 'plot.roc'
- Improved validation of input class 'levels' and 'direction'; messages when auto-detecting, use 'quiet' to turn on
- Removed extraneous 'name' attribute on the 'p.value' (thanks Paweł Kleka for the report)
- Faster DeLong algorithm (code contributed by Stefan Siegert)
pROC 1.8 (2015-05-05)
- NAMESPACE now properly exports the methods as S3 methods.
- Now uses and works with 'requireNamespace'
- Add ability to supply two ordered factors with identical levels as control / cases
- Deprecate dangerous use of a matrix as response / predictor with a warning
- Forward 'best.method' and 'best.weights' arguments to 'coords' in 'ci.thresholds'
- Fix CITATION file as per CRAN request
- pAUC correction is undefined for partial AUC below the diagonal (result < 0.5) and now returns NA (with a warning). Thanks Vincenzo Lagani for the report.
pROC 1.7.3 (2014-06-13)
- Fixed AUC of binomial-smoothed ROC off by 100^2 (thanks Bao-Li Chang for the report)
- Fix print of logcondens-smoothed ROC
pROC 1.7.2 (2014-04-06)
- Fixed bug where 'ci.coords' with 'x="best"' would fail if one or more resampled ROC curve had multiple "best" thresholds
- Fixed bug in 'ci.coords': passing more than one value in 'x' now works
- Fixed typo in documentation of 'direction' argument to 'roc' (thanks Le Kang for the report)
- Add a warning when computing statistics of ROC curve with AUC = 1
- Require latest version of Rcpp to avoid weird errors (thanks Tom Liptrot for the report)
pROC 1.7.1 (2014-02-21)
- Close SOCK cluster on Windows with parallel=TRUE
- Fixed really use algorithm 1 when microbenchmark fails
pROC 1.7
- Faster algorithm for DeLong 'roc.test', 'power.roc.test', 'ci.auc', 'var' and 'cov' function (no large matrix allocation)
- Handling Math and Operations correctly on 'auc' and 'ci' objects (see '?groupGeneric.pROC')
- The 'formula' for 'roc.formula' can now provide several predictors and a list of ROC curves will be returned
- Fixed documentation of 'ci.coords' with examples
- Fixed binormal AUC computed with triangulation despite the claim in the documentation
- Fixed unstated requirement on Rcpp >= 0.10.5
pROC 1.6.0.1 (2013-12-28)
- Removed erroneous error message displayed when predictors and responses were not vectors
pROC 1.6 (2013-12-26)
- New 'power.roc.test' function for sample size and power computations
- New 'cov' and 'var' functions supports new "obuchowski" method
- New 'ci.coords' function to compute CI of arbitrary coords
- 'coords' accepts new 'ret' value "1-accuracy"
- Introducing various algorithms to compute sensitivities and specificites, with a more vectorized code or Rcpp. See 'algorithm' in ?roc for more details on the trade-offs of the different methods.
- Faster algorithm for DeLong 'roc.test', 'ci', 'var' and 'cov' function (thanks Kazuki Yoshida).
- '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)
pROC 1.5.4 (2012-09-10)
- Running less smooth.roc examples with logcondens because they take too much time (requested by Uwe Ligges)
pROC 1.5.3
- AUC specification was lost when roc.test, cov or var was passed an 'auc' object.
- Correct computation of "accuracy" in 'coords' (thanks to Kosuke Yoshihara for the report)
pROC 1.5.1 (2012-03-09)
- Faster loading of the package (thanks to Prof Brian Ripley and Glenn Lawyer for the report)
pROC 1.5 (2011-12-12)
- New 'cov' and 'var' functions
- 'coords' accepts new 'ret' values: "accuracy", "tn", "tp", "fn", "fp", "npv", "ppv", "1-specificity", "1-sensitivity", "1-npv", "1-ppv", "npe" and "ppe"
- New 'legacy.axes' argument to 'plot' 1-specificity rather than specificity
- New 'axes' argument to turn off the plotting of the axis
- New 'logcondens' and 'logcondens.smooth' (Univariate Log-Concave Density Estimation) smoothing methods
- New function 'has.partial.auc' to determine if an AUC is full or partial
- New argument 'drop' for 'coords'
- 'auc' and 'multiclass.auc' objects now also have secondary class 'numeric'
- Updated load call
- Delong's CI reversed in ROC curves with direction=">"
- Delong's CI AUC returned values > 1 or < 0 in some rare cases
- Minor improvements in documentation
pROC 1.4.4 (2011-08-10)
- Fixed alternative for one-tailed tests (thanks to Lisa Koch for the report)
- Removed COPYING file to fix a warning in r-devel.
pROC 1.4.3 (2011-03-19)
pROC 1.4.2 (2011-03-04)
- Fixed bootstrap 'roc.test' generating NAs when 'smooth.roc's were used with 'reuse.auc=FALSE' (thanks to Buddy for the report)
- Documented a warning that was missing in roc.test
- Updated citation
pROC 1.4.1 (2011-01-27)
- 'venkatraman”s test for unpaired ROC curves
pROC 1.4 (2011-01-21)
- 'smooth' does not apply on 'ordered' factors anymore
- Multi-class AUC support
- Can choose how 'best' thresold is determined ('best.method' and 'best.weights' in 'coords' and 'print.thres.best.method' and 'print.thres.best.weights' in 'plot.roc')
- Minor fixes in documentation
- 'print' now prints the response instead of "response" and more informative data in 'htest's
- Bootstrap with 'ci.auc' consumes much less memory
- Unpaired bootstrap and DeLong's test
- Specificity and sensitivity tests (in 'roc.test')
pROC 1.3.2 (2010-08-24)
- 'print.auc' printed incorrect CI in 'plot.roc' (thanks to Alexander B. Leichtle for the report)
- Failed to detect local maximas in 'coords' when 2 or less points were selected
- Don't consider ROC extremities (+-Inf at 1.0/0.0 SE<->SP) as local maximas
pROC 1.3.1 (2010-08-18)
- Sensitivity and specificity were inverted in coords when results were reported as list
- Faster checks with '\dontrun{}' in 'roc.test'
pROC 1.3 (2010-08-13)
- '...' not passed correctly in 'plot.ci.se' with 'type="bars"' resulting in an error
- CI is not re-computed by default in 'smooth.roc'. You can still turn it on with 'reuse.ci=TRUE'
- New function 'are.paired'
- Local maximas could be incorrectly detected in 'coords' (and 'plot.roc') with 'predictor's containing more than 2 levels.
- New method 'venkatraman' for 'roc.test'
- MASS and tcltk packages are now only suggested instead of required
pROC 1.2.1 (2010-05-11)
- Handle 'method' arguments for 'smooth.roc' and 'ci.auc' separately in 'roc.default'
- Added 'auc.polygon.*' and 'max.auc.polygon.*' arguments for 'polygon' in 'plot.roc'
pROC 1.2 (2010-05-09)
- Added DeLong method in 'ci.auc'
- Return value of 'ci.auc' does not contain an 'aucs' item anymore
- Put most examples with bootstrap within '\dontrun{}' blocks for faster (but less useful) checks execution
pROC 1.1 (2010-05-06)
- Added 'lines.roc' functions for ROC
- Added 'type' argument for both 'lines.roc' and 'plot.roc'
- Added 'print.auc.col' argument to 'plot.roc'
- Fixed a warning in 'roc.test.default' when the class of 'predictor1' had several elements
- Fixed an encoding failure during the checks on MacOS X
pROC 1.0.1 (2010-04-28)
- Reduced examples execution time. Added low 'boot.n' in the slowest examples and 'reuse.auc' and 'reuse.ci' arguments in smooth.roc.roc
pROC 1.0