pROC version 1.16.0 is available on CRAN now. Besides several bug fixes, the main change is the switch of the default value of the transpose argument to the coords function from TRUE to FALSE. As announced earlier, this is a backward incompatible change that will break any script that did not previously set the transpose argument and for now comes with a warning to make debugging easier. Scripts that set transpose explicitly are not unaffected.

New return values of coords and ci.coords

With transpose = FALSE, the coords returns a tidy data.frame suitable for use in pipelines:

data(aSAH)
rocobj <- roc(aSAH$outcome, aSAH$s100b)
coords(rocobj, c(0.05, 0.2, 0.5), transpose = FALSE)
#      threshold specificity sensitivity
# 0.05      0.05  0.06944444   0.9756098
# 0.2       0.20  0.80555556   0.6341463
# 0.5       0.50  0.97222222   0.2926829

The function doesn't drop dimensions, so the result is always a data.frame, even if it has only one row and/or one column.

If speed is of utmost importance, you can get the results as a non-transposed matrix instead:

coords(rocobj, c(0.05, 0.2, 0.5), transpose = FALSE, as.matrix = TRUE)
#      threshold specificity sensitivity
# [1,]      0.05  0.06944444   0.9756098
# [2,]      0.20  0.80555556   0.6341463
# [3,]      0.50  0.97222222   0.2926829

In some scenarios this can be a tiny bit faster, and is used internally in ci.coords.

Type help(coords_transpose) for additional information.

ci.coords

The ci.coords function now returns a list-like object:

ciobj <- ci.coords(rocobj, c(0.05, 0.2, 0.5))
ciobj$accuracy
#        2.5%       50%     97.5%
# 1 0.3628319 0.3982301 0.4424779
# 2 0.6637168 0.7433628 0.8141593
# 3 0.6725664 0.7256637 0.7787611

The print function prints a table with all the results, however this table is generated on the fly and not available directly.

ciobj
# 95% CI (2000 stratified bootstrap replicates):
#      threshold sensitivity.low sensitivity.median sensitivity.high
# 0.05      0.05          0.9268             0.9756           1.0000
# 0.2       0.20          0.4878             0.6341           0.7805
# 0.5       0.50          0.1707             0.2927           0.4390
#      specificity.low specificity.median specificity.high accuracy.low
# 0.05         0.01389            0.06944           0.1250       0.3628
# 0.2          0.70830            0.80560           0.8889       0.6637
# 0.5          0.93060            0.97220           1.0000       0.6726
#      accuracy.median accuracy.high
# 0.05          0.3982        0.4425
# 0.2           0.7434        0.8142
# 0.5           0.7257        0.7788

The following code snippet can be used to obtain all the information calculated by the function:

for (ret in attr(ciobj, "ret")) {
	print(ciobj[[ret]])
}
#        2.5%       50%     97.5%
# 1 0.9268293 0.9756098 1.0000000
# 2 0.4878049 0.6341463 0.7804878
# 3 0.1707317 0.2926829 0.4390244
#         2.5%        50%     97.5%
# 1 0.01388889 0.06944444 0.1250000
# 2 0.70833333 0.80555556 0.8888889
# 3 0.93055556 0.97222222 1.0000000
#        2.5%       50%     97.5%
# 1 0.3628319 0.3982301 0.4424779
# 2 0.6637168 0.7433628 0.8141593
# 3 0.6725664 0.7256637 0.7787611

Getting the update

The update his available on CRAN now. You can update your installation by simply typing:

install.packages("pROC")

Here is the full changelog:

• 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.