coords
This help page desribes recent and upcoming changes in the
return values of the coords
function.
Untile the release of pROC 1.16, the coords
has was returning
a matrix with thresholds in columns, and the coordinate variables in rows.
data(aSAH) rocobj <- roc(aSAH$outcome, aSAH$s100b) coords(rocobj, c(0.05, 0.2, 0.5)) # 0.05 0.2 0.5 # threshold 0.05000000 0.2000000 0.5000000 # specificity 0.06944444 0.8055556 0.9722222 # sensitivity 0.97560976 0.6341463 0.2926829
This format didn't conform to the grammar of the tidyverse which has become prevalent in modern R language.
In addition, the dropping of dimensions by default makes it difficult to guess
what type of data coords
is going to return.
coords(rocobj, "best") # threshold specificity sensitivity # 0.2050000 0.8055556 0.6341463 # A numeric vector
Although it is possible to pass drop = FALSE
, the fact that it is not the
default makes the behaviour unintuitive.
In pROC version 1.16, this was changed and coords
now returns
a data.frame
with the thresholds in rows and measurement in colums by default.
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
Addition of the transpose
argument.
Display a warning if transpose
is missing. Pass transpose
explicitly to silence the warning.
Deprecation of as.list
.
Change of the default transpose
to TRUE
.
THIS CHANGE IS BACKWARDS INCOMPATIBLE AND IS EXPECTED TO BREAK LEGACY CODE.
It is expected that the following major version (1.17) will remove the warning and drop support for the as.list
argument altogether.
The transpose
and drop
arguments will be deprecated in 1.17, but will remain available for a few additional major versions.
In version 1.16, the format of the ci.coords
return value was changed from a matrix-like object with mixed x
and ret
in rows and 3 columns, into a list-like object which should be easier to use programatically.
If you are writing a new script calling the coords
function, set transpose = FALSE
to silence the warning and benefit from the latest improvements in pROC and obtain a tidy data.
The GitHub issue tracking the changes described in this manual page.