pROC (version 1.3.1)

coords: Coordinates of a ROC curve

Description

This function returns the coordinates of the ROC curve at the specified point.

Usage

coords(...)
## S3 method for class 'roc':
coords(roc, x, input=c("threshold", "specificity",
"sensitivity"), ret=c("threshold", "specificity", "sensitivity"),
as.list=FALSE, ...)
## S3 method for class 'smooth.roc':
coords(smooth.roc, x, input=c("specificity",
"sensitivity"), ret=c("specificity", "sensitivity"), as.list=FALSE, ...)

Arguments

roc, smooth.roc

a roc object from the roc function, or a smooth.roc object from the smooth.roc function.

x

the coordinates to look for. Numeric (if so, their meaning is defined by the input argument) or one of all (all the points of the ROC curve), local maximas (the local maximas of the ROC curve) or

input

If x is numeric, the kind of input coordinate (x). One of threshold, specificity or sensitivity. Can be shortenend (for example to thr, sens and

ret

The coordinates to return. One or more of threshold, specificity or sensitivity. Can be shortenend (for example to thr, sens and spec, or eve

as.list

If the returned object must be a list. If FALSE (default), a named numeric vector is returned.

...

further arguments passed to or from other methods. Ignored.

Value

• Depending on the length of x and as.list argument.

  lll{ length(x) == 1 length(x) > 1 as.list=TRUE a list of the length of, in the order of, and named after, ret. a list of the length of, and named after, x. Each element of this list is a list of the length of, in the order of, and named after, ret. as.list=FALSE a numeric vector of the length of, in the order of, and named after, ret. a numeric matrix with one row for each ret and one column for each x } In all cases if input="specificity" or input="sensitivity" and interpolation was required, threshold is returned as NA.

  Note that if giving a character as x (all, local maximas or best), you cannot predict the dimension of the return value, so be prepared to receive either a numeric vector or a matrix (if as.list=FALSE) or either a list of numeric or a list of lists (if as.list=TRUE). Even best may return more than one value (for example if the ROC curve is below the identity line, both extreme points).

encoding

UTF-8

Details

This function takes a roc or smooth.roc object as first argument, on which the coordinates will be determined. The coordinates are defined by the x and input arguments. threshold coordinates cannot be determined in a smoothed ROC.

If input="threshold", the coordinates for the threshold are reported, even if the exact threshold do not define the ROC curve. The following convenience characters are allowed: all, local maximas and best. They will return all the thresholds, only the thresholds defining local maximas (angles of the ROC curve), or only the threshold(s) corresponding to the best sum of sensitivity + specificity respectively. Note that best can return more than one threshold. If x is a character, the coordinates are limited to the thresholds within the partial AUC if it has been defined, and not necessarily to the whole curve. For input="specificity" and input="sensitivity", the function checks if the specificity or sensitivity is one of the points of the ROC curve (in roc$sensitivities or roc$specificities). More than one point may match (in step curves), then only the upper-left-most point coordinates are returned. Otherwise, the specificity and specificity of the point is interpolated and NA is returned as threshold.

The coords function in this package is a generic, but it might be superseded by functions in other packages such as colorspace or spatstat if they are loaded after pROC. In this case, call the coords.roc or coords.smooth.roc functions directly.

See Also

roc

Examples

data(aSAH)

# Print a roc object:
rocobj <- roc(aSAH$outcome, aSAH$s100b)

coords(rocobj, 0.55)
coords(rocobj, 0.9, "specificity", as.list=TRUE)
coords(rocobj, 0.5, "se", ret="se")
# fully qualified but identical:
coords(roc=rocobj, x=0.5, input="sensitivity", ret="sensitivity")

# Same in percent
rocobj <- roc(aSAH$outcome, aSAH$s100b,
              percent=TRUE)

coords(rocobj, 0.55)
coords(rocobj, 90, "specificity", as.list=TRUE)
coords(rocobj, x=50, input="sensitivity", ret=c("sen", "spec"))

# Get the sensitivities for all thresholds
sensitivities <- coords(rocobj, rocobj$thresholds, "thr", "se")
# This is equivalent to taking sensitivities from rocobj directly
stopifnot(all.equal(as.vector(rocobj$sensitivities), as.vector(sensitivities)))
# You could also write:
sensitivities <- coords(rocobj, "all", ret="se")
stopifnot(all.equal(as.vector(rocobj$sensitivities), as.vector(sensitivities)))

# Get the best threshold
coords(rocobj, "b", ret="t")