Compute the confidence interval of arbitrary coordinates
Description
This function computes the confidence interval (CI) of the coordinates
of a ROC curves with the coords
function.
By default, the 95% CI are computed with 2000 stratified bootstrap replicates.
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20  # ci.coords(...)
## S3 method for class 'roc'
ci.coords(roc, x,
input=c("threshold", "specificity", "sensitivity"),
ret=c("threshold", "specificity", "sensitivity"),
best.method=c("youden", "closest.topleft"), best.weights=c(1, 0.5),
conf.level=0.95, boot.n=2000,
boot.stratified=TRUE,
progress=getOption("pROCProgress")$name, ...)
## S3 method for class 'formula'
ci.coords(formula, data, ...)
## S3 method for class 'smooth.roc'
ci.coords(smooth.roc, x,
input=c("specificity", "sensitivity"), ret=c("specificity", "sensitivity"),
best.method=c("youden", "closest.topleft"), best.weights=c(1, 0.5),
conf.level=0.95, boot.n=2000,
boot.stratified=TRUE,
progress=getOption("pROCProgress")$name, ...)
## Default S3 method:
ci.coords(response, predictor, ...)

Arguments
roc, smooth.roc 
a “roc” object from the

response, predictor 
arguments for the 
formula, data 
a formula (and possibly a data object) of type
response~predictor for the 
x, input, ret, best.method, best.weights 
Arguments passed to 
conf.level 
the width of the confidence interval as [0,1], never in percent. Default: 0.95, resulting in a 95% CI. 
boot.n 
the number of bootstrap replicates. Default: 2000. 
boot.stratified 
should the bootstrap be stratified (default, same number of cases/controls in each replicate than in the original sample) or not. 
progress 
the name of progress bar to display. Typically
“none”, “win”, “tk” or “text” (see the

... 
further arguments passed to or from other methods,
especially arguments for 
Details
ci.coords.formula
and ci.coords.default
are convenience methods
that build the ROC curve (with the roc
function) before
calling ci.coords.roc
. You can pass them arguments for both
roc
and ci.coords.roc
. Simply use ci.coords
that will dispatch to the correct method.
This function creates boot.n
bootstrap replicate of the ROC
curve, and evaluates the coordinates specified by the x
, input
,
ret
, best.method
and best.weights
arguments. Then it computes the
confidence interval as the percentiles given by conf.level
.
For more details about the bootstrap, see the Bootstrap section in this package's documentation.
Value
A matrix of class “ci.coords”, “ci” and “matrix” (in this order), with the confidence
intervals of the CI. The matrix has 3 columns (lower bound, median and upper bound) and
as many rows as x
* ret
were requested. Rows are sorted by x
and then by ret
and named as “input x: return”.
Additionally, the list has the following attributes:
conf.level 
the width of the CI, in fraction. 
boot.n 
the number of bootstrap replicates. 
boot.stratified 
whether or not the bootstrapping was stratified. 
roc 
the object of class “roc” that was used to compute the CI. 
Warnings
If boot.stratified=FALSE
and the sample has a large imbalance between
cases and controls, it could happen that one or more of the replicates
contains no case or control observation, producing a NA
area.
The warning “NA value(s) produced during bootstrap were ignored.”
will be issued and the observation will be ignored. If you have a large
imbalance in your sample, it could be safer to keep
boot.stratified=TRUE
.
References
James Carpenter and John Bithell (2000) “Bootstrap condence intervals: when, which, what? A practical guide for medical statisticians”. Statistics in Medicine 19, 1141–1164. DOI: 10.1002/(SICI)10970258(20000515)19:9<1141::AIDSIM479>3.0.CO;2F.
Tom Fawcett (2006) “An introduction to ROC analysis”. Pattern Recognition Letters 27, 861–874. DOI: 10.1016/j.patrec.2005.10.010.
Hadley Wickham (2011) “The SplitApplyCombine Strategy for Data Analysis”. Journal of Statistical Software, 40, 1–29. URL: www.jstatsoft.org/v40/i01.
See Also
roc
,
coords
,
ci
CRAN package plyr, employed in this function.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24  data(aSAH)
## Not run:
# Syntax (response, predictor):
ci.coords(aSAH$outcome, aSAH$s100b, x="best", input = "threshold",
ret=c("specificity", "ppv", "tp"))
# With a roc object:
rocobj < roc(aSAH$outcome, aSAH$s100b)
ci.coords(rocobj, x=0.9, input = "sensitivity", ret="specificity")
ci.coords(rocobj, x=0.9, input = "sensitivity", ret=c("specificity", "ppv", "tp"))
ci.coords(rocobj, x=c(0.1, 0.5, 0.9), input = "sensitivity", ret="specificity")
ci.coords(rocobj, x=c(0.1, 0.5, 0.9), input = "sensitivity", ret=c("specificity", "ppv", "tp"))
# With a smoothed roc:
rocobj < roc(aSAH$outcome, aSAH$s100b)
ci.coords(smooth(rocobj), x=0.9, input = "sensitivity", ret=c("specificity", "ppv", "tp"))
# Return everything we can:
rets < c("threshold", "specificity", "sensitivity", "accuracy", "tn", "tp", "fn", "fp", "npv",
"ppv", "1specificity", "1sensitivity", "1accuracy", "1npv", "1ppv")
ci.coords(rocobj, x="best", input = "threshold", ret=rets)
## End(Not run)
