ci.coords  R Documentation 
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.
# 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),
best.policy = c("stop", "omit", "random"),
conf.level=0.95, boot.n=2000,
boot.stratified=TRUE,
progress=getOption("pROCProgress")$name, ...)
## S3 method for class 'formula'
ci.coords(formula, data, ...)
## S3 method for class 'smooth.roc'
ci.coords(smooth.roc, x,
input=c("specificity", "sensitivity"), ret=c("specificity", "sensitivity"),
best.method=c("youden", "closest.topleft"), best.weights=c(1, 0.5),
best.policy = c("stop", "omit", "random"),
conf.level=0.95, boot.n=2000,
boot.stratified=TRUE,
progress=getOption("pROCProgress")$name, ...)
## Default S3 method:
ci.coords(response, predictor, ...)
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 
best.policy 
The policy follow when multiple “best” thresholds are returned by 
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 
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
.
When x="best"
, the best threshold is determined at each bootstrap
iteration, effectively assessing the confidence interval of choice of the "best"
threshold itself. This differs from the behavior of ci.thresholds
,
where the "best" threshold is assessed on the given ROC curve before
resampling.
For more details about the bootstrap, see the Bootstrap section in this package's documentation.
Note: changed in version 1.16.
A list of the same length as ret
and named as ret
, and of
class “ci.thresholds”, “ci” and “list” (in this order).
Each element of the list is a matrix of the confidence intervals with
rows given by x
and with 3 columns, the lower bound of the CI,
the median, and the upper bound of the CI.
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. 
input 
the input coordinate, as given in argument. 
x 
the coordinates used to calculate the CI, as given in argument. 
ret 
the return values, as given in argument or substituted by

roc 
the object of class “roc” that was used to compute the CI. 
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
.
This warning will also be displayed if you chose best.policy = "omit"
and a ROC curve with multiple “best” threshold was generated
during at least one of the replicates.
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: \Sexpr[results=rd]{tools:::Rd_expr_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: \Sexpr[results=rd]{tools:::Rd_expr_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: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.18637/jss.v040.i01")}.
roc
,
coords
,
ci
CRAN package plyr, employed in this function.
# Create a ROC curve:
data(aSAH)
roc1 < roc(aSAH$outcome, aSAH$s100b)
## Basic example ##
## Not run:
ci.coords(roc1, x="best", input = "threshold",
ret=c("specificity", "ppv", "tp"))
## More options ##
ci.coords(roc1, x=0.9, input = "sensitivity", ret="specificity")
ci.coords(roc1, x=0.9, input = "sensitivity", ret=c("specificity", "ppv", "tp"))
ci.coords(roc1, x=c(0.1, 0.5, 0.9), input = "sensitivity", ret="specificity")
ci.coords(roc1, x=c(0.1, 0.5, 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(roc1, x="best", input = "threshold", ret=rets)
## End(Not run)
## On smoothed ROC curves with bootstrap ##
## Not run:
ci.coords(smooth(roc1), x=0.9, input = "sensitivity", ret=c("specificity", "ppv", "tp"))
## End(Not run)
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