Message-ID: <07E228A5BE53C24CAD490193A7381BBBF2AD02@LP-EXCHVS07.CO.IHC.COM>
Date: 2008-03-03T21:07:29Z
From: Greg Snow
Subject: need help in calculating confidence intervals forsensitivity, specificity, PPV & NPV
In-Reply-To: <708592.65199.qm@web52104.mail.re2.yahoo.com>
I am not a physician, but most of the people who ask me for confidence
intervals on sensitivity and specificity are.
My prefered approach (not the only one), is to use the Bayesian interval
using a uniform prior (beta(1,1) distribution) with the binomial (it is
easier to do than it looks).
Basically find the HPD interval from a beta distribution with parameters
s+1 and f+1, where s and f are successes (correct test results) and
failures (incorrect test results).
I use the hpd function from the TeachingDemos package, but there are
others as well (I'm a bit biased towards that package).
For example, to calculate the 95% confidence interval for sensitivity
when you have 95 true positives and 5 false negatives you would just
type (after installing and loading the package):
> hpd(qbeta, shape1=96, shape2=6)
And the 2 numbers are limits of a 95% confidence interval.
I like this approach because it still gives sensible results when you
have no false negatives (or false positives for specificity).
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.snow at imail.org
(801) 408-8111
> -----Original Message-----
> From: r-sig-epi-bounces at stat.math.ethz.ch
> [mailto:r-sig-epi-bounces at stat.math.ethz.ch] On Behalf Of
> Smita Pakhale
> Sent: Friday, February 29, 2008 12:34 PM
> To: r-sig-epi at stat.math.ethz.ch
> Subject: [R-sig-Epi] need help in calculating confidence
> intervals forsensitivity, specificity, PPV & NPV
>
> Hello,
>
> I am a physician and a novice in R.
>
> I am trying to calculate sensitivity, specificity, positive
> predictive and negative predictive values. I could do that
> using the package caret. However, I need to get confidence
> intervals around these estimates and I do not know how to do that.
>
> Please help me find a way to calculate confidence intervals
> for these parameters.
>
> thank you.
> Sincerely,
> Dr. Smita Pakhale
>
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