need help in calculating confidence intervals forsensitivity, specificity, PPV & NPV
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 > > _______________________________________________ > R-sig-Epi at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-sig-epi >