# Re: [R] Calculate Specificity and Sensitivity for a given threshold value

Date: Thu, 13 Nov 2008 17:59:56 +0100

Pierre-Jean

-----Original Message-----
From: Frank E Harrell Jr [mailto:f.harrell_at_vanderbilt.edu] Sent: Thursday, November 13, 2008 5:00 PM To: Breton, Pierre-Jean-EXT R&D/FR
Cc: r-help_at_r-project.org
Subject: Re: [R] Calculate Specificity and Sensitivity for a given threshold value

Kaliss wrote:
> Hi list,
>
>
> I'm new to R and I'm currently using ROCR package.
> Data in input look like this:
>
> DIAGNOSIS SCORE
> 1 0.387945
> 1 0.50405
> 1 0.435667
> 1 0.358057
> 1 0.583512
> 1 0.387945
> 1 0.531795
> 1 0.527148
> 0 0.526397
> 0 0.372935
> 1 0.861097
>
> And I run the following simple code:

> d\$DIAGNOSIS); perf <- performance( pred, "tpr", "fpr");
> plot(perf)
>
> So building the curve works easily.
> My question is: can I have the specificity and the sensitivity for a
> score threshold = 0.5 (for example)? How do I compute this ?
>

Beware of the utility/loss function you are implicitly assuming with this approach. It is quite oversimplified. In clinical practice the cost of a false positive or false negative (which comes from a cost function and the simple forward probability of a positive diagnosis, e.g., from a basic logistic regression model if you start with a cohort study) vary with the type of patient being diagnosed.

Frank

```--
Frank E Harrell Jr   Professor and Chair           School of Medicine
Department of Biostatistics   Vanderbilt
University

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Received on Thu 13 Nov 2008 - 17:05:03 GMT

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