From: <Pierre-Jean-EXT.Breton_at_sanofi-aventis.com>

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

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

Thank you for your answer.

In fact, I don't use this for clinical research practice.
I am currently testing several scoring methods and I'd like
to know which one is the most effective and which threshold
value I should apply to discriminate positives and negatives.
So, any idea for my problem ?

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 <- read.table("inputFile", header=TRUE); pred <- prediction(d$SCORE,
*

> 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 ?
**>
**> Thank you in advance
*

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 ______________________________________________ R-help_at_r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.Received on Thu 13 Nov 2008 - 17:05:03 GMT

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