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

From: <Pierre-Jean-EXT.Breton_at_sanofi-aventis.com>
Date: Thu, 13 Nov 2008 17:59:56 +0100


Hi Frank,

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

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Thu 13 Nov 2008 - 19:31:23 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive