[EMAIL PROTECTED] wrote:
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 ?
The use of thresholds gets in the way of finding a good solution because
you will have predictor values in the "gray zone". I tend to rank
methods by the most sensitive index available such as the log likelihood
in the binary logistic model. You can extend ordinary logistic models
to allow for nonlinear effects on the log odds scale using regression
splines.
Frank
Pierre-Jean
-----Original Message-----
From: Frank E Harrell Jr [mailto:[EMAIL PROTECTED]
Sent: Thursday, November 13, 2008 5:00 PM
To: Breton, Pierre-Jean-EXT R&D/FR
Cc: r-help@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@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.
