Kaliss
2008-Nov-13 15:03 UTC
[R] Calculate Specificity and Sensitivity for a given threshold value
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 -- View this message in context: http://www.nabble.com/Calculate-Specificity-and-Sensitivity-for-a-given-threshold-value-tp20481633p20481633.html Sent from the R help mailing list archive at Nabble.com.
Frank E Harrell Jr
2008-Nov-13 16:00 UTC
[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 advanceBeware 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