Dear R-help and ROCR developers (Tobias Sing and Oliver Sander) - I think my first question is generic and could apply to many methods, which is why I'm directing this initially to R-help as well as Tobias and Oliver.
Question 1. The plot function in ROCR will average your cross validation data if asked. I'd like to use that averaged data to find a "best" cutoff but I can't figure out how to grab the actual data that get plotted. A simple redirect of the plot (such as test <- plot(mydata)) doesn't do it. Question 2. I am asking ROCR to average lists with varying lengths for each list entry. See my example below. None of the ROCR examples have data structured in this manner. Can anyone speak to whether the averaging methods in ROCR allow for this? If I can't easily grab the data as desired from Question 1, can someone help me figure out how to average the lists, by threshold, similarly? Question 3. If my cross validation data happen to have a list entry whose length = 2, ROCR errors out. Please see the second part of my example. Any suggestions? #reproducible examples exemplifying my questions ##part one## library(ROCR) data(ROCR.xval) # set up data so it looks more like my real data sampSize <- c(4, 55, 20, 75, 350, 250, 6, 120, 200, 25) testSet <- ROCR.xval # do the extraction for (i in 1:length(ROCR.xval[[1]])){ y <- sample(c(1:350),sampSize[i]) testSet$predictions[[i]] <- ROCR.xval$predictions[[i]][y] testSet$labels[[i]] <- ROCR.xval$labels[[i]][y] } # now massage the data using ROCR, set up for a ROC plot # if it errors out here, run the above sample again. pred <- prediction(testSet$predictions, testSet$labels) perf <- performance(pred,"tpr","fpr") # create the ROC plot, averaging by cutoff value plot(perf, avg="threshold") # check out the structure of the data str(perf) # note the ragged edges of the list and that I assume averaging # whether it be vertical, horizontal, or threshold, somehow # accounts for this? ## part two ## # add a list entry with only two values p...@x.values[[1]] <- c(0,1) p...@y.values[[1]] <- c(0,1) p...@alpha.values[[1]] <- c(Inf,0) plot(perf, avg="threshold") ##output results in an error with this message # Error in if (from == to) rep.int(from, length.out) else as.vector(c(from, : # missing value where TRUE/FALSE needed Thanks in advance for your help Tim Howard New York Natural Heritage Program ______________________________________________ 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.