Re: [R] ROC curve in R
You might also want to try the ROCR package (http://rocr.bioinf.mpi-sb.mpg.de/). Tutorial slides: http://rocr.bioinf.mpi-sb.mpg.de/ROCR_Talk_Tobias_Sing.ppt Overview paper: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/20/3940 Good luck, Tobias On 7/26/07, Rithesh M. Mohan [EMAIL PROTECTED] wrote: Hi, I need to build ROC curve in R, can you please provide data steps / code or guide me through it. Thanks and Regards Rithesh M Mohan [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- Tobias Sing Computational Biology and Applied Algorithmics Max Planck Institute for Informatics Saarbrucken, Germany Phone: +49 681 9325 315 Fax: +49 681 9325 399 http://www.tobiassing.net __ R-help@stat.math.ethz.ch 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.
[R] [R-pkgs] ROCR 1.0-2
Dear useRs, an update of the ROCR package is available on CRAN. ROCR helps in evaluating the performance of scoring classifiers using ROC graphs, precision/recall plots, lift charts and many other performance metrics. For further information check http://rocr.bioinf.mpi-sb.mpg.de and http://bioinformatics.oxfordjournals.org/cgi/reprint/21/20/3940 NEWS: - added an optional parameter 'fpr.stop' to the performance measure 'auc', allowing to calculate the partial area under the ROC curve up to the false positive rate given by 'fpr.stop'. - fixed bug in 'prediction' function which caused ROCR to halt in the context of a custom label.ordering (thanks to Roberto Perdisci for pointing out) As usual, any feedback is more than welcome! - Tobias -- Tobias Sing Computational Biology and Applied Algorithmics Max Planck Institute for Informatics Saarbrucken, Germany Phone: +49 681 9325 315 Fax: +49 681 9325 399 http://www.tobiassing.net ___ R-packages mailing list R-packages@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch 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.
Re: [R] Probabilities calibration error ROCR
Roberto, On 1/24/07, Roberto Perdisci [EMAIL PROTECTED] wrote: [...]. Do you know of any reference where I can find the details of the algorithm that computes the calibration error implemented in ROCR (apart from ROCR's source code)? we use it as defined in Caruana Niculescu-Mizil: Data mining in metric space: An empirical evaluation of supervised learning performance criteria. Knowledge Discovery and Data Mining (KDD) 2006. http://www.cs.cornell.edu/~caruana/perfs.rocai04.revised.rev1.ps Also, have a look at ?performance. HTH, Tobias __ R-help@stat.math.ethz.ch 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.
[R] [R-pkgs] New package: ROCR (Visualizing classifier performance)
Dear R users, we are glad to announce the release of our new R package ROCR, for visualizing the performance of scoring classifiers (available on CRAN). We hope that the package might be useful for those of you working on classification problems. For details, see the package description below, or the ROCR website: http://rocr.bioinf.mpi-sb.mpg.de. You can get a short overview by typing 'demo(ROCR)'. Any kind of feedback (questions, comments, suggestions, bug reports) is very welcome. Best regards, the ROCRs (Tobias Sing, Oliver Sander, Niko Beerenwinkel, Thomas Lengauer) Package description: - ROC graphs, sensitivity/specificity curves, lift charts, and precision/recall plots are popular examples of trade-off visualizations for specific pairs of performance measures. ROCR is a flexible tool for creating cutoff-parametrized 2D performance curves by freely combining two from over 25 performance measures (new performance measures can be added using a standard interface). Curves from different cross-validation or bootstrapping runs can be averaged by different methods, and standard deviations, standard errors or box plots can be used to visualize the variability across the runs. The parametrization can be visualized by printing cutoff values at the corresponding curve positions, or by coloring the curve according to cutoff. All components of a performance plot can be quickly adjusted using a flexible parameter dispatching mechanism. Despite its flexibility, ROCR is easy to use, with only three commands and reasonable default values for all optional parameters. __ Tobias Sing phone: +49 681 9325 315 Max-Planck-Institut für Informatik fax : +49 681 9325 399 Stuhlsatzenhausweg 85 email:[EMAIL PROTECTED] 66123 Saarbrücken, Germany web : http://www.tobiassing.net ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] association rules in R
I think there is no R package for association rules yet. You might want to write a wrapper around one of the many freely available association rule miners instead, e.g. Christian Borgelt's nice implementation of the apriori algorithm: http://fuzzy.cs.uni-magdeburg.de/~borgelt/apriori.html HTH, Tobias. Christoph Lehmann wrote: Hi I am interested in data mining problems. Has anybody ever programmed and worked with association rules in R? I am very grateful for any hint. Best regards Christoph __ Tobias Sing phone: +49 681 9325 315 Max-Planck-Institut für Informatik fax : +49 681 9325 399 Stuhlsatzenhausweg 85 email:[EMAIL PROTECTED] 66123 Saarbrücken, Germany web : http://www.mpi-sb.mpg.de/~tsing __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Debugging R Code
Hi all, is there a more convenient way to debug R code than the built in debug() function? (so that one can set breakpoints, step in and out of function calls,...). I read the section on debugging compiled code in the manual Writing R Extensions (I only want to debug ordinary code but thought that maybe the advice there could help), but didn't find out how I can start debugging my code after typing R -d gdb, which brought me to the gdb prompt (I'm using R 1.6.2 in xemacs via ESS). Thanks, Tobias __ Tobias Sing Computational Biology Group Max-Planck-Institut für Informatik Stuhlsatzenhausweg 85 66123 Saarbrücken, Germany Phone: +49 681 9325 314 Fax: +49 681 9325 399 E-mail: [EMAIL PROTECTED] WWW: http://www.mpi-sb.mpg.de/units/ag3/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] graph algorithms in R
I was wondering if there are any packages available that can represent mathematical graphs along with functions to manipulate them? Google did'nt turn up anything ( I may be asking too much of R :-/ ) I was looking for the same thing the other day, and found that a graph package for R is being developed as part of the bioconductor project. However, I haven't tried it yet, so I don't know about the status (judging from the function list one shouldn't expect a comprehensive collection of graph algorithms, but at least the base structures and some random graph stuff seem to be implemented already). There is also a package for visualization, Rgraphviz. http://www.bioconductor.org/ http://www.bioconductor.org/repository/release1.3/package/html/graph.html http://www.bioconductor.org/repository/release1.2/package/html/Rgraphviz.html Tobias __ Tobias Sing Diploma Student Computational Biology Group Max-Planck-Institut für Informatik Stuhlsatzenhausweg 85 66123 Saarbrücken, Germany Also affiliated with: Machine Learning and Natural Language Processing Group Institut für Informatik Albert-Ludwigs-Universität Freiburg, Germany Phone: +49 681 9325 314 Fax: +49 681 9325 399 E-mail: [EMAIL PROTECTED] WWW: http://www.mpi-sb.mpg.de/units/ag3/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
