On Wed, 23 Mar 2011, Jonas Kaplan wrote: > have successfully installed 0.6rc2 on OSX, which I consider a great > achievement. :)
congratulations ;) > I miss the old nperlabel option in the NFoldSplitter... is there > an easy way to recreate this behavior with the new NFoldPartitioner? in the quest for the modularization and thus flexibility, all such options were pulled out of *Splitters and have their own classes which you would need to chain to achieve virtually any effect you like: e.g. for nperlabel: Balancer http://www.pymvpa.org/generated/mvpa.generators.resampling.Balancer.html so, just chain the NFoldPartitioner an Balancer with something like: partitioner = ChainNode([NFoldPartitioner(), Balancer()], space='partitions') Such chaining, although might be looking like an unnecessary inconvenience, allows to greater flexibility, e.g. see http://www.pymvpa.org/examples/permutation_test.html for permutations generators > Also, I've been wanting to give RFE a try... I have been reading > through all the messages on this list about it and I *think* I am starting to > understand the many layers. However, all of the code examples seem to be > written with the older syntax. It would be helpful to see a working version > of oy -- which ones? I guess these guys: $> ls -l doc/source/*txt -rw-rw-r-- 1 yoh yoh 1990 Mar 5 15:36 doc/source/authors.txt -rw-rw-r-- 1 yoh yoh 26629 Mar 4 17:38 doc/source/classifiers.txt -rw-rw-r-- 1 yoh yoh 15677 Mar 4 17:38 doc/source/datasets.txt -rw-rw-r-- 1 yoh yoh 10696 Mar 4 17:38 doc/source/featsel.txt -rw-rw-r-- 1 yoh yoh 797 Mar 5 15:36 doc/source/mappers.txt -rw-rw-r-- 1 yoh yoh 9099 Mar 5 15:36 doc/source/measures.txt which managed to escape our daily testing because of old-fashioned .txt extension (instead of .rst) so they were not part of the daily tests we thought to convert (nearly) or deprecate all of them. > RFE written under .6, does anything like that exist? well, if documentation might be lagging behind in covering the features, the unittests are staying quite in sync; so you could find plenty of constructs in there with a simple query: $> git grep RFE mvpa/tests mvpa/tests/test_datameasure.py:from mvpa.featsel.rfe import RFE mvpa/tests/test_datameasure.py: # Proper RFE: aggregate sensitivities across multiple splits, mvpa/tests/test_datameasure.py: rfe = RFE(sensitivity_analyzer= mvpa/tests/test_rfe.py:from mvpa.featsel.rfe import RFE mvpa/tests/test_rfe.py:class RFETests(unittest.TestCase): mvpa/tests/test_rfe.py: rfe = RFE(sens_ana, mvpa/tests/test_rfe.py: RFE(rfesvm_split.get_sensitivity_analyzer(), mvpa/tests/test_rfe.py: # on features selected via RFE mvpa/tests/test_rfe.py: self.fail('CrossValidation cannot handle classifier with RFE ' mvpa/tests/test_rfe.py: feature_selection = RFE( mvpa/tests/test_rfe.py: return unittest.makeSuite(RFETests) could you have a look at mvpa/tests/test_rfe.py ? if you do not have a local clone, then see https://github.com/PyMVPA/PyMVPA/blob/master/mvpa/tests/test_rfe.py -- =------------------------------------------------------------------= Keep in touch www.onerussian.com Yaroslav Halchenko www.ohloh.net/accounts/yarikoptic _______________________________________________ Pkg-ExpPsy-PyMVPA mailing list Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa