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On Sat, Dec 17, 2011 at 11:20 AM, Warren Weckesser <warren.weckesser@enthought.com> wrote:
On Wed, Nov 30, 2011 at 3:25 PM, <josef.pktd@gmail.com> wrote:
On Wed, Nov 30, 2011 at 4:10 PM, Warren Weckesser <warren.weckesser@enthought.com> wrote:
On Wed, Nov 30, 2011 at 3:05 PM, <josef.pktd@gmail.com> wrote:
On Wed, Nov 30, 2011 at 4:02 PM, Warren Weckesser <warren.weckesser@enthought.com> wrote:
On Wed, Nov 30, 2011 at 2:54 PM, <josef.pktd@gmail.com> wrote:
On Wed, Nov 30, 2011 at 3:45 PM, <josef.pktd@gmail.com> wrote: > On Wed, Nov 30, 2011 at 3:25 PM, Alacast <alacast@gmail.com> > wrote: >> axis=0 (the default) works fine. axis=1, etc, is clearly wrong. >> Am I >> misunderstanding how to use this, or is this a bug? >> >> In [16]: i = rand(4,4) >> >> In [17]: i >> Out[17]: >> array([[ 0.85367762, 0.25348857, 0.23572615, 0.50403358], >> [ 0.70199066, 0.81872151, 0.47357357, 0.20425537], >> [ 0.31042673, 0.25837984, 0.73550134, 0.57970176], >> [ 0.42828877, 0.60988596, 0.04059321, 0.73944219]]) >> >> In [18]: zscore(i, axis=0) >> Out[18]: >> array([[ 1.30128758, -0.96195723, -0.52119142, -0.01453907], >> [ 0.59653471, 1.38544585, 0.39284654, -1.55756529], >> [-1.22271057, -0.94164388, 1.39942427, 0.37494213], >> [-0.67511172, 0.51815526, -1.27107939, 1.19716222]]) >> >> In [19]: zscore(i[:,0]) >> Out[19]: array([ 1.30128758, 0.59653471, -1.22271057, >> -0.67511172]) >> >> In [20]: zscore(i[:,0])==zscore(i,axis=0)[:,0] >> Out[20]: array([ True, True, True, True], dtype=bool) >> >> In [21]: zscore(i, axis=1) >> Out[21]: >> array([[-0.99378502, -1.59397407, -1.61173649, -1.34342906], >> [-1.6379836 , -1.52125275, -1.86640069, -2.13571889], >> [-2.09968257, -2.15172946, -1.67460796, -1.83040754], >> [-1.29796925, -1.11637205, -1.68566481, -0.98681582]]) >> #The above is obviously wrong, as everything has a negative z >> score >> >> In [22]: zscore(i[0,:]) >> Out[22]: array([ 1.56824016, -0.83321371, -0.90428403, >> 0.16925757]) >> >> In [23]: zscore(i[0,:])==zscore(i,axis=1)[0,:] >> Out[23]: array([False, False, False, False], dtype=bool) >> #Using axis=1 produces different results from taking a row >> directly. >> >> In [24]: zscore(i, axis=-1) >> Out[24]: >> array([[-0.99378502, -1.59397407, -1.61173649, -1.34342906], >> [-1.6379836 , -1.52125275, -1.86640069, -2.13571889], >> [-2.09968257, -2.15172946, -1.67460796, -1.83040754], >> [-1.29796925, -1.11637205, -1.68566481, -0.98681582]]) >> #Getting rows by using axis=-1 is no better (this is the same >> result >> as >> axis=1 > > This looks like a serious bug to me. I don't know what happened > here > (. > > The docstring example also has negative numbers only. > > ??? > > I'm looking into it > > Thanks for reporting
a misplaced axis: if axis>0 then it calculates x - mean/std instead of (x - mean) / std
now, how did this go through the testing ?
There is only one test for zscore, on a 1-d sample without the axis keyword.
which just show that we shouldn't trust changesets that say
"stats: rewrite of zscore functions, ticket:1083 regression tests pass, still need tests for enhancements"
http://projects.scipy.org/scipy/changeset/6169
my mistake (maybe January 2nd wasn't a good day.)
Josef
Thanks for the link. Looks like zmap has the same bug. :(
copy paste errors?
I just don't know why I didn't do basic checks like this in the final version
assert_equal(zscore(x.T, axis=0).T, zscore(x, axis=1)) a = zscore(x, axis=1) a.var(1) array([ 1., 1., 1., 1.]) a.mean(1) array([ 0.00000000e+00, -1.11022302e-16, 0.00000000e+00, 1.94289029e-16])
Josef
Ticket: http://projects.scipy.org/scipy/ticket/1575 Pull request: https://github.com/scipy/scipy/pull/116
Thanks Warren, good to see you and Ralf taking care of stats. Josef
Warren
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