Re: [SciPy-dev] Problem with F distribution, or with me? - ticket 422 might apply for discrete distributions
On Tue, Aug 26, 2008 at 8:18 PM, <josef.pktd@gmail.com> wrote:
Can somebody run:
stats.zipf.pmf(range(10),1.5) stats.zipf.cdf(10,1.5) stats.zipf.cdf(range(10),1.5)
stats.zipf.cdf(10,1.5) Traceback (most recent call last): File "<stdin>", line 1, in ? File "C:\Josef\_progs\Subversion\scipy_trunk\dist\Programs\Python24\Lib\site-p ackages\scipy\stats\distributions.py", line 3549, in cdf
I get place(output,cond,self._cdf(*goodargs)) File "C:\Josef\_progs\Subversion\scipy_trunk\dist\Programs\Python24\Lib\site-p ackages\scipy\stats\distributions.py", line 3458, in _cdf return self._cdfvec(k,*args) File "C:\Programs\Python24\Lib\site-packages\numpy\lib\function_base.py", line 1092, in __call__ raise ValueError, "mismatch between python function inputs"\ ValueError: mismatch between python function inputs and received arguments
but this might be, because I am running either an older version of scipy or from my own faulty (?) build from subversion. If the current version still has this error, then I think it is related to the generic calculation of the cdf, similar to ticket 422, changeset 3797 for the moment calculation.
In my tests I get many value errors, but again I don't know whether it is my version/setup, whether the parameters are not ruled out but don't make sense, or whether there is actually a bug somewhere.
Josef
in changeset 3797 this was added to the continuous random variable: 315 self.generic_moment.nin = self.numargs+1 # Because of the *args argument 316 # of _mom0_sc, vectorize cannot count the number of arguments correctly. in current trunk these are lines 318 and 319 I don't understand the details of numpy and vectorize, but I think that the same problem with the number of arguments also applies to the generic calculation for the discrete distribution, i.e. lines 3401 self._ppf = new.instancemethod(sgf(_drv_ppf,otypes='d'), 3402 self, rv_discrete) 3403 self._pmf = new.instancemethod(sgf(_drv_pmf,otypes='d'), 3404 self, rv_discrete) 3405 self._cdf = new.instancemethod(sgf(_drv_cdf,otypes='d'), 3406 self, rv_discrete) since all _drv_??? methods also use the *args argument and the exception message I get looks the same as in ticket 422. Josef
I just saw the report by Alan McIntyre that this fails check_rvs (scipy.stats.tests.test_distributions.test_rv_discrete) Looking briefly at the current trunk source, I think now that the problem with the generic cdf for defined distributions such as zipf is in 3383 self._cdfvec = sgf(self._cdfsingle,otypes='d') which calls 3469 def _cdfsingle(self, k, *args): If the explanation in ticket 422 applies more generally, then all calls to vectorize, i.e. to sgf, would need to be checked in scipy.stats.distribution. I'm sorry if I'm barking up the wrong tree, I am just looking at the pattern without knowing the internals. Josef On 8/26/08, josef.pktd@gmail.com <josef.pktd@gmail.com> wrote:
On Tue, Aug 26, 2008 at 8:18 PM, <josef.pktd@gmail.com> wrote:
Can somebody run:
stats.zipf.pmf(range(10),1.5) stats.zipf.cdf(10,1.5) stats.zipf.cdf(range(10),1.5)
stats.zipf.cdf(10,1.5) Traceback (most recent call last): File "<stdin>", line 1, in ? File "C:\Josef\_progs\Subversion\scipy_trunk\dist\Programs\Python24\Lib\site-p ackages\scipy\stats\distributions.py", line 3549, in cdf
I get place(output,cond,self._cdf(*goodargs)) File "C:\Josef\_progs\Subversion\scipy_trunk\dist\Programs\Python24\Lib\site-p ackages\scipy\stats\distributions.py", line 3458, in _cdf return self._cdfvec(k,*args) File "C:\Programs\Python24\Lib\site-packages\numpy\lib\function_base.py", line 1092, in __call__ raise ValueError, "mismatch between python function inputs"\ ValueError: mismatch between python function inputs and received arguments
but this might be, because I am running either an older version of scipy or from my own faulty (?) build from subversion. If the current version still has this error, then I think it is related to the generic calculation of the cdf, similar to ticket 422, changeset 3797 for the moment calculation.
In my tests I get many value errors, but again I don't know whether it is my version/setup, whether the parameters are not ruled out but don't make sense, or whether there is actually a bug somewhere.
Josef
in changeset 3797 this was added to the continuous random variable: 315 self.generic_moment.nin = self.numargs+1 # Because of the *args argument 316 # of _mom0_sc, vectorize cannot count the number of arguments correctly. in current trunk these are lines 318 and 319
I don't understand the details of numpy and vectorize, but I think that the same problem with the number of arguments also applies to the generic calculation for the discrete distribution, i.e. lines
3401 self._ppf = new.instancemethod(sgf(_drv_ppf,otypes='d'), 3402 self, rv_discrete) 3403 self._pmf = new.instancemethod(sgf(_drv_pmf,otypes='d'), 3404 self, rv_discrete) 3405 self._cdf = new.instancemethod(sgf(_drv_cdf,otypes='d'), 3406 self, rv_discrete)
since all _drv_??? methods also use the *args argument and the exception message I get looks the same as in ticket 422.
Josef
patch that works for me with scipy 0.6.0 follwing the pattern of Changeset 3797 in class rv_discrete add a line, adapted from Changeset 3797 def _cdf(self, x, *args): line 3456 in scipy 0.6.0, line 3473 in trunk k = floor(x) + self._cdfvec.nin = self.numargs+1 #JP return self._cdfvec(k,*args) I could do this without recompile now zipf works:
stats.zipf._cdf(10,1.5) array(0.7638016085053122) stats.zipf.cdf(10,1.5) array(0.7638016085053122)
all test in scipy 0.6.0 stats still pass (but that's not very reliable) stats.test() Found 73/73 tests for scipy.stats.tests.test_distributions Found 10/10 tests for scipy.stats.tests.test_morestats Found 107/107 tests for scipy.stats.tests.test_stats ...........................................................................Ties preclude use of exact statistic. ..Ties preclude use of exact statistic. ................................................................................................................. ---------------------------------------------------------------------- Ran 190 tests in 0.469s OK <unittest._TextTestResult run=190 errors=0 failures=0> Josef On 8/28/08, josef.pktd@gmail.com <josef.pktd@gmail.com> wrote:
I just saw the report by Alan McIntyre that this fails check_rvs (scipy.stats.tests.test_distributions.test_rv_discrete)
Looking briefly at the current trunk source, I think now that the problem with the generic cdf for defined distributions such as zipf is in
3383 self._cdfvec = sgf(self._cdfsingle,otypes='d') which calls 3469 def _cdfsingle(self, k, *args):
If the explanation in ticket 422 applies more generally, then all calls to vectorize, i.e. to sgf, would need to be checked in scipy.stats.distribution.
I'm sorry if I'm barking up the wrong tree, I am just looking at the pattern without knowing the internals.
Josef
On 8/26/08, josef.pktd@gmail.com <josef.pktd@gmail.com> wrote:
On Tue, Aug 26, 2008 at 8:18 PM, <josef.pktd@gmail.com> wrote:
Can somebody run:
stats.zipf.pmf(range(10),1.5) stats.zipf.cdf(10,1.5) stats.zipf.cdf(range(10),1.5)
stats.zipf.cdf(10,1.5) Traceback (most recent call last): File "<stdin>", line 1, in ? File "C:\Josef\_progs\Subversion\scipy_trunk\dist\Programs\Python24\Lib\site-p ackages\scipy\stats\distributions.py", line 3549, in cdf
I get place(output,cond,self._cdf(*goodargs)) File "C:\Josef\_progs\Subversion\scipy_trunk\dist\Programs\Python24\Lib\site-p ackages\scipy\stats\distributions.py", line 3458, in _cdf return self._cdfvec(k,*args) File "C:\Programs\Python24\Lib\site-packages\numpy\lib\function_base.py", line 1092, in __call__ raise ValueError, "mismatch between python function inputs"\ ValueError: mismatch between python function inputs and received arguments
but this might be, because I am running either an older version of scipy or from my own faulty (?) build from subversion. If the current version still has this error, then I think it is related to the generic calculation of the cdf, similar to ticket 422, changeset 3797 for the moment calculation.
In my tests I get many value errors, but again I don't know whether it is my version/setup, whether the parameters are not ruled out but don't make sense, or whether there is actually a bug somewhere.
Josef
in changeset 3797 this was added to the continuous random variable: 315 self.generic_moment.nin = self.numargs+1 # Because of the *args argument 316 # of _mom0_sc, vectorize cannot count the number of arguments correctly. in current trunk these are lines 318 and 319
I don't understand the details of numpy and vectorize, but I think that the same problem with the number of arguments also applies to the generic calculation for the discrete distribution, i.e. lines
3401 self._ppf = new.instancemethod(sgf(_drv_ppf,otypes='d'), 3402 self, rv_discrete) 3403 self._pmf = new.instancemethod(sgf(_drv_pmf,otypes='d'), 3404 self, rv_discrete) 3405 self._cdf = new.instancemethod(sgf(_drv_cdf,otypes='d'), 3406 self, rv_discrete)
since all _drv_??? methods also use the *args argument and the exception message I get looks the same as in ticket 422.
Josef
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