sampling failure

[Lorna Le Stanc]

Hello everyone,

I get an error when trying to sample, does someone have any idea of what is going on ? For other dataset, it is perfectly working.

Many thanks to you all.

Lorna


Here is the code :

dat_pass = data.loc[data['stade'].isin([g])]

m = hddm.HDDMStimCoding(dat_pass, include = 'z', p_outlier = 0.05, stim_col = 'true_response',split_param = 'v',depends_on = ll[0])

m.find_starting_values()

m.sample(20000, burn = 10000, thin = 5, dbname = '/home/lorna/These/Projets/analyses_comite/stm_comite/data/ddm/acoustic/%s_m%i_%i_db' %(g,0,1), db = 'pickle')

Here is the output :

/home/lorna/These/Tools/anaconda2/lib/python2.7/site-packages/pymc/Node.py:403: VisibleDeprecationWarning: using a non-integer number instead of an integer will result in an error in the future
  self.__name__ = input['__name__']
Traceback (most recent call last):

  File "<ipython-input-10-5a0f731e9f64>", line 1, in <module>
    m.sample(20000, burn = 10000, thin = 5, dbname = '/home/lorna/These/Projets/analyses_comite/stm_comite/data/ddm/acoustic/%s_m%i_%i_db' %(g,0,1), db = 'pickle')

  File "/home/lorna/These/Tools/anaconda2/lib/python2.7/site-packages/kabuki/hierarchical.py", line 651, in sample
    self.mc.sample(*args, **kwargs)

  File "/home/lorna/These/Tools/anaconda2/lib/python2.7/site-packages/pymc/MCMC.py", line 279, in sample
    Sampler.sample(self, iter, length, verbose)

  File "/home/lorna/These/Tools/anaconda2/lib/python2.7/site-packages/pymc/Model.py", line 251, in sample
    self._loop()

  File "/home/lorna/These/Tools/anaconda2/lib/python2.7/site-packages/pymc/MCMC.py", line 315, in _loop
    step_method.step()

  File "/home/lorna/These/Tools/anaconda2/lib/python2.7/site-packages/kabuki/step_methods.py", line 383, in step
    assert iter < self.maxiter, "Step-out procedure failed"

AssertionError: Step-out procedure failed

[Thomas Wiecki]

Hi,

Most likely those are caused by outliers in your data, or using miliseconds instead of seconds.

Best,

Thomas

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[Lorna Le Stanc]

Hi Thomas,

Thanks for your quick reply.

I do use seconds and even by removing outliers(  I tried 4s and 2 seconds as cutoff for slow outliers and 0.5s  and 0.2s for small outliers), I still get this error message. Any other idea ?

Lorna

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[Thomas Wiecki]

Sure you coded response and stimulus columns correctly?

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