[SciPy-User] R vs Python for simple interactive data analysis

Christopher Jordan-Squire cjordan1@uw....
Mon Aug 29 10:34:06 CDT 2011


On Mon, Aug 29, 2011 at 10:27 AM,  <josef.pktd@gmail.com> wrote:
> On Mon, Aug 29, 2011 at 11:10 AM, Skipper Seabold <jsseabold@gmail.com> wrote:
>> On Mon, Aug 29, 2011 at 10:57 AM, Christopher Jordan-Squire
>> <cjordan1@uw.edu> wrote:
>>> On Sun, Aug 28, 2011 at 2:54 PM, Skipper Seabold <jsseabold@gmail.com> wrote:
>>>> On Sat, Aug 27, 2011 at 10:15 PM, Bruce Southey <bsouthey@gmail.com> wrote:
>>>>> On Sat, Aug 27, 2011 at 5:06 PM, Wes McKinney <wesmckinn@gmail.com> wrote:
>>>>>> On Sat, Aug 27, 2011 at 5:03 PM, Jason Grout
>>>>>> <jason-sage@creativetrax.com> wrote:
>>>>>>> On 8/27/11 1:19 PM, Christopher Jordan-Squire wrote:
>>>>>>>> This comparison might be useful to some people, so I stuck it up on a
>>>>>>>> github repo. My overall impression is that R is much stronger for
>>>>>>>> interactive data analysis. Click on the link for more details why,
>>>>>>>> which are summarized in the README file.
>>>>>>>
>>>>>>>  From the README:
>>>>>>>
>>>>>>> "In fact, using Python without the IPython qtconsole is practically
>>>>>>> impossible for this sort of cut and paste, interactive analysis.
>>>>>>> The shell IPython doesn't allow it because it automatically adds
>>>>>>> whitespace on multiline bits of code, breaking pre-formatted code's
>>>>>>> alignment. Cutting and pasting works for the standard python shell,
>>>>>>> but then you lose all the advantages of IPython."
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> You might use %cpaste in the ipython normal shell to paste without it
>>>>>>> automatically inserting spaces:
>>>>>>>
>>>>>>> In [5]: %cpaste
>>>>>>> Pasting code; enter '--' alone on the line to stop.
>>>>>>> :if 1>0:
>>>>>>> :    print 'hi'
>>>>>>> :--
>>>>>>> hi
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Jason
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> SciPy-User mailing list
>>>>>>> SciPy-User@scipy.org
>>>>>>> http://mail.scipy.org/mailman/listinfo/scipy-user
>>>>>>>
>>>>>>
>>>>>> This strikes me as a textbook example of why we need an integrated
>>>>>> formula framework in statsmodels. I'll make a pass through when I get
>>>>>> a chance and see if there are some places where pandas would really
>>>>>> help out.
>>>>>
>>>>> We used to have a formula class is scipy.stats and I do not follow
>>>>> nipy (http://nipy.sourceforge.net/nipy/stable/index.html) as it also
>>>>> had this (extremely flexible but very hard to comprehend). It was what
>>>>> I had argued was needed ages ago for statsmodel. But it needs a
>>>>> community effort because the syntax required serves multiple
>>>>> communities with different annotations and needs. That is also seen
>>>>> from the different approaches taken by the stats packages from S/R,
>>>>> SAS, Genstat (and those are just are ones I have used).
>>>>>
>>>>
>>>> We have held this discussion at _great_ length multiple times on the
>>>> statsmodels list and are in the process of trying to integrate
>>>> Charlton (from Nathaniel) and/or Formula (from Jonathan / NiPy) into
>>>> the statsmodels base.
>>>>
>>>> http://statsmodels.sourceforge.net/dev/roadmap_todo.html#formula-framework
>>>>
>>>> and more recently
>>>>
>>>> https://groups.google.com/group/pystatsmodels/browse_thread/thread/a76ea5de9e96964b/fd85b80ae46c4931?
>>>>
>>>> https://github.com/statsmodels/formula
>>>> https://github.com/statsmodels/charlton
>>>>
>>>> Wes and I made some effort to go through this at SciPy. From where I
>>>> sit, I think it's difficult to disentangle the data structures from
>>>> the formula implementation, or maybe I'd just prefer to finish
>>>> tackling the former because it's much more straightforward. So I'd
>>>> like to first finish the pandas-integration branch that we've started
>>>> and then focus on the formula support. This is on my (our, I hope...)
>>>> immediate long-term goal list. Then I'd like to come back to the
>>>> community and hash out the 'rules of the game' details for formulas
>>>> after we have some code for people to play with, which promises to be
>>>> "fun."
>>>>
>>>> https://github.com/statsmodels/statsmodels/tree/pandas-integration
>>>>
>>>> FWIW, I could also improve the categorical function to be much nicer
>>>> for the given examples (ie., take a list, drop a reference category),
>>>> but I don't know that it's worth it, because it's really just a
>>>> stop-gap and ideally users shouldn't have to rely on it. Thoughts on
>>>> more stop-gap?
>>>>
>>>
>>> I want more usability, but I agree that a stop-gap probably isn't the
>>> right way to go, unless it has things we'd eventually want anyways.
>>>
>>>> If I understand Chris' concerns, I think pandas + formula will go a
>>>> long way towards bridging the gap between Python and R usability, but
>>>
>>> Yes, I agree. pandas + formulas would go a long, long way towards more
>>> usability.
>>>
>>> Though I really, really want a scatterplot smoother (i.e., lowess) in
>>> statsmodels. I use it a lot, and the final part of my R file was
>>> entirely lowess. (And, I should add, that was the part people liked
>>> best since one of the main goals of the assignment was to generate
>>> nifty pictures that could be used to summarize the data.)
>>>
>>
>> Working my way through the pull requests. Very time poor...
>>
>>>> it's a large effort and there are only a handful (at best) of people
>>>> writing code -- Wes being the only one who's more or less "full time"
>>>> as far as I can tell. The 0.4 statsmodels release should be very
>>>> exciting though, I hope. I'm looking forward to it, at least. Then
>>>> there's only the small problem of building an infrastructure and
>>>> community like CRAN so we can have specialists writing and maintaining
>>>> code...but I hope once all the tools are in place this will seem much
>>>> less daunting. There certainly seems to be the right sentiment for it.
>>>>
>>>
>>> At the very least creating and testing models would be much simpler.
>>> For weeks I've been wanting to see if gmm is the same as gee by
>>> fitting both models to the same dataset, but I've been putting it off
>>> because I didn't want to construct the design matrices by hand for
>>> such a simple question. (GMM--Generalized Method of Moments--is a
>>> standard econometrics model and GEE--Generalized Estimating
>>> Equations--is a standard biostatics model. They're both
>>> generalizations of quasi-likelihood and appear very similar, but I
>>> want to fit some models to figure out if they're exactly the same.)
>
> Since GMM is still in the sandbox, the interface is not very polished,
> and it's missing some enhancements. I recommend asking on the mailing
> list if it's not clear.
>
> Note GMM itself is very general and will never be a quick interactive
> method. The main work will always be to define the moment conditions
> (a bit similar to non-linear function estimation, optimize.leastsq).
>
> There are and will be special subclasses, eg. IV2SLS, that have
> predefined moment conditions, but, still, it's up to the user do
> construct design and instrument arrays.
> And as far as I remember, the GMM/GEE package in R doesn't have a
> formula interface either.
>

Both of the two gee packages in R I know of have formula interfaces.

http://cran.r-project.org/web/packages/geepack/
http://cran.r-project.org/web/packages/gee/index.html

-Chris JS

> Josef
>
>>>
>>
>> Oh, it's not *that* bad. I agree, of course, that it could be better,
>> but I've been using mainly Python for my work, including GMM and
>> estimating equations models (mainly empirical likelihood and
>> generalized maximum entropy) for the last ~two years.
>>
>> Skipper
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>>
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