Re: Re: [babel] R questions

Re: Re: [babel] R questions

[Thomas S. Dye]

Aloha Sebasien,

On Dec 7, 2009, at 11:50 PM, Sébastien Vauban wrote:

> But what's a "NA" value in general?  Is 0 always a meaningful value as
> numeric?  Context-sensitive..
>

NA is a logical constant of length 1 which contains a missing value  
indicator.  Whether or not 0 is a meaningful value as numeric depends  
on your data and the questions you are asking of it.  You don't ask  
this question, but if I read this thread correctly and you are trying  
to workaround a data input problem with R in Org-babel, then replacing  
missing values with 0 in a numeric context to get around the Org-babel  
problem is NOT a good idea.

HTH,
Tom

Re: Re: [babel] R questions

[Dan Davison]

Sébastien Vauban <wxhgmqzgwmuf@spammotel.com> writes:

> Hi Dan and Eric,
>
> I have a side question, but I think this is of general interest for others as
> well.
>
> I almost don't know GnuPlot neither R -- yes, before seeing the light, I used
> Excel for all my graphs.
>
> So, my question is: for typical small plots (piecharts and barplots), is there
> any Org-babel reason that would advocate for doing it in one of the two above
> language preferably than in the other one?

> Reasons could be better integration (for editing or (re-)generating the
> graphs), simpler semantics (with NA values, for example), etc.

Org-babel wants to support both languages as well as possible. So there
is no such purely org-babel reason; or if there is, there shouldn't be,
so tell us about it and we'll try to fix it.

With respect to graphics, I'm sure that each one has things it can do
better than the other (e.g. I get the impression that gnuplot is better
for "3D" graphics).

But yes, if there was someone who (a) didn't know either language, and
(b) were limited in the amount of time they could devote to learning
computer languages, and (c) thought they might one day have some use for
some of the things that R can do and gnuplot can't, then I would suggest
that they start using R over gnuplot.

R is a fully-featured programming language with a very large amount of
numerical/statistical/scientific procedures available. (2094 add-on
packages currently listed at http://cran.r-project.org/). One wouldn't
normally compare R with gnuplot; more appropriate comparisons might be
to the scientific libraries for python, perl and C++, and to things like
Excel, SAS, and Matlab, Mathematica (although R is not a symbolic
mathematics engine).

Dan

>
>
> Best regards,
>   Seb

Re: Re: [babel] R questions

[Thomas S. Dye]

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Hi Sebastien,

On Dec 8, 2009, at 11:37 AM, Sébastien Vauban wrote:

> Hi Thomas,
>
> "Thomas S. Dye" wrote:
>> On Dec 7, 2009, at 11:50 PM, Sébastien Vauban wrote:
>>
>>>> [2] I guess one could potentially think about dealing with  
>>>> missing values
>>>>    more explicitly in org-babel. E.g. there could be a header arg
>>>>    specifying what values are to be treatyed as missing. Nothing  
>>>> like
>>>>    that exists currently.
>>>
>>> I guess such a feature would be required on the long term. Of  
>>> course, even
>>> specifying what would be the needed behavior is already difficult,  
>>> I think.
>>> One must have good knowledge of the multiple languages and  
>>> environments,
>>> and try to abstract the best behavior out of these.
>>>
>>> Side note -- I know, for example, that there is an option in  
>>> Access to let
>>> it consider the empty string ('') as the NULL value, or not. Clear.
>>>
>>> But what's a "NA" value in general?  Is 0 always a meaningful  
>>> value as
>>> numeric?  Context-sensitive..
>>
>> NA is a logical constant of length 1 which contains a missing value
>> indicator. Whether or not 0 is a meaningful value as numeric  
>> depends on your
>> data and the questions you are asking of it. You don't ask this  
>> question,
>
> ?  I thought I addressed that when asking (to myself) "Is 0 always a
> meaningful value as numeric?" and answering [that it certainly is]
> "context-sensitive.."
>
>
>> but if I read this thread correctly and you are trying to  
>> workaround a data
>> input problem with R in Org-babel,
>
> No, you misread, or I mis-wrote ;-)
>
> I wasn't speaking of R only, saying that "such a feature would be  
> required on
> the long term [... for] the multiple languages".
>
> Thinking at shell-script (with empty strings), SQL code (with empty  
> strings
> and NULL values), etc.
>
>
>> then replacing missing values with 0 in a numeric context to get  
>> around the
>> Org-babel problem is NOT a good idea.
>
> Implementing a fixed interpretation is NOT a good idea. I share your  
> point of
> view.
>
> My comments were:
>
> - I think we must be able to write a rule for interpreting  
> "empty" (whatever
>  it means) values;
>
> - We should think at what's needed to cover the current and future  
> needs, not
>  focusing on one specific language (R), but thinking at all of them  
> (shell
>  commands, SQL, etc.).
>
> Best regards,
>  Seb
>
> -- 
> Sébastien Vauban

I agree with you on the importance of having some way to represent  
missing values in Org-babel that can be translated cleanly and  
transparently to the representations used by specific languages.

I was responding to one part of your longer message in the context of  
the message subject, "R questions."  I see now that you were asking a  
more general question.  Mea culpa.

All the best,
Tom

Thomas S. Dye, Ph.D.
T. S. Dye & Colleagues, Archaeologists, Inc.
Phone: (808) 529-0866 Fax: (808) 529-0884
http://www.tsdye.com


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Re: [babel] R questions

[Sébastien Vauban]

Hi Thomas,

"Thomas S. Dye" wrote:
> On Dec 8, 2009, at 11:37 AM, Sébastien Vauban wrote:
>> "Thomas S. Dye" wrote:
>>> On Dec 7, 2009, at 11:50 PM, Sébastien Vauban wrote:
>>>
>>>>> [2] I guess one could potentially think about dealing with missing values
>>>>>    more explicitly in org-babel. E.g. there could be a header arg
>>>>>    specifying what values are to be treatyed as missing. Nothing like
>>>>>    that exists currently.
>>>>
>>>> I guess such a feature would be required on the long term. Of course,
>>>> even specifying what would be the needed behavior is already difficult, I
>>>> think.
>>>> One must have good knowledge of the multiple languages and environments,
>>>> and try to abstract the best behavior out of these.
>>>>
>>>> But what's a "NA" value in general? Is 0 always a meaningful value as
>>>> numeric? Context-sensitive..
>>>
>>> [...] but if I read this thread correctly and you are trying to workaround
>>> a data input problem with R in Org-babel,
>>
>> No, you misread, or I mis-wrote ;-)
>>
>> I wasn't speaking of R only, saying that "such a feature would be required
>> on the long term [... for] the multiple languages".
>>
>> Thinking at shell-script (with empty strings), SQL code (with empty strings
>> and NULL values), etc.
>>
>> Implementing a fixed interpretation is NOT a good idea. I share your point
>> of view.
>>
>> My comments were:
>>
>> - I think we must be able to write a rule for interpreting "empty"
>>   (whatever it means) values;
>>
>> - We should think at what's needed to cover the current and future needs,
>>   not focusing on one specific language (R), but thinking at all of them
>>   (shell commands, SQL, etc.).
>
> I agree with you on the importance of having some way to represent missing
> values in Org-babel that can be translated cleanly and transparently to the
> representations used by specific languages.

We're on the same wavelength for such a need. Remains to specify what we would
want, in order to be simple and generic enough...

Best regards,
  Seb

-- 
Sébastien Vauban



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