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Re: [O] [babel][PATCHES] ob-R patches for review

From: Rainer M Krug
Subject: Re: [O] [babel][PATCHES] ob-R patches for review
Date: Fri, 09 May 2014 14:02:58 +0200
User-agent: Gnus/5.13 (Gnus v5.13) Emacs/24.3 (darwin)

Rainer M Krug <address@hidden> writes:

> Rainer M Krug <address@hidden> writes:
>> Envoyé de mon iPhone
>>> Le 8 mai 2014 à 04:26, Charles Berry <address@hidden> a écrit :
>>> Eric Schulte <schulte.eric <at> gmail.com> writes:
>>>> Rainer M Krug <Rainer <at> krugs.de> writes:
>>>>> Hi
>>>>> Attached please find seven patches for review to implement the storing
>>>>> of org variables in their own environment and to make the org-issued R
>>>>> code look nicer in the R session.
>>>>> Thanks,
>>>>> Rainer
>>>> Hi Rainer,
>>>> Thanks for these patches.  I don't have the R experience to review or
>>>> maintain them, but I'm happy to apply them.
>>>> I missed some previous discussion in this thread.  Are these patches
>>>> ready to be applied as is?
>>> IMO, the patches hard coded behaviors that would better be customizable
>>> and optional. 
>> I'll give feedback tomorrow and let you know about customization of
>> the name of the environment. The general behavior of storing the
>> variables in an environment should not be customizable as it is
>> 1) safer then the behavior of storing each variable separately
>> 2) no changes for the user are introduced 
> OK. Concerning customization options:
> There are a few points where customizations could be introduced:
> 1) transfer of variables from org to R, i.e. old behavior (variables in
> .GlobalEnv) or new behavior (in own environment (.org_variables_)) or
> own defined function
> 2) name of new environment
> 3) name of file into which to save the  variables (org_variables.RData)
> Some comments to each:
> 1) As outlined above, I see neither changes in behavior for the user
> nor disadvantages of the new behavior. As only one object is created in
> R (.org_variables_) instead of one for each variable, the chances of
> name clashes are much smaller. As the name of the variable starts with a
> dot (.), ends with an underscore (_), it is very unlikely that there is
> a nameclash in existing scripts (but you are right, one does not know).
> So I don't think, that it is necessary to include an option for
> disabling the old behavior. 
> Concerning defining an own function for data transfer, I am thinking of
> putting the variable transfer into an R function which can then be
> customized from R. My reasoning is that users using this feature are
> more likely to be fluent in R then in lisp, so more able to change these
> functions in R. In org, the whole R code would then simply replaced with
> one function call. These functions would reside in a new environment (or
> in the ESSR environment as offered by Vitalie).
> In addition, as it was not asked before to have this function
> customizable, I don't think there would be a large need for it.
> 2) I don't think name clashes are likely, so I don't see a real need to
> have the name of the org environment in R configurable. Especially when
> using these variables in R, one can always use
> .org_variables_::VARIABLENAME to access the original value. If the
> environment name is customizable, this will be different between
> customizations and not that easily reproducible between
> org-installations.
> It would be easy to configure it, but I think it is rather a
> disadvantage and would make the code (slightly) more complex.
> 3) The name into which the variables are saved could be configurable,
> but again, I do not think this is such an issue. The saved environment
> is anyway only of limited usage when the variables in org are not
> defined file wide but per source block / tree. I am actually thinking of
> removing this saving, although it is quite useful to make tangled code
> usable on a non-org system when org variables are used - comments?
> So please let me know if you see the need of customization and for
> which aspect.

I started looking into ESS in more detail and I got some useful ideas. 

I am including them at the moment in org, so please do not yet apply the



>> Cheers
>> Rainer
>>> Rainer and I had some back and forth about this -- see the thread.
>>> Best,
>>> Chuck

Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

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