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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 11:11:32 +0200
User-agent: Gnus/5.13 (Gnus v5.13) Emacs/24.3 (darwin)

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

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.

> 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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