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

[Rainer M Krug]

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.

>
> 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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