From: Rainer M Krug <Rainer@krugs.de>
To: Charles Berry <ccberry@ucsd.edu>
Cc: "emacs-orgmode@gnu.org" <emacs-orgmode@gnu.org>, schulte.eric@gmail.com
Subject: Re: [babel][PATCHES] ob-R patches for review
Date: Fri, 09 May 2014 11:11:32 +0200 [thread overview]
Message-ID: <m2k39vwc3f.fsf@krugs.de> (raw)
In-Reply-To: <C5F03688-8A03-449D-85FC-A89B57555E42@gmail.com> (Rainer M. Krug's message of "Thu, 8 May 2014 12:02:36 +0200")
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Rainer M Krug <r.m.krug@gmail.com> writes:
> Envoyé de mon iPhone
>
>> Le 8 mai 2014 à 04:26, Charles Berry <ccberry@ucsd.edu> 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
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D): +49 - (0)3 21 21 25 22 44
email: Rainer@krugs.de
Skype: RMkrug
PGP: 0x0F52F982
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next prev parent reply other threads:[~2014-05-09 9:11 UTC|newest]
Thread overview: 24+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-04-29 12:43 [babel][PATCHES] ob-R patches for review Rainer M Krug
2014-04-29 18:15 ` Charles Berry
2014-04-30 12:28 ` Rainer M Krug
2014-04-30 22:49 ` Charles C. Berry
2014-05-01 9:10 ` Rainer M Krug
2014-05-07 10:27 ` Eric Schulte
2014-05-08 2:26 ` Charles Berry
2014-05-08 10:02 ` Rainer M Krug
2014-05-09 9:11 ` Rainer M Krug [this message]
2014-05-09 12:02 ` Rainer M Krug
2014-05-08 9:57 ` Rainer M Krug
2014-05-09 13:03 ` Bastien
2014-05-09 13:45 ` Rainer M Krug
2014-05-09 14:34 ` Eric Schulte
2014-05-12 8:33 ` Rainer M Krug
2014-05-12 12:23 ` Suvayu Ali
2014-05-12 12:41 ` Rainer M Krug
2014-05-12 14:01 ` Queestion concerning lists - was: " Rainer M Krug
2014-05-12 15:23 ` Eric Schulte
2014-05-12 15:21 ` Eric Schulte
2014-05-12 19:08 ` Rainer M Krug
2014-05-12 22:05 ` Charles C. Berry
[not found] ` <m2y4y2f499.fsf@krugs.de>
2014-05-16 18:22 ` Charles C. Berry
2014-06-06 16:11 ` Eric Schulte
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