Queestion concerning lists - was: [babel][PATCHES] ob-R patches for review

[Rainer M Krug <Rainer@krugs.de>]

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Rainer M Krug <Rainer@krugs.de> writes:

> Eric Schulte <schulte.eric@gmail.com> writes:
>
>> Rainer M Krug <Rainer@krugs.de> writes:
>>
>>> Bastien <bzg@gnu.org> writes:
>>>
>>>> Hi Rainer,
>>>>
>>>> Rainer M Krug <r.m.krug@gmail.com> writes:
>>>>
>>>>> I'll look at it again tomorrow and let you know as I made some changes
>>>>> since then. Do you prefer one patch to several?
>>>>
>>>> Up to Eric's taste -- but in general I think a series of patches
>>>> is better, it allows you to isolate and fix conflicts more easily.
>>>
>>
>> I agree, multiple patches make future maintenance easier.
>>
>
> OK - I'll do so.
>
> A little bit off-topic, is there a "git way" of splitting one patch into
> several patches, if it was a single commit?
>
>>>> 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. 
>>>
>>> Rainer and I had some back and forth about this -- see the thread.
>>
>> With respect to these points, I'm inclined to agree with Charles in the
>> following.
>
> OK - see further comments below.
>
>>
>>> All you have to do is add this:
>>>
>>> (defvar org-babel-R-assign-elisp-function 'org-babel-R-assign-elisp
>>>   "Name or definition of function to handle `:var name=value'
>>> header args."
>>>   )
>>>
>>> and change one line in org-babel-variable-assignments:R from
>>>
>>>     (org-babel-R-assign-elisp to
>>>
>>>    (funcall org-babel-R-assign-elisp-function
>>>
>>> and the user can provide her own elisp assignment function.
>>>
>>> This gives users who want special behavior like creating something
>>> other than a data.frame the option of providing their own function.
>>
>> Would such a customization variable be difficult to add to your patches?
>
> I don't think so - I'll look into it.
>
>> If not would you mind submitting a version of the patches split into
>> multiple commits with as much of the hard-coded R code as feasible
>> placed into customizable variables along the lines of the
>> `org-babel-R-assign-elisp-function' variable suggested by Charles.  
>
> I am thinking of actually not providing the R code in org-variables, but
> to put them into R files and to source them. By doing this, the
> customization could be done in R, which will be much easier for R users
> then to customize emacs variables.
>
> These would be sourced and stored into an environment "org:functions",
> using the same approach as ESS is using to store functions into an
> environment "ESSR". I would then put the variables transfered into
> "org:variables". These environments would only exist in the search path,
> and not overwrite any user set objects in R.

I am working on it, but I have a question concerning strings and lists
in elisp.

In the function  org-babel-execute:R it says:

,----
| (inside
| 		   (list (org-babel-expand-body:R body params graphics-file)))
`----

I now want to convert "inside" to a comma separated string. I am doing
now the following:

,----
| (replace-regexp-in-string "\n" ", " (format "%s" inside))
`----

but this does not look elegant to me, as I am converting inside to a
string and then do a replace. There is the function mapconcat, but I
don't get it to work:

,----
| (replace-regexp-in-string "\n" ", " (format "%s" inside))
| "(     createOrgVariablesEnvironment(), plot(1))"
| 
| (mapconcat 'identity inside ", ")
| "     createOrgVariablesEnvironment()
| plot(1)"
`----

What am I missing?

Thanks,

Rainer

>
> As it needs to be sourced for each R process once, the right place would
> be in  org-babel-R-initiate-session - correct?
>
> What would be the best place to put these R files? 
>
>> One lesson I've certainly learned from the Org-mode mailing list is
>> that you can't anticipate all of the ways that your code will be used,
>> so up-front customizability generally pays off.
>
> OK - point taken - and I am definitely one of those users who thinks
> about unusual usages of certain features.
>
> Cheers,
>
> Rainer
>
>>
>> Thanks,
>> Eric
>>
>>>
>>> Thanks
>>>
>>> Rainer

-- 
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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email:      Rainer@krugs.de

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