[BABEL] evaluation of R code in export

[BABEL] evaluation of R code in export

[Rainer M Krug]

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Hi

assuming I have the following in an org buffer (and enabled evaluation
of R code), and export it to html.

The exported html looks perfect, but when I go into the *R_test* buffer,
I see all the commands evaluated in the export (which is not such a
problem), but they are also inserted in the history.

When evaluating a line of code in ESS, this line is evaluated, but NOT
added to the history. Would that be possible for evaluation of R code
during export as well?

My reasoning is, that I have a report in an .org file, which is using an
existing R session in which I conduct simulations. When creating the
report from a finished simulation, my command history in the *R* buffer
contains all the commands evaluated for the export, and if I want to
change one parameter for the simulation, I either have to go back
several commands to find it, or type it in again. If the evaluated
commands would not appear in the history, I could simply go one command
back.

If it is not to much work, it would be great if this could be changed.

Cheers and thanks for an excellent tool,

Rainer

############################################

#+BABEL: session *R_test*
** test
#+begin_src R :exports both
  x <- 5
  x
#+end_src

############################################

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

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Tel:        +33 - (0)9 53 10 27 44
Cell:       +27 - (0)8 39 47 90 42
Fax (SA):   +27 - (0)8 65 16 27 82
Fax (D) :   +49 - (0)3 21 21 25 22 44
Fax (FR):   +33 - (0)9 58 10 27 44
email:      Rainer@krugs.de

Skype:      RMkrug
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Re: [BABEL] evaluation of R code in export

[Eric Schulte]

Hi Rainer,

I general it is useful to have the results of Babel-evaluated code
appear in the session history as it can help for debugging.

Maybe (if you are specifying the session on a subtree or file wide
bases) it would be possible to change the session name to a different
name so that your normal working session won't be polluted.

This is butting up against a more general feature which has been dancing
in the twilight of Babel's glow for some time now.  Namely the ability
to specify header arguments which are conditional on the export state,
where export state can be something like
- nil :: not currently export, this is the default
- t :: an export is taking place
- html :: exporting to html
- latex :: exporting to latex
- ascii :: exporting to ascii
etc...

How exactly this should best be folded into the existing header argument
resolution schema is not immediately clear, so this development may take
some time.

If anyone has suggestions on syntax or behavior for this functionality
please do share.

Thanks -- Eric

Rainer M Krug <r.m.krug@gmail.com> writes:

> Hi
>
> assuming I have the following in an org buffer (and enabled evaluation
> of R code), and export it to html.
>
> The exported html looks perfect, but when I go into the *R_test* buffer,
> I see all the commands evaluated in the export (which is not such a
> problem), but they are also inserted in the history.
>
> When evaluating a line of code in ESS, this line is evaluated, but NOT
> added to the history. Would that be possible for evaluation of R code
> during export as well?
>
> My reasoning is, that I have a report in an .org file, which is using an
> existing R session in which I conduct simulations. When creating the
> report from a finished simulation, my command history in the *R* buffer
> contains all the commands evaluated for the export, and if I want to
> change one parameter for the simulation, I either have to go back
> several commands to find it, or type it in again. If the evaluated
> commands would not appear in the history, I could simply go one command
> back.
>
> If it is not to much work, it would be great if this could be changed.
>
> Cheers and thanks for an excellent tool,
>
> Rainer
>
> ############################################
>
> #+BABEL: session *R_test*
> ** test
> #+begin_src R :exports both
>   x <- 5
>   x
> #+end_src
>
> ############################################

Re: [BABEL] evaluation of R code in export

[Rainer M Krug]

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Hash: SHA1

Hi Eric,

On 23/07/2010 19:45, Eric Schulte wrote:
> Hi Rainer,
> 
> I general it is useful to have the results of Babel-evaluated code
> appear in the session history as it can help for debugging.

Ok - agreed. The results are quite useful - but I would prefer the
history of the commands in the R session which is accessible by C-up to
not include the commands issued - but I can live with it as it is now.

> 
> Maybe (if you are specifying the session on a subtree or file wide
> bases) it would be possible to change the session name to a different
> name so that your normal working session won't be polluted.

Wouldn't work, as I am creating a report of an object created in the
other R session - unless I save it and load it, which would be an
option. I'll think about it.

> 
> This is butting up against a more general feature which has been dancing
> in the twilight of Babel's glow for some time now.  Namely the ability
> to specify header arguments which are conditional on the export state,
> where export state can be something like
> - nil :: not currently export, this is the default
> - t :: an export is taking place
> - html :: exporting to html
> - latex :: exporting to latex
> - ascii :: exporting to ascii
> etc...

I think that would be really useful - in addition, when I want to
include a graph in the export, I would prefer to be able to specify one
format for html (png) and pdf for latex / pdf export.

> 
> How exactly this should best be folded into the existing header argument
> resolution schema is not immediately clear, so this development may take
> some time.
> 
> If anyone has suggestions on syntax or behavior for this functionality
> please do share.

Unfortunately not,

Cheers and thanks,

Rainer

> 
> Thanks -- Eric
> 
> Rainer M Krug <r.m.krug@gmail.com> writes:
> 
>> Hi
>>
>> assuming I have the following in an org buffer (and enabled evaluation
>> of R code), and export it to html.
>>
>> The exported html looks perfect, but when I go into the *R_test* buffer,
>> I see all the commands evaluated in the export (which is not such a
>> problem), but they are also inserted in the history.
>>
>> When evaluating a line of code in ESS, this line is evaluated, but NOT
>> added to the history. Would that be possible for evaluation of R code
>> during export as well?
>>
>> My reasoning is, that I have a report in an .org file, which is using an
>> existing R session in which I conduct simulations. When creating the
>> report from a finished simulation, my command history in the *R* buffer
>> contains all the commands evaluated for the export, and if I want to
>> change one parameter for the simulation, I either have to go back
>> several commands to find it, or type it in again. If the evaluated
>> commands would not appear in the history, I could simply go one command
>> back.
>>
>> If it is not to much work, it would be great if this could be changed.
>>
>> Cheers and thanks for an excellent tool,
>>
>> Rainer
>>
>> ############################################
>>
>> #+BABEL: session *R_test*
>> ** test
>> #+begin_src R :exports both
>>   x <- 5
>>   x
>> #+end_src
>>
>> ############################################


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

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Tel:        +33 - (0)9 53 10 27 44
Cell:       +27 - (0)8 39 47 90 42
Fax (SA):   +27 - (0)8 65 16 27 82
Fax (D) :   +49 - (0)3 21 21 25 22 44
Fax (FR):   +33 - (0)9 58 10 27 44
email:      Rainer@krugs.de

Skype:      RMkrug
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Re: [BABEL] evaluation of R code in export

[Eric Schulte]

Rainer M Krug <r.m.krug@gmail.com> writes:

> Hi Eric,
>
> On 23/07/2010 19:45, Eric Schulte wrote:
>> Hi Rainer,
>> 
>> I general it is useful to have the results of Babel-evaluated code
>> appear in the session history as it can help for debugging.
>
> Ok - agreed. The results are quite useful - but I would prefer the
> history of the commands in the R session which is accessible by C-up to
> not include the commands issued - but I can live with it as it is now.
>

Hi Rainer,

I have found no good answer for sending commands to an inferior process
w/o adding them to the history ring.  There is one possible way forward,
the investigation of which is now on the task stack for babel
development but probably won't happen in the near future.

Best -- Eric

Re: [BABEL] evaluation of R code in export

[Rainer M Krug]

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Hash: SHA1

On 28/07/10 15:53, Eric Schulte wrote:
> Rainer M Krug <r.m.krug@gmail.com> writes:
> 
>> Hi Eric,
>>
>> On 23/07/2010 19:45, Eric Schulte wrote:
>>> Hi Rainer,
>>>
>>> I general it is useful to have the results of Babel-evaluated code
>>> appear in the session history as it can help for debugging.
>>
>> Ok - agreed. The results are quite useful - but I would prefer the
>> history of the commands in the R session which is accessible by C-up to
>> not include the commands issued - but I can live with it as it is now.
>>
> 

Hi Eric

> Hi Rainer,
> 
> I have found no good answer for sending commands to an inferior process
> w/o adding them to the history ring.  There is one possible way forward,
> the investigation of which is now on the task stack for babel
> development but probably won't happen in the near future.

ESS is doing it, when submitting and evaluating a line of R code - maybe
that could help? but as I said before, I don't know anything about
emacs-lisp, and less about how emacs and the modes work, so it might not
be applicable.

As I said - I can easily live with that.

Cheers,

Rainer


> 
> Best -- Eric


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

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Tel:        +33 - (0)9 53 10 27 44
Cell:       +27 - (0)8 39 47 90 42
Fax (SA):   +27 - (0)8 65 16 27 82
Fax (D) :   +49 - (0)3 21 21 25 22 44
Fax (FR):   +33 - (0)9 58 10 27 44
email:      Rainer@krugs.de

Skype:      RMkrug
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