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Re: Efficiently reuse code in org babel with R


From: Naresh Gurbuxani
Subject: Re: Efficiently reuse code in org babel with R
Date: Thu, 7 Jul 2022 12:09:47 +0000

Thanks for providing a detailed solution.  

I also learned from other responses.

Sent from my iPhone

> On Jul 7, 2022, at 4:42 AM, Jeremie Juste <jeremiejuste@gmail.com> wrote:
> 
> ´╗┐Hello Naresh,
> 
> Many thanks for sharing.
> If I'm looking for efficiency, I tend not to use noweb and use an R
> session instead.
> 
> One reason is that caching does not work with noweb
> 
> #+name: test
> #+begin_src R  :cache yes :session *R*
> Sys.sleep(10)
>  a <- 1
> #+end_src
> 
> #+RESULTS[36c41617bf9aa447ecc28fca8207eab38340d418]: test
> : 1
> 
> 
> #+name: add1
> #+begin_src R :noweb yes :cache no :session *R*
> <<test>>
> a + 1
> #+end_src
> 
> #+RESULTS: add1
> : 2
> 
> 
> I would proceed in the following way
> 
>    #+name: connection
>    #+begin_src R :exports results :results output :session *R* 
>     ## my code here
>    #+end_src
> 
>    #+begin_src R :exports results :results output graphics file
>    :session *R* :file figures/fig1.png
>    ## my code here
>    #+end_src
> 
>    #+begin_src R :exports results output graphics file :file figures/fig2.png 
> :session *R*
>    ## my code here
>    #+end_src
> 
> this will require running the first code chunk once only to run the rest
> 
>> On Thursday,  7 Jul 2022 at 09:22, Greg Minshall wrote:
>> you'd have to be careful to not get bitten by the code
>> *not* being evaluated, and by it being evaluated too often.  (probably
>> too clever by half.)
> 
> The comment of Greg is very relevant here as you'll have to manage
> updates yourself, and it can get complex very quickly. A potential
> pitfall is when the tables in database you are referring to, change.
> So in this case I would avoid using :cache yes in the first code chunk
> 
> 
> I'm also tempted to adopt the following organization
> 
>    * setup table
>    #+name: connection
>    #+begin_src R :exports results :results output :session *R* 
>     ## my code here
>    #+end_src
> 
>    * output graphs
>     :PROPERTIES:
>     :header-args:R: :exports results output graphics file  :session *R*
>     :END:
> 
>    #+begin_src R  :file figures/fig2.png
>    ## my code here
>    #+end_src
> 
>    #+begin_src R  :file figures/fig1.png 
>    ## my code here
>    #+end_src
> 
> then I would use (org-babel-execute-subtree) which is bound to C-c C-v
> s on the subheading output graphs to regenerate the graphs.
> 
> 
> HTH,
> Jeremie

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