Re: Tangling with variables in R

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

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Andreas Leha <andreas.leha@med.uni-goettingen.de> writes:

> Hi Rainer,

Hi Andreas,

>
> Rainer M Krug <Rainer@krugs.de> writes:
>
>> Hi
>>
>> I just realized (again) that tangling with variables in R contains many
>> particularities.
>>
>> 1) it only works with non-tables, i.e. single values.
>>
>> When defining the following variables:
>>
>> #+NAME: YEARS
>> |   | year          |
>> |---+---------------|
>> | 1 | 1990          |
>> | 2 | 2000          |
>> #+PROPERTY: var+ YEARS=YEARS
>> #+PROPERTY: var+ PRESENT=2008
>>
>>
>> I get the following code in the tangled .R file:
>>
>> ,----
>> | YEARS <- read.table("/var/folders/50/wcr5bjwn75q595n6x82gxj280000gn/T/babel-97151aBD/R-import-97151vpn",
>> |                       header=TRUE,
>> |                       row.names=1,
>> |                       sep="\t",
>> |                       as.is=TRUE)
>> | PRESENT <- 2008
>> `----
>>
>> Variable transfer from tables does not work, as it is based on a
>> temporary file, which is not easy to distribute together with the
>> tangled.R file and requires manual work as the path will be different.
>>
>> I consider this as a bug which should be fixed.
>
> Me too, see http://thread.gmane.org/gmane.emacs.orgmode/51067
>

OK - then I will include a fix to the tangling of tables issue in one of
my first patches.

>
>>
>> 2) With regards to variables which are defined non-file wide, (i.e. in
>> properties in a subtree and variables defined per code block and
>> function call), these are set when they occur in the tangled code, but
>> they are not unset *for the next code block* or *for R code in the next
>> subtree* (I hope you know what I mean). They are therefore similar to
>> the use of a session header argument instead of non-session evaluation
>> of the code.
>>
>> This is a (conceptually) a more complex issue, and requires some initial
>> thought on how this should be dealt with and how the tangled code should
>> relate to the executed code.
>>
>> - Should the tangled .R file result in the same output as the execution in
>> the org file, i.e. an accompanying .R file to a exported pdf, so that
>> the .R file can be used to reproduce the graphs and analysis in the .pdf
>> exported from the .org? or
>>
>> - Is tangling a completely thing to execution, and the resulting R code
>> in the .R file is not expected to reproduce the results in the org file?
>>
>> - Finally, does tangling with variables makes sense?
>>
>> My opinions are 
>>
>> a) *All* variables should be transferred to the .R file. This can be
>> already disabled via the :no-expand header argument. Unfortunately, this
>> is combined with noweb expansion, and it might be useful to split these
>> two, i.e. to be able to only disable variable expansion but to keep
>> noweb (I don't use noweb so far, so it is not a problem to me as it is
>> now).
>>
>> b) The variable assignments should be per code block / function call. So
>> a tangled block should look as follow:
>>
>> #+NAME: YEARS
>> |   | year          |
>> |---+---------------|
>> | 1 | 1990          |
>> | 2 | 2000          |
>> #+PROPERTY: var+ YEARS=YEARS
>> #+PROPERTY: var+ PRESENT=2008
>>
>> #+begin_src R
>> x <- 4
>> cat(x^2)
>> #+end_src
>>
>> should result in something like the following:
>>
>> ,----
>> | ## # Set the variables
>> | YEARS <- TRANSFER_TABLE()
>> | PRESENT <- TRANSFER_VALUE()
>> | ## Here begins the real code
>> | x <- 4
>> | cat(x^2)
>> | ## # Unset all variables previously set
>> `----
>>
>> but I prefer the following approach, as the result would be very
>> similar, only that the variables are still present afterwards which
>> would make debugging easier:
>>
>> ,----
>> | ## # Unset all variables previously set
>> | ## # Set the variables
>> | YEARS <- TRANSFER_TABLE()
>> | PRESENT <- TRANSFER_VALUE()
>> | ## Here begins the real code
>> | x <- 4
>> | cat(x^2)
>> `----
>>
>> This is effectively already implemented by using R environments. See [1]
>> and particularly [2] and [3] for how it is implemented. This does not
>> yet address the concern about the transfer of tables, but I will look at
>> this.
>
> These are good thoughts!

Thanks.

>
> For the general question on whether tangling should directly reflect
> weaving, there was a long (and fruitless) discussion or R-devel lately.
> See http://thread.gmane.org/gmane.comp.lang.r.devel/36031 and maybe
> http://thread.gmane.org/gmane.comp.lang.r.devel/36031/focus=36075 where
> Yihui states that it is very hard to tangle code that produces the
> same result as weaving.  This might actually be easier in org than in
> Sweave/knitr, but still the org setup will have a big impact, that would
> be hard to replicate in the tangled R code.

I agree completely - but it might be worth to try to go into this
direction rather then blocking it with choosing the wrong approach
initially.

>
> Setting aside the general question:
> In my opinion, it should definitely be possible to tangle with
> variables.  I think the approach of the environments to address (2) is a
> good one.

OK - I will put some thoughts into this and see how it could be done
easily and with limited rewuirements to supplementary files.

>
>
>
>>
>> Apologies for a long post, but I would like to know which direction of
>> the tangling / variable transfer from org to R should take - I don't
>> want to spend a lot of time solving a problem which does not really
>> exist.
>>
>> So - any comments? Suggestions?
>>
>
> See above.  And thanks for your work on ob-R!  Keep it up!

Thanks - I will do. Your email comes at the right moment, as I was
wondering if I am the only one using R and ESS and org. But I guess it
is rather the inner workings do not impact on most users.

I will see that I get the first set of patches together before the end
of June (after this it is holidays).

Cheers,

Rainer

>
>> Thanks,
>>
>> Rainer
>>
>> Footnotes: 
>> [1]  https://github.com/rkrug/orgmode-dev
>>
>> [2]  https://github.com/rkrug/orgmode-dev/blob/R-env/lisp/ob-R.el
>>
>> [3]  https://github.com/rkrug/orgmode-dev/blob/R-env/etc/R/org_functions.R
>
>
> Best,
> Andreas
>
>

-- 
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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