Re: [O] org tables into R?

[Rainer M Krug]

Aaron Ecay <address@hidden> writes:

> Hi Rainer and Andreas,
>
> 2015ko urtarrilak 6an, Rainer M Krug-ek idatzi zuen:
>> What would definitely solve the issue is if the string containing the
>> tabs would use \t instead - but I have no idea how this could be
>> achieved easily.
>
> This could be achieved by modifying the call to orgtbl-to-csv in
> org-babel-R-assign-elisp:
>
> diff --git i/lisp/ob-R.el w/lisp/ob-R.el
> index 6f76aa5..ec3f110 100644
> --- i/lisp/ob-R.el
> +++ w/lisp/ob-R.el
> @@ -239,7 +239,10 @@ This function is called by 
> `org-babel-execute-src-block'."
>              (min (if lengths (apply 'min lengths) 0)))
>          ;; Ensure VALUE has an orgtbl structure (depth of at least 2).
>          (unless (listp (car value)) (setq value (list value)))
> -       (let ((file (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
> +       (let ((file (replace-regexp-in-string
> +                    "\t" "\\t"
> +                    (orgtbl-to-tsv value '(:raw t :fmt 
> org-babel-R-quote-tsv-field))
> +                    nil t))
>               (header (if (or (eq (nth 1 value) 'hline) colnames-p)
>                           "TRUE" "FALSE"))
>               (row-names (if rownames-p "1" "NULL")))
>
> (This is just a quick hack; if it works then the code should actually
> use orgtbl-to-generic to do the conversion in a single step.)

That looks like it would work. 

>
>> ,----
>> |   ...  
>> |        sep       = \"\",   ;;;;;<<<<<<<<< was before  sep = \"\\t\"
>> |   ...
>> `----
>> 
>> This will set the separator to "whitespace", i.e. "that is one or more
>> spaces, tabs, newlines or carriage returns" (from R help).
>
> This was the approach that Michael took in his original patch.  It
> introduces new bugs related to the handling of quotes, though – see the
> “Details” section of ?scan in R for the gory details (beginning with “If
> ‘sep’ is the default”...).

I agree completely - it would not be a final solution but possibly solve
the problem temporarily in an emacs.org file.

But the real question is: why are on some setups the tabs converted to
spaces?

>
> Andreas raised a bug a while ago that indicates to me that this code
> should switch to csv rather than a whitespace-delimited format.  But
> there are lots of corner cases, and I have not had time to work on a
> patch that I am confident could cover them all.

Might be a solution - but I do not know how commas are working under
different locales. In MS Office, a csv file is a semicolon (;)
separated file when in the chosen language settings a comma is used as
decimal separator - and and I have no idea if language settings affect
emacs in the same way (I actually don't hope so).

This makes me think - why not use "|" as a separator (as it is the case
in org)? In this way, all tables which are in org can be directly given
to R as strings without the hassle of to much of conversion?

Rainer

>
> Andreas’s original report (also referenced earlier in this thread):
> http://news.gmane.org/find-root.php?message_id=olulhmmtei5.fsf%40med.uni%2dgoettingen.de
>
> Thanks,

-- 
Rainer M. Krug
email: Rainer<at>krugs<dot>de
PGP: 0x0F52F982

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