One more question concerning the variable transfer of tables:

,----
| 	(let ((file (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
| 	      (header (if (or (eq (nth 1 value) 'hline) colnames-p)
| 			  "TRUE" "FALSE"))
| 	      (row-names (if rownames-p "1" "NULL")))
| 	  (if (= max min)
| 	      (format "%s <- local({
|                         con <- textConnection(
|                           %S
|                         )
|                         res <- read.table(
|                           con,
|                           header    = %s,
|                           row.names = %s,
|                           sep       = \"\\t\",
|                           as.is     = TRUE
|                         )
|                         close(con)
|                         res
|                         })" name file header row-names)
| 	    (format "%s <- local({
|                        con <- textConnection(
|                          %S
|                        )
|                        res <- read.table(
|                          con,
|                          header    = %s,
|                          row.names = %s,
|                          sep       = \"\\t\",
|                          as.is     = TRUE,
|                          fill      = TRUE,
|                          col.names = paste(\"V\", seq_len(%d), sep =\"\")
|                        )
|                        close(con)
|                        res
|                        })" name file header row-names max))))
`----

It seems that the two variable transfer routines only differ slightly:

1. routine: =header= is present (TRUE) and defined in table when passed
as =colnames= while

2. routine: =header= is not present (FALSE) and =colnames= is generated
as V1 .. Vn

This generation is actually not needed as this is the R default value
which is used when =colnames= is not supplied.

Also: I do not undestand why the argument =fill= is TRUE in the second
routine. From R:

,----
|     fill: logical. If ‘TRUE’ then in case the rows have unequal length,
|           blank fields are implicitly added.  See ‘Details’.
`----

If I understands tables in org correctly, this is not needed as the rows
always have equal length?

so if I am not mistaken the following lines could be deleted:

,----
|                            row.names = %s,
|                            sep       = \"\\t\",
|                            as.is     = TRUE,
| -                          fill      = TRUE,
| -                          col.names = paste(\"V\", seq_len(%d), sep =\"\")
`----

Or am I missing something here?

Cheers,

Rainer


"Charles C. Berry" <ccberry@ucsd.edu> writes:

> On Fri, 20 Jun 2014, Rainer M Krug wrote:
>
>> Attached please find =the reworked patch.
>>
>> 1) uses local() and closes connection
>> 2) does not leave a variable cal;led file behind
>>
>
> Seems to work on a few test cases.
>
> I'd move the strings to defconsts.
>
> Putting a newline before each `%S' will outdent the first line of 
> :var value when it is echoed in the session log so it will be easier to 
> view.
>
> ===
>
> With Eric's input on this:
>
> Would you also change this at the end of org-babel-R-assign-elisp:
>
>                          res})" name file header row-names max))))
> -    (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
> +    (format "%s <- %S" name
> +	    (if (stringp value) value (prin1-to-string value)))))
>
> ??
>
> I think this is innocuous for plain strings with no internal quotes, but 
> allows almost anything to be passed to R as a string.
>
> So
>  	:var x=[1 2 3 "4" 5]
>
> will be passed to R as x <- "[1 2 3 \"4\" 5]"
>
> instead of x <- "[1 2 3 "4" 5] which throws an error.
>
> And this just works:
>
> #+NAME: latex-capt
> #+BEGIN_SRC latex
>    \begin{math}
>      y = X\beta,
>      \mbox{where } \beta = %beta%
>    \end{math}
> #+END_SRC
>
> #+BEGIN_SRC R :var ytxt=latex-capt :results raw :wrap latex
> beta <- 1.234
> sub("%beta%",beta,ytxt)
> #+END_SRC
>
>
> HTH,
>
> Chuck

-- 
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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