Re: [Orgmode] [PATCH] babel: add a :rownames argument to R code blocks

[Eric Schulte]

Hi Julien,

Thanks for the patch, however it looks like the attached patch breaks
columnname support for R source code blocks.  I'm pasting in the
relevant portion of our test suite, from the development.org file in our
development repository [1].  Could you please sort this issue out before
we apply the patch?

Thanks -- Eric

relevant test... the final source block should return 169

#+tblname: test-table-colnames
| var1 | var2 | var3 |
|------+------+------|
|    1 |   22 |   13 |
|   41 |   55 |   67 |

#+srcname: R-square(x=default-name-doesnt-exist)
#+begin_src R :colnames yes
x^2
#+end_src

This should return 169. The fact that R is able to use the column name
to index the data frame (x$var3) proves that a table with column names
(a header row) has been recognised as input for the R-square function
block, and that the R-square block has output an elisp table with
column names, and that the colnames have again been recognised when
creating the R variables in this block.
#+srcname: table-R-colnames-org(x = R-square(x=test-table-colnames))
#+begin_src R
x$var3[1]
#+end_src


Julien Barnier <address@hidden> writes:

> Hi,
>
> The following simple patch add a :rownames argument to R source code
> blocks in org-babel. With :rownames yes it allows to export the row
> names when the result is a table.
>
> For example :
>
> #+BEGIN_SRC R :session :colnames yes :rownames yes
> table(d$sexe,d$cuisine)
> #+END_SRC
>
> #+results:
> |       | Non | Oui |
> |-------+-----+-----|
> | Homme |   2 |   2 |
> | Femme |   4 |   2 |
>
> Thanks a lot for all your work !
>
> Julien
>
> ---
>  contrib/babel/lisp/langs/org-babel-R.el |   12 +++++++-----
>  1 files changed, 7 insertions(+), 5 deletions(-)
>
> diff --git a/contrib/babel/lisp/langs/org-babel-R.el 
> b/contrib/babel/lisp/langs/org-babel-R.el
> index a8071b2..f0d79b9 100644
> --- a/contrib/babel/lisp/langs/org-babel-R.el
> +++ b/contrib/babel/lisp/langs/org-babel-R.el
> @@ -46,6 +46,8 @@ called by `org-babel-execute-src-block'."
>             (vars (second processed-params))
>          (column-names-p (and (cdr (assoc :colnames params))
>                               (string= "yes" (cdr (assoc :colnames params)))))
> +        (row-names-p (and (cdr (assoc :rownames params))
> +                             (string= "yes" (cdr (assoc :rownames params)))))
>          (out-file (cdr (assoc :file params)))
>          (augmented-body
>           (concat
> @@ -53,7 +55,7 @@ called by `org-babel-execute-src-block'."
>            (mapconcat ;; define any variables
>             (lambda (pair) (org-babel-R-assign-elisp (car pair) (cdr pair))) 
> vars "\n")
>            "\n" body "\n" (if out-file "dev.off()\n" "")))
> -        (result (org-babel-R-evaluate session augmented-body result-type 
> column-names-p)))
> +        (result (org-babel-R-evaluate session augmented-body result-type 
> column-names-p row-names-p)))
>        (or out-file result))))
>  
>  (defun org-babel-prep-session:R (session params)
> @@ -133,9 +135,9 @@ called by `org-babel-execute-src-block'."
>  (defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
>  (defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
>  (defvar org-babel-R-wrapper-method "main <- function ()\n{\n%s\n}
> -write.table(main(), file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, 
> col.names=%s, quote=FALSE)")
> +write.table(main(), file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=%s, 
> col.names=%s, quote=FALSE)")
>  
> -(defun org-babel-R-evaluate (session body result-type column-names-p)
> +(defun org-babel-R-evaluate (session body result-type column-names-p 
> row-names-p)
>    "Pass BODY to the R process in SESSION.  If RESULT-TYPE equals
>  'output then return a list of the outputs of the statements in
>  BODY, if RESULT-TYPE equals 'value then return the value of the
> @@ -153,7 +155,7 @@ last statement in BODY, as elisp."
>               (stderr
>                (with-temp-buffer
>                  (insert (format org-babel-R-wrapper-method
> -                                body tmp-file (if column-names-p "TRUE" 
> "FALSE")))
> +                                body tmp-file (if row-names-p "TRUE" 
> "FALSE") (if column-names-p (if row-names-p "NA" "TRUE") "FALSE")))
>                  (setq exit-code (org-babel-shell-command-on-region
>                                   (point-min) (point-max) "R --no-save" nil 
> 'replace (current-buffer)))
>                  (buffer-string))))
> @@ -168,7 +170,7 @@ last statement in BODY, as elisp."
>             (case result-type
>               (value
>                (mapconcat #'org-babel-chomp (list body
> -                                                 (format 
> "write.table(.Last.value, file=\"%s\", sep=\"\\t\", 
> na=\"nil\",row.names=FALSE, col.names=%s, quote=FALSE)" tmp-file (if 
> column-names-p "TRUE" "FALSE"))
> +                                                 (format 
> "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=%s, 
> col.names=%s, quote=FALSE)" tmp-file (if row-names-p "TRUE" "FALSE") (if 
> column-names-p  (if row-names-p "NA" "TRUE") "FALSE"))
>                                                   org-babel-R-eoe-indicator) 
> "\n"))
>               (output
>                (mapconcat #'org-babel-chomp (list body 
> org-babel-R-eoe-indicator) "\n"))))

Footnotes: 
[1]  http://eschulte.github.com/babel-dev/