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Re: [Orgmode] [PATCH] babel: add a :rownames argument to R code blocks
From: |
Eric Schulte |
Subject: |
Re: [Orgmode] [PATCH] babel: add a :rownames argument to R code blocks |
Date: |
Thu, 25 Mar 2010 07:39:18 -0600 |
User-agent: |
Gnus/5.13 (Gnus v5.13) Emacs/23.1.90 (gnu/linux) |
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/