"Charles C. Berry" <ccbe...@ucsd.edu> writes:
V> 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_SRCOK - attached please find two patches: 0001-lisp-ob-R.el-Fix-tangling-with-tables.patch 0002-Make-transfer-of-values-from-R-type-aware.patch The first one fixes tangling with tables including discussed suggestions, the second one moves the definition of the R code into defconst and introduces type awareness for the transfer of *values*, but not tables. I reworked your suggestion and now integer are transferred to R as integers (L) and float as double. This already worked for tables. Could you please check the second patch? In my checks everything worked as expected. Cheers, Rainer > > > 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 Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D): +49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug PGP: 0x0F52F982
From 38c029b38c85d9f9d35d0867b332eebc3daf1aca Mon Sep 17 00:00:00 2001
From: "Rainer M. Krug" <r.m.k...@gmail.com>
Date: Fri, 20 Jun 2014 22:19:59 +0200
Subject: [PATCH 1/2] lisp/ob-R.el: Fix tangling with tables
* lisp/ob-R.el (org-babel-R-assign-elisp): Fix variable transfer of
tables by using text connections in R instead of files. Variable
transfer of tables does not depend on files anymore, i.e. works also
when tangling.
---
lisp/ob-R.el | 52 ++++++++++++++++++++++++++++++++--------------------
1 file changed, 32 insertions(+), 20 deletions(-)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index a3ae1ec..c77a103 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -190,32 +190,44 @@ This function is called by `org-babel-execute-src-block'."
(if (listp value)
(let* ((lengths (mapcar 'length (org-remove-if-not 'sequencep value)))
(max (if lengths (apply 'max lengths) 0))
- (min (if lengths (apply 'min lengths) 0))
- (transition-file (org-babel-temp-file "R-import-")))
+ (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)))
- (with-temp-file transition-file
- (insert
- (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))
- "\n"))
- (let ((file (org-babel-process-file-name transition-file 'noquote))
+ (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 <- read.table(\"%s\",
- header=%s,
- row.names=%s,
- sep=\"\\t\",
- as.is=TRUE)" name file header row-names)
- (format "%s <- read.table(\"%s\",
- header=%s,
- row.names=%s,
- sep=\"\\t\",
- as.is=TRUE,
- fill=TRUE,
- col.names = paste(\"V\", seq_len(%d), sep =\"\"))"
- name file header row-names max))))
+ (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))))
(format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
(defvar ess-ask-for-ess-directory) ; dynamically scoped
--
2.0.0
From e62a75e7227027c406d23fa9f8ac594db2ce81d6 Mon Sep 17 00:00:00 2001
From: "Rainer M. Krug" <r.m.k...@gmail.com>
Date: Mon, 23 Jun 2014 12:11:59 +0200
Subject: [PATCH 2/2] Make transfer of values from R type aware
* lisp/ob-R.el (org-babel-R-assign-elisp): Added different cases for
transfer of integer, float, string and other variables to R so that
now integer values are transferred as integers (L) and stored in R as
such. This change is backward compatible as integer values are
numerical values in R.
Moved definition of R functions for transfer of tables into defconst
ob-R-transfer-variable-table-with-header and
ob-R-transfer-variable-table-without-header.
---
lisp/ob-R.el | 78 ++++++++++++++++++++++++++++++++++++------------------------
1 file changed, 47 insertions(+), 31 deletions(-)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index c77a103..92c1dbc 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -93,6 +93,44 @@ this variable.")
(when (and session (string-match "^\\*\\(.+?\\)\\*$" session))
(save-match-data (org-babel-R-initiate-session session nil)))))
+(defconst ob-R-transfer-variable-table-with-header
+ "%s <- local({
+ con <- textConnection(
+ %S
+ )
+ res <- read.table(
+ con,
+ header = %s,
+ row.names = %s,
+ sep = \"\\t\",
+ as.is = TRUE
+ )
+ close(con)
+ res
+ })"
+ "R code used to transfer a table defined as a variable from org to R.
+This function is used when the table contains a header.")
+
+(defconst ob-R-transfer-variable-table-without-header
+ "%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
+ })"
+ "R code used to transfer a table defined as a variable from org to R.
+This function is used when the table does not contain a header.")
+
(defun org-babel-expand-body:R (body params &optional graphics-file)
"Expand BODY according to PARAMS, return the expanded body."
(mapconcat 'identity
@@ -198,37 +236,15 @@ This function is called by `org-babel-execute-src-block'."
"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))))
- (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
+ (format ob-R-transfer-variable-table-with-header
+ name file header row-names)
+ (format ob-R-transfer-variable-table-without-header
+ name file header row-names max))))
+ (if (integerp value) (format "%s <- %s" name (concat (number-to-string value) "L"))
+ (if (floatp value) (format "%s <- %s" name value)
+ (if (stringp value) (format "%s <- %S" name value)
+ (format "%s <- %S" name (prin1-to-string value)))))))
+
(defvar ess-ask-for-ess-directory) ; dynamically scoped
(defun org-babel-R-initiate-session (session params)
--
2.0.0
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