* [babel] org mode tables and tangling
@ 2012-01-12 18:42 Andreas Leha
2012-01-14 17:55 ` Eric Schulte
0 siblings, 1 reply; 2+ messages in thread
From: Andreas Leha @ 2012-01-12 18:42 UTC (permalink / raw)
To: emacs-orgmode
Hi all,
What is the suggested way to use org mode tables in connection with tangling?
Example: If I tangle this org mode file
/====<org-file>=====================================\
| * org-tables and reproducibility |
| #+name: params |
| | number | param | |
| |--------+-------| |
| | 0 | 1 | |
| | 1 | 1 | |
| |
| #+begin_src R :var params=params :tangle test.R |
| apply(params, 1, print) |
| #+end_src |
\====</org-file>====================================/
the tangled file looks like
/====<test.R>===============================================================\
| params <- read.table("/tmp/babel-19196cip/R-import-19196ILE", |
| header=TRUE, row.names=NULL, sep="\t", as.is=TRUE) |
| attach(params) |
| apply(params, 1, print) |
\====</test.R>==============================================================/
which depends on a temporary file. I could distribute that along with the
tangled file, of course.
But I'd like a distributable, ideally self-contained version, that my
co-workers can work with.
Something like this, maybe:
/====<sample.R>=======================================================\
| # generated with R dput()... |
| babel_tmp_1238h098 <- structure(list(means = 0:1, sds = c(1L, 1L)), |
| .Names = c("means", "sds"), |
| class = "data.frame", |
| row.names = c(NA, -2L)) |
| params <- dget(textConnection("babel_tmp_1238h098", "r")) |
\====</sample.R>======================================================/
Is such a mode of tangling already available for R?
Best,
Andreas
^ permalink raw reply [flat|nested] 2+ messages in thread
* Re: [babel] org mode tables and tangling
2012-01-12 18:42 [babel] org mode tables and tangling Andreas Leha
@ 2012-01-14 17:55 ` Eric Schulte
0 siblings, 0 replies; 2+ messages in thread
From: Eric Schulte @ 2012-01-14 17:55 UTC (permalink / raw)
To: Andreas Leha; +Cc: emacs-orgmode
Andreas Leha <andreas.leha@med.uni-goettingen.de> writes:
> Hi all,
>
> What is the suggested way to use org mode tables in connection with tangling?
>
Currently there is no support for including table values literally
inline in tangled R code. While some languages (e.g., the lisps) do
include table values literally, R is not one of those. You could
customize (read rewrite) the `org-babel-R-assign-elisp' function to use
literal R tables instead of importing values from an external file.
Alternately, if not too many values need to be included into the code,
you may want to simply assign individual cells of the table as scalars
in your R code.
Hope this helps, sorry no pre-built solution exists
>
> Example: If I tangle this org mode file
>
> /====<org-file>=====================================\
> | * org-tables and reproducibility |
> | #+name: params |
> | | number | param | |
> | |--------+-------| |
> | | 0 | 1 | |
> | | 1 | 1 | |
> | |
> | #+begin_src R :var params=params :tangle test.R |
> | apply(params, 1, print) |
> | #+end_src |
> \====</org-file>====================================/
>
> the tangled file looks like
>
> /====<test.R>===============================================================\
> | params <- read.table("/tmp/babel-19196cip/R-import-19196ILE", |
> | header=TRUE, row.names=NULL, sep="\t", as.is=TRUE) |
> | attach(params) |
> | apply(params, 1, print) |
> \====</test.R>==============================================================/
>
> which depends on a temporary file. I could distribute that along with the
> tangled file, of course.
>
> But I'd like a distributable, ideally self-contained version, that my
> co-workers can work with.
>
> Something like this, maybe:
>
> /====<sample.R>=======================================================\
> | # generated with R dput()... |
> | babel_tmp_1238h098 <- structure(list(means = 0:1, sds = c(1L, 1L)), |
> | .Names = c("means", "sds"), |
> | class = "data.frame", |
> | row.names = c(NA, -2L)) |
> | params <- dget(textConnection("babel_tmp_1238h098", "r")) |
> \====</sample.R>======================================================/
>
> Is such a mode of tangling already available for R?
>
> Best,
> Andreas
>
>
--
Eric Schulte
http://cs.unm.edu/~eschulte/
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