Writing a ConTeXt module for R

Writing a ConTeXt module for R

[Johan Sandblom]

[-- Attachment #1: Type: text/plain, Size: 1465 bytes --]

Since I sometimes use the open-source statistics environment R
(http://www.r-project.org) as well as ConTeXt, I thought a module that
could typeset R code as well as evaluate it on the fly would be
useful. Borrowing largely without understanding but lots of trial and
eror from m-gnustep.tex, I came up with the attached. Limited testing
indicates it works, but at least one problem is apparent: the R code
snippets have one unnecessary line break to start them and two after
the end. How can I fix that? Of course, any other suggestions are also
welcome.

A recent R needs to be in the path, but given that, it seems to work
on Windows XP as well as Linux.

Regards, Johan

PS Emacs users may appreciate the following to get r-mode where appropriate:
(require 'mmm-mode)
(setq mmm-global-mode 'maybe)
(setq mmm-submode-decoration-level 2)
(mmm-add-group
 'context-plus
 '((context-MP
    :submode metapost-mode
    :face mmm-code-submode-face
    :front ".*\\\\start\\w*MP\\w*\\({\\w*}\\|\\[\\w*\\]\\|\\)\\W"
    :back  ".*\\\\stop\\w*MP")
   (context-R
    :submode r-mode
    :face mmm-comment-submode-face
    :front ".*\\\\startR.*\\W"
    :back  ".*\\\\stopR.*")))
(add-to-list
 'mmm-mode-ext-classes-alist '(context-mode nil context-plus))

-- 
Johan Sandblom  N8, MRC, Karolinska sjh
t +46851776108  17176 Stockholm
m +46735521477  Sweden
"What is wanted is not the will to believe, but the
will to find out, which is the exact opposite"
- Bertrand Russell

[-- Attachment #2: t-rweave.tex --]
[-- Type: application/x-tex, Size: 2337 bytes --]

[-- Attachment #3: Type: text/plain, Size: 139 bytes --]

_______________________________________________
ntg-context mailing list
ntg-context@ntg.nl
http://www.ntg.nl/mailman/listinfo/ntg-context

Re: Writing a ConTeXt module for R

[Johan Sandblom]

Attachment seems to have failed  I put the content of the file below.

2006/6/6, Johan Sandblom <jsandblom@gmail.com>:
> Since I sometimes use the open-source statistics environment R
> (http://www.r-project.org) as well as ConTeXt, I thought a module that
> could typeset R code as well as evaluate it on the fly would be
> useful. Borrowing largely without understanding but lots of trial and
> eror from m-gnustep.tex, I came up with the attached. Limited testing
> indicates it works, but at least one problem is apparent: the R code
> snippets have one unnecessary line break to start them and two after
> the end. How can I fix that? Of course, any other suggestions are also
> welcome.
>
> A recent R needs to be in the path, but given that, it seems to work
> on Windows XP as well as Linux.
>
> Regards, Johan
>
> PS Emacs users may appreciate the following to get r-mode where appropriate:
> (require 'mmm-mode)
> (setq mmm-global-mode 'maybe)
> (setq mmm-submode-decoration-level 2)
> (mmm-add-group
>  'context-plus
>  '((context-MP
>     :submode metapost-mode
>     :face mmm-code-submode-face
>     :front ".*\\\\start\\w*MP\\w*\\({\\w*}\\|\\[\\w*\\]\\|\\)\\W"
>     :back  ".*\\\\stop\\w*MP")
>    (context-R
>     :submode r-mode
>     :face mmm-comment-submode-face
>     :front ".*\\\\startR.*\\W"
>     :back  ".*\\\\stopR.*")))
> (add-to-list
>  'mmm-mode-ext-classes-alist '(context-mode nil context-plus))
>
> --
> Johan Sandblom  N8, MRC, Karolinska sjh
> t +46851776108  17176 Stockholm
> m +46735521477  Sweden
> "What is wanted is not the will to believe, but the
> will to find out, which is the exact opposite"
> - Bertrand Russell
>
>
>

% Copyright Johan Sandblom, distributed and redistributable under the
% terms of the GNU Lesser General Public License.
\unprotect

\newcounter\Rnumber

% I would like to reduce this two-stage call, but then line-endings disappear
\def\startR%
  {\bgroup
   \obeylines
   \catcode`\%=\@@letter
   \catcode`\#=\@@letter
   \dostartR%
  }%

\def\dostartR#1\stopR%
  {\doglobal\increment\Rnumber%
   \letgvalue{rcs:n:\Rnumber}\Rnumber%
   \setgvalue{rcs:d:\Rnumber}{#1}%
      \edef\Rfile  {\bufferprefix R-\Rnumber}%
      \bgroup%
      \the\everyR%
      \immediate\openout\scratchwrite=\Rfile.r%
      \def\par{\rawcharacter{10}}%
      \immediate\write\scratchwrite{\getvalue{rcs:d:\Rnumber}}%
      \immediate\closeout\scratchwrite%
      \egroup%
      \startmode[*\v!first]%
      \runR%
      \stopmode
      \typeRout%
   \egroup}%

\def\startRhidden%
  {\bgroup
   \obeylines
   \catcode`\%=\@@letter
   \dostartRhidden{}}

\def\dostartRhidden#1\stopRhidden
  {\doglobal\increment\Rnumber
   \letgvalue{rcs:n:\Rnumber}\Rnumber
   \setgvalue{rcs:d:\Rnumber}{#1}%
      \edef\Rfile  {\bufferprefix R-\Rnumber}%
      \bgroup
      \the\everyR%
      \immediate\openout\scratchwrite=\Rfile.r%
      \def\par{\rawcharacter{10}}%
      \immediate\write\scratchwrite{\getvalue{rcs:d:\Rnumber}}%
      \immediate\closeout\scratchwrite%
      \egroup
      \startmode[*\v!first]%
      \runR%
      \stopmode
   \egroup}

\newtoks\everyR

\appendtoks
    \obeylines
\to \everyR

% The call to R has -q in order to prevent banner, --save to make sure
% it saves the workspace after the run, --restore to make sure it
% reads any workspace from a previous session
\def\runR
     {\executesystemcommand{R -q --save --restore < \Rfile.r > \Rfile.Rout}}

\def\typeRout
  {\typefile{\Rfile.Rout}}

\protect \doifnotmode{demo}{\endinput}

\starttext

\startR
a <- "bla"
b <- "blabla"
ls()
\stopR

bla bla

\startRhidden
rm(list=ls())
save.image()
\stopRhidden

bla

\startR
ls()
ushape <- c(rexp(500000), 12-rexp(500000))
pdf("ushape.pdf")
par(mfrow=c(1,2))
hist(ushape)
plot(density(ushape), main="Density")
dev.off()
\stopR

\input tufte

\input knuth

\startR
x <- rnorm(900)
y <- rexp(900)
# test comment
f <- gl(9,9,900)
summary(aov(y~x+Error(f)))
library(lattice)
pdf("lattice.pdf")
xyplot(y~x|f)
dev.off()
\stopR

\placefigure[here]{}{\externalfigure[lattice]}
\placefigure[here]{}{\externalfigure[ushape]}

\input tufte

\startR
(test <- ".*\\\\ []{}=?!+%#|<|>@$")
cat(test)
\stopR

\input bryson

\input knuth

\startR
a.df <- data.frame(a=1:2, b=rnorm(2))
a.df$a
testfunction <- function(a=NULL, ...) {
  for(i in 1:length(a)) {
    gsub(a[[i]], "([a-r]|[A-R])", "bla")}
  print(a)}
\stopR

\stoptext

-- 
Johan Sandblom  N8, MRC, Karolinska sjh
t +46851776108  17176 Stockholm
m +46735521477  Sweden
"What is wanted is not the will to believe, but the
will to find out, which is the exact opposite"
- Bertrand Russell

Re: Writing a ConTeXt module for R

[Taco Hoekwater]

I do not have R installed here. but:

Johan Sandblom wrote:
> 
> % I would like to reduce this two-stage call, but then line-endings disappear

This two-stage approach is required unless each statement in R is
terminated uniquely, by something like a semicolon because then
you could redefine the semicolon at the writing stage.

> \def\startR%
>   {\bgroup
>    \obeylines
>    \catcode`\%=\@@letter
>    \catcode`\#=\@@letter
>    \dostartR%
>   }%

Don't you need percent signs at the end of the @@letter lines?

>       \stopmode
>       \typeRout%
>    \egroup}%

You can make that

        \stopmode
        \egroup
        \typeRout }

because \typefile doesnt need \obeylines

Cheers, Taco

Re: Writing a ConTeXt module for R

[Johan Sandblom]

Thank you for your explanations, and yes I probably do need percent
signs if my test case had been more severe. Hans, with characteristic
swiftness, already sent me back a vastly improved version which I will
test as soon as I get a chance.

Johan

2006/6/7, Taco Hoekwater <taco@elvenkind.com>:
>
> I do not have R installed here. but:
>
> Johan Sandblom wrote:
> >
> > % I would like to reduce this two-stage call, but then line-endings disappear
>
> This two-stage approach is required unless each statement in R is
> terminated uniquely, by something like a semicolon because then
> you could redefine the semicolon at the writing stage.
>
> > \def\startR%
> >   {\bgroup
> >    \obeylines
> >    \catcode`\%=\@@letter
> >    \catcode`\#=\@@letter
> >    \dostartR%
> >   }%
>
> Don't you need percent signs at the end of the @@letter lines?
>
> >       \stopmode
> >       \typeRout%
> >    \egroup}%
>
> You can make that
>
>        \stopmode
>        \egroup
>        \typeRout }
>
> because \typefile doesnt need \obeylines
>
> Cheers, Taco
>


-- 
Johan Sandblom  N8, MRC, Karolinska sjh
t +46851776108  17176 Stockholm
m +46735521477  Sweden
"What is wanted is not the will to believe, but the
will to find out, which is the exact opposite"
- Bertrand Russell