Re: [NTG-context] Writing a ConTeXt module for R

6 Jun 2006


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

2006/6/6, Johan Sandblom :
...
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