[Rd] requesting a mentor for R development

2011-06-20 Thread Paul Johnson 
I'd like to learn the process of revising R functions & packages and
then submitting proposed patches to the R Core team.  Would someone be
willing to mentor me through one example?

For starters, consider an example.  I'd like to revise the t.test
function to return the stderr value to the user.  We only need to
change the "rval" in the third-from-the end line of
stats:::t.test.default.

Change this:

 rval <- list(statistic = tstat, parameter = df, p.value = pval,
conf.int = cint, estimate = estimate, null.value = mu,
alternative = alternative, method = method, data.name = dname)
class(rval) <- "htest"
return(rval)

To this:

 rval <- list(statistic = tstat, parameter = df, stderr=stderr, p.value = pval,
conf.int = cint, estimate = estimate, null.value = mu,
alternative = alternative, method = method, data.name = dname)
class(rval) <- "htest"
return(rval)

Here is where I need help.

1. What other changes in the R code & documents would be required for
consistency?

2. How does R Core Team expect/accept patches?
I do understand a bit about SVN and CVS.  I think I could mark this up
and make a diff, but I'm uncertain about the details.

3. How would I best  prepare a suggestion like this so as to get it
accepted into R?

If somebody will raise a hand, I'm willing to do the work to learn.

pj
-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas

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Re: [Rd] arbitrary size data frame or other stcucts, curious about issues invovled.

2011-06-20 Thread Jay Emerson 
Mike,


Neither bigmemory nor ff are "drop in" solutions -- though useful,
they are primarily for data storage and management and allowing
convenient access to subsets of the data.  Direct analysis of the full
objects via most R functions is not possible.  There are many issues
that could be discussed here (and have, previously), including the use
of 32-bit integer indexing.  There is a nice section "Future
Directions" in the R Internals manual that you might want to look at.

Jay


-  Original message:

We keep getting questions on r-help about memory limits  and
I was curious to know what issues are involved in making
common classes like dataframe work with disk and intelligent
swapping? That is, sure you can always rely on OS for VM
but in theory it should be possible to make a data structure
that somehow knows what pieces you will access next and
can keep thos somewhere fast. Now of course algorithms
"should" act locally and be block oriented but in any case
could communicate with data structures on upcoming
access patterns, see a few ms into the future and have the
right stuff prefetched.

I think things like "bigmemory" exist but perhaps one
issue was that this could not just drop in for data.frame
or does it already solve all the problems?

Is memory management just a non-issue or is there something
that needs to be done  to make large data structures work well?


-- 
John W. Emerson (Jay)
Associate Professor of Statistics
Department of Statistics
Yale University
http://www.stat.yale.edu/~jay

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[Rd] Quote the path of graphics output in Sweave when it contains spaces

2011-06-20 Thread Yihui Xie 
Hi,

I'm aware of the definition of a "valid filename" in
.SweaveValidFilenameRegexp, but I think it might be better to quote
the filename when it contains spaces instead of just giving a warning.
This should bring us safer LaTeX code (although I never use spaces in
paths).

Here is the simple patch:

Index: src/library/utils/R/SweaveDrivers.R
===
--- src/library/utils/R/SweaveDrivers.R (revision 56193)
+++ src/library/utils/R/SweaveDrivers.R (working copy)
@@ -390,6 +390,8 @@
 }

 if (options$include) {
+if (grepl("[[:space:]]", chunkprefix))
+chunkprefix = shQuote(chunkprefix, type = "cmd")
 cat("\\includegraphics{", chunkprefix, "}\n", sep = "",
 file = object$output)
 linesout[thisline + 1L] <- srcline

Thanks!

Regards,
Yihui
--
Yihui Xie 
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA

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Re: [Rd] Quote the path of graphics output in Sweave when it contains spaces

2011-06-20 Thread Duncan Murdoch 

On 11-06-20 5:57 PM, Yihui Xie wrote:

Hi,

I'm aware of the definition of a "valid filename" in
.SweaveValidFilenameRegexp, but I think it might be better to quote
the filename when it contains spaces instead of just giving a warning.
This should bring us safer LaTeX code (although I never use spaces in
paths).


That works in MikTeX 2.9's version of pdflatex, but not in latex.  I 
imagine in 5 years it's possible all the different latex versions will 
consistently handle quotes, but it hasn't happened yet.


Duncan Murdoch



Here is the simple patch:

Index: src/library/utils/R/SweaveDrivers.R
===
--- src/library/utils/R/SweaveDrivers.R (revision 56193)
+++ src/library/utils/R/SweaveDrivers.R (working copy)
@@ -390,6 +390,8 @@
  }

  if (options$include) {
+if (grepl("[[:space:]]", chunkprefix))
+chunkprefix = shQuote(chunkprefix, type = "cmd")
  cat("\\includegraphics{", chunkprefix, "}\n", sep = "",
  file = object$output)
  linesout[thisline + 1L]<- srcline

Thanks!

Regards,
Yihui
--
Yihui Xie
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA

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