Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
On 19/08/2010 5:25 PM, Duncan Murdoch wrote:
On 19/08/2010 5:07 PM, Kevin Coombes wrote:
I use it, frequently. The idea for it goes back to some of Knuth's
original literate programming ideas for developing weave and tangle when
he was writing TeX (the program). I want to be able to document the
pieces of some complex algorithm without having to see all of the gory
details. For instance, I have code that looks like the following.
(Note that this is typed on the fly rather than copied from actual
source, so there may be typos.)
Okay, thanks. I'll keep it in. So now I have a question: suppose
you have an error (syntax error at this point, maybe some other kinds of
error in the future) in the getInfoAboutThisSample chunk, but that
chunk wasn't eval'd, mainloop was eval'd. So the error is going to be
reported as occurring in chunk mainloop, but with a line number from
somewhere else in the file. Is that a problem?
I was out of town for a week, but I'm back now, and have just committed
these changes. Hopefully the reports of syntax errors will be a little
more helpful now. I don't think I'll have time to make the reports of
execution time errors better before the 2.12.0 release.
Duncan Murdoch
Duncan Murdoch
mainloop,keep.source=TRUE,expand=FALSE=
for (i in 1:nSamples) {
getInfoAboutThisSample
for (j in 1:nChromosomes) {
getChromosomeDataForCurrentSample
normalizeChromosomeData
findSegments
computeSignificance
writeResults
}
}
@
Each of the chunks is itself a fairly long piece of code defined and
documented somewhere else. (Some of them may themselves be written in
the same form to reduce the final size of a chunk to something a human
has a chance of understanding. That's the difference between weave and
tangle in the original implementation.) By blocking expansion, I can
focus on the main steps without having them lost in pages and pages of code.
So I vote strongly for retaining expand=FALSE.
Best,
Kevin
Duncan Murdoch wrote:
On 19/08/2010 4:29 PM, Claudia Beleites wrote:
I never used it.
I got curious, though. What would be a situation that benefits of
this option?
When I put it in, I thought it would be for people who were writing
about Sweave.
Duncan Murdoch
Maybe a use case could be found by brute force (grep all .Rnw files
on CRAN for the option?
Claudia
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Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
Duncan, I use noweb for my R source code on the more complex projects (see the coxme package). I currently have my own noweb.R functions to do the work, but the overlap is so great with Sweave that I have hopes that they will one day merge. A note on abc recursion: for documentation this is very well designed; it's better than a macro or a function would be. And of course, documentation of code is what the system was designed for. And a general query: I currently have the .Rnw source files in the inst/noweb directory. Do people have a better suggestion? Remember these .Rnw files are the source of my .R files and of document explaining the code, not the source of vignettes or manual pages. Terry Therneau __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
On Aug 19, 2010, at 2:07 PM, Duncan Murdoch wrote: I am trying to improve the error reporting in Sweave documents, so that if you have a syntax error in a code chunk, it will tell you which line of your input file contained the error. For example, currently you get this: Error: chunk 1 (label=named) Error in parse(text = chunk) : unexpected symbol in x - foo bar Execution halted and I'd like errors to be more like this: Error: chunk 1 (label=named) Error in parse(text = chunk, srcfile = srcfile) : test.Rnw:9:10: unexpected symbol 9: x - foo bar ^ Execution halted It turns out that this requires changes that make the expand=FALSE option quite hard to implement. Is anyone using it? For those who don't know it, expand=FALSE means that a code chunk like echo=TRUE, keep.source=TRUE,expand=FALSE= z - 3 named @ will be displayed as z - 3 named rather than expanding the named chunk. I'd like to drop the option, so that the default behaviour (which has always been equivalent to expand = TRUE) would be the only behaviour. Duncan Murdoch I don't. So 1 go ahead and drop it vote... You may want to post this to R-Help though Duncan, as I suspect there may be more Sweave users there than here... Thanks and regards, Marc Schwartz __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
I have read a significant number of vignettes from Bioconductor packages and I have never seen it used. Kasper On Thu, Aug 19, 2010 at 3:17 PM, Marc Schwartz marc_schwa...@me.com wrote: On Aug 19, 2010, at 2:07 PM, Duncan Murdoch wrote: I am trying to improve the error reporting in Sweave documents, so that if you have a syntax error in a code chunk, it will tell you which line of your input file contained the error. For example, currently you get this: Error: chunk 1 (label=named) Error in parse(text = chunk) : unexpected symbol in x - foo bar Execution halted and I'd like errors to be more like this: Error: chunk 1 (label=named) Error in parse(text = chunk, srcfile = srcfile) : test.Rnw:9:10: unexpected symbol 9: x - foo bar ^ Execution halted It turns out that this requires changes that make the expand=FALSE option quite hard to implement. Is anyone using it? For those who don't know it, expand=FALSE means that a code chunk like echo=TRUE, keep.source=TRUE,expand=FALSE= z - 3 named @ will be displayed as z - 3 named rather than expanding the named chunk. I'd like to drop the option, so that the default behaviour (which has always been equivalent to expand = TRUE) would be the only behaviour. Duncan Murdoch I don't. So 1 go ahead and drop it vote... You may want to post this to R-Help though Duncan, as I suspect there may be more Sweave users there than here... Thanks and regards, Marc Schwartz __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
On 19/08/2010 3:17 PM, Marc Schwartz wrote: On Aug 19, 2010, at 2:07 PM, Duncan Murdoch wrote: I am trying to improve the error reporting in Sweave documents, so that if you have a syntax error in a code chunk, it will tell you which line of your input file contained the error. For example, currently you get this: Error: chunk 1 (label=named) Error in parse(text = chunk) : unexpected symbol in x - foo bar Execution halted and I'd like errors to be more like this: Error: chunk 1 (label=named) Error in parse(text = chunk, srcfile = srcfile) : test.Rnw:9:10: unexpected symbol 9: x - foo bar ^ Execution halted It turns out that this requires changes that make the expand=FALSE option quite hard to implement. Is anyone using it? For those who don't know it, expand=FALSE means that a code chunk like echo=TRUE, keep.source=TRUE,expand=FALSE= z - 3 named @ will be displayed as z - 3 named rather than expanding the named chunk. I'd like to drop the option, so that the default behaviour (which has always been equivalent to expand = TRUE) would be the only behaviour. Duncan Murdoch I don't. So 1 go ahead and drop it vote... You may want to post this to R-Help though Duncan, as I suspect there may be more Sweave users there than here... I probably will before I go ahead with this, but I may as well start on this group. Duncan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
I never used it. I got curious, though. What would be a situation that benefits of this option? Maybe a use case could be found by brute force (grep all .Rnw files on CRAN for the option? Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
On 19/08/2010 4:29 PM, Claudia Beleites wrote: I never used it. I got curious, though. What would be a situation that benefits of this option? When I put it in, I thought it would be for people who were writing about Sweave. Duncan Murdoch Maybe a use case could be found by brute force (grep all .Rnw files on CRAN for the option? Claudia __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
I use it, frequently. The idea for it goes back to some of Knuth's
original literate programming ideas for developing weave and tangle when
he was writing TeX (the program). I want to be able to document the
pieces of some complex algorithm without having to see all of the gory
details. For instance, I have code that looks like the following.
(Note that this is typed on the fly rather than copied from actual
source, so there may be typos.)
mainloop,keep.source=TRUE,expand=FALSE=
for (i in 1:nSamples) {
getInfoAboutThisSample
for (j in 1:nChromosomes) {
getChromosomeDataForCurrentSample
normalizeChromosomeData
findSegments
computeSignificance
writeResults
}
}
@
Each of the chunks is itself a fairly long piece of code defined and
documented somewhere else. (Some of them may themselves be written in
the same form to reduce the final size of a chunk to something a human
has a chance of understanding. That's the difference between weave and
tangle in the original implementation.) By blocking expansion, I can
focus on the main steps without having them lost in pages and pages of code.
So I vote strongly for retaining expand=FALSE.
Best,
Kevin
Duncan Murdoch wrote:
On 19/08/2010 4:29 PM, Claudia Beleites wrote:
I never used it.
I got curious, though. What would be a situation that benefits of
this option?
When I put it in, I thought it would be for people who were writing
about Sweave.
Duncan Murdoch
Maybe a use case could be found by brute force (grep all .Rnw files
on CRAN for the option?
Claudia
__
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https://stat.ethz.ch/mailman/listinfo/r-devel
__
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https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
On 19/08/2010 5:07 PM, Kevin Coombes wrote:
I use it, frequently. The idea for it goes back to some of Knuth's
original literate programming ideas for developing weave and tangle when
he was writing TeX (the program). I want to be able to document the
pieces of some complex algorithm without having to see all of the gory
details. For instance, I have code that looks like the following.
(Note that this is typed on the fly rather than copied from actual
source, so there may be typos.)
Okay, thanks. I'll keep it in. So now I have a question: suppose
you have an error (syntax error at this point, maybe some other kinds of
error in the future) in the getInfoAboutThisSample chunk, but that
chunk wasn't eval'd, mainloop was eval'd. So the error is going to be
reported as occurring in chunk mainloop, but with a line number from
somewhere else in the file. Is that a problem?
Duncan Murdoch
mainloop,keep.source=TRUE,expand=FALSE=
for (i in 1:nSamples) {
getInfoAboutThisSample
for (j in 1:nChromosomes) {
getChromosomeDataForCurrentSample
normalizeChromosomeData
findSegments
computeSignificance
writeResults
}
}
@
Each of the chunks is itself a fairly long piece of code defined and
documented somewhere else. (Some of them may themselves be written in
the same form to reduce the final size of a chunk to something a human
has a chance of understanding. That's the difference between weave and
tangle in the original implementation.) By blocking expansion, I can
focus on the main steps without having them lost in pages and pages of code.
So I vote strongly for retaining expand=FALSE.
Best,
Kevin
Duncan Murdoch wrote:
On 19/08/2010 4:29 PM, Claudia Beleites wrote:
I never used it.
I got curious, though. What would be a situation that benefits of
this option?
When I put it in, I thought it would be for people who were writing
about Sweave.
Duncan Murdoch
Maybe a use case could be found by brute force (grep all .Rnw files
on CRAN for the option?
Claudia
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
__
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Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
I picked the example from segmenting chromosomes for a reason. I have a
fair chunk of code that deals with not quite exceeding the amount of RAM
available in the machine sitting on my desktop. If I use functions,
then the pass-by-value semantics of R will push me beyond the limits at
some points. (This is an empirical statement, not a theoretical one. I
was bitten by it several times while trying to analyze a couple of these
datasets. And, yes, I know I can get around this by buying a bigger and
better machine; it's on order...) The real point is that using
functions can be detrimental to the efficiency of the program, in ways
that have real world consequences.
I haven't thought about doing the same thing with expressions.
Expressions don't have quite the same semantics as chunks, and you'd
have to make sure the evaluation was delayed so that you cold use the
current values of things that were computed in the meantime and I
already know how to do this with chunks without having to think so hard.
Using expressons would, however, help with the one difficulty that I
have with reusing chunks (independent of whether or not I use
'expand=FALSE'). I usually work inside emacs, using the
emacs-speaks-statistics (ESS) package. ESS doesn't know how to evaluate
the chunk call inside another chunk. so if I want to step through
the code during development, I have to jump around myself to locate the
source chunks. With expressions that wouldn't matter.
As I ramble on about this, it occurs to me that the underlying issue is
that chunks are not first class objects either in the LaTeX world or
in the R world part of Sweave. If there were a way to promote them to
first class objects somehow, then it might make my use of ESS easier
while simultaneously making it easier for Duncan to figure out how to
report the correct line numbers. But I only have an extremely vague
idea of how one might start to do that...
Kevin
Matt Shotwell wrote:
On Thu, 2010-08-19 at 17:07 -0400, Kevin Coombes wrote:
I use it, frequently. The idea for it goes back to some of Knuth's
original literate programming ideas for developing weave and tangle when
he was writing TeX (the program). I want to be able to document the
pieces of some complex algorithm without having to see all of the gory
details. For instance, I have code that looks like the following.
(Note that this is typed on the fly rather than copied from actual
source, so there may be typos.)
mainloop,keep.source=TRUE,expand=FALSE=
for (i in 1:nSamples) {
getInfoAboutThisSample
for (j in 1:nChromosomes) {
getChromosomeDataForCurrentSample
normalizeChromosomeData
findSegments
computeSignificance
writeResults
}
}
@
Each of the chunks is itself a fairly long piece of code defined and
documented somewhere else. (Some of them may themselves be written in
the same form to reduce the final size of a chunk to something a human
has a chance of understanding. That's the difference between weave and
tangle in the original implementation.) By blocking expansion, I can
focus on the main steps without having them lost in pages and pages of code.
Couldn't you achieve the same amount of abstraction using function
calls, rather than embedded code chunks? The reader can then see real
code, rather than non-code, or meta-code, or whatever. Alternatively,
represent the code chunks as R expressions, then evaluate the
expressions at the appropriate points.
-Matt
So I vote strongly for retaining expand=FALSE.
Best,
Kevin
Duncan Murdoch wrote:
On 19/08/2010 4:29 PM, Claudia Beleites wrote:
I never used it.
I got curious, though. What would be a situation that benefits of
this option?
When I put it in, I thought it would be for people who were writing
about Sweave.
Duncan Murdoch
Maybe a use case could be found by brute force (grep all .Rnw files
on CRAN for the option?
Claudia
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
__
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__
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Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
On Thu, Aug 19, 2010 at 6:21 PM, Kevin Coombes kevin.r.coom...@gmail.com wrote: I picked the example from segmenting chromosomes for a reason. I have a fair chunk of code that deals with not quite exceeding the amount of RAM available in the machine sitting on my desktop. If I use functions, then the pass-by-value semantics of R will push me beyond the limits at some points. (This is an empirical statement, not a theoretical one. I was bitten by it several times while trying to analyze a couple of these datasets. And, yes, I know I can get around this by buying a bigger and better machine; it's on order...) The real point is that using functions can be detrimental to the efficiency of the program, in ways that have real world consequences. I haven't thought about doing the same thing with expressions. Expressions don't have quite the same semantics as chunks, and you'd have to make sure the evaluation was delayed so that you cold use the current values of things that were computed in the meantime and I already know how to do this with chunks without having to think so hard. Using expressons would, however, help with the one difficulty that I have with reusing chunks (independent of whether or not I use 'expand=FALSE'). I usually work inside emacs, using the emacs-speaks-statistics (ESS) package. ESS doesn't know how to evaluate the chunk call inside another chunk. so if I want to step through the code during development, I have to jump around myself to locate the source chunks. With expressions that wouldn't matter. As I ramble on about this, it occurs to me that the underlying issue is that chunks are not first class objects either in the LaTeX world or in the R world part of Sweave. If there were a way to promote them to first class objects somehow, then it might make my use of ESS easier while simultaneously making it easier for Duncan to figure out how to report the correct line numbers. But I only have an extremely vague idea of how one might start to do that... You could try a macro instead and see how it performs. There is an article by Thomas Lumley in R News 2003-1 and an implementation in the gtools package. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
On Thu, 19 Aug 2010, Kevin Coombes wrote:
I picked the example from segmenting chromosomes for a reason. I have a fair
chunk of code that deals with not quite exceeding the amount of RAM available
in the machine sitting on my desktop. If I use functions, then the
pass-by-value semantics of R will push me beyond the limits at some points.
(This is an empirical statement, not a theoretical one. I was bitten by it
several times while trying to analyze a couple of these datasets. And, yes, I
know I can get around this by buying a bigger and better machine; it's on
order...) The real point is that using functions can be detrimental to the
efficiency of the program, in ways that have real world consequences.
I haven't thought about doing the same thing with expressions. Expressions
don't have quite the same semantics as chunks, and you'd have to make sure
the evaluation was delayed so that you cold use the current values of things
that were computed in the meantime and I already know how to do this with
chunks without having to think so hard.
Using expressons would, however, help with the one difficulty that I have
with reusing chunks (independent of whether or not I use 'expand=FALSE').
I usually work inside emacs, using the emacs-speaks-statistics (ESS) package.
ESS doesn't know how to evaluate the chunk call inside another chunk. so
if I want to step through the code during development, I have to jump around
myself to locate the source chunks. With expressions that wouldn't matter.
emacs org-mode might help.
You can define a chunk, ch1 (say), then place it in a subsequent
chunk, ch2 (say), inside an eval() and refer to ch2 inside an
eval() inside another chunk, ch3, and so on. The only trick is to
write the chunk so that the chunk it refers to is on its own line, like
this:
#+source: ch3
#+begin_src R :session :noweb yes
eval(
ch2
)
z - mean(y)+1
#+end_src
as the noweb expansion will repeat any other text on the line with the
named chunk for each line of code in the referenced chunk.
You can define a library of chunks separately, which might help you if you
reuse them in different places.
You can use ess-mode to edit the chunks and execute them with the usual
ess-eval-* commands, or run them in org-mode with the results optionally
returned to the edit buffer, but outside the code block.
If you want to debug a bunch of nested chunks and 'step through the code
during development', you can tangle the chunk you wish to execute to
produce a *.R file. The nested chunks are expanded into R. Open that *.R
file and debug away.
With a recent emacs, I think this gets you going:
C-h i m Org Mode RET C-s source RET RET
or Google 'org-babel R' or some such or just go look here:
http://blogisticreflections.wordpress.com/
As I ramble on about this, it occurs to me that the underlying issue is that
chunks are not first class objects either in the LaTeX world or in the R
world part of Sweave. If there were a way to promote them to first class
objects somehow, then it might make my use of ESS easier while simultaneously
making it easier for Duncan to figure out how to report the correct line
numbers. But I only have an extremely vague idea of how one might start to
do that...
org-mode might be the path of least resistance.
FWIW, the code chunks are objects processed by emacs-lisp before they are
handed off to R, so there might be a slicker way to handle the nesting
than dropping chunks inside eval()s in R blocks. If that interests you,
there is a very active listserv for orgmode, where you might inqure.
HTH,
Chuck
Kevin
Matt Shotwell wrote:
On Thu, 2010-08-19 at 17:07 -0400, Kevin Coombes wrote:
I use it, frequently. The idea for it goes back to some of Knuth's
original literate programming ideas for developing weave and tangle when
he was writing TeX (the program). I want to be able to document the
pieces of some complex algorithm without having to see all of the gory
details. For instance, I have code that looks like the following.
(Note that this is typed on the fly rather than copied from actual
source, so there may be typos.)
mainloop,keep.source=TRUE,expand=FALSE=
for (i in 1:nSamples) {
getInfoAboutThisSample
for (j in 1:nChromosomes) {
getChromosomeDataForCurrentSample
normalizeChromosomeData
findSegments
computeSignificance
writeResults
}
}
@
Each of the chunks is itself a fairly long piece of code defined and
documented somewhere else. (Some of them may themselves be written in
the same form to reduce the final size of a chunk to something a human
has a chance of understanding. That's the difference between weave and
tangle in the original implementation.) By blocking expansion, I can
focus on the main steps without having them lost in pages and pages of
code.
Couldn't you achieve the same amount of abstraction using function
