From kevin.r.coombes at gmail.com  Fri Aug 20 00:21:40 2010
From: kevin.r.coombes at gmail.com (Kevin Coombes)
Date: Thu, 19 Aug 2010 17:21:40 -0500
Subject: [Rd] Does anyone use Sweave (RweaveLatex) option "expand=FALSE"?
In-Reply-To: <1282253385.1554.5.camel@matt-laptop>
References: <4C6D80E3.2090806@gmail.com> <4C6D9431.4020104@units.it>	
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	<1282253385.1554.5.camel@matt-laptop>
Message-ID: <4C6DAE74.7010002@gmail.com>

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 at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>       
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>     
>
>



[Rd] Does anyone use Sweave (RweaveLatex) option "expand=FALSE"?
Kevin Coombes