[R] (structured) programming style

Spencer Graves spencer.graves at pdf.com
Fri Sep 12 03:03:04 CEST 2003

You asked, "Where and what is Bioconductor... ."  See:  www.bioconductor.org

spencer graves

Ross Boylan wrote:
> Thanks for your response.  Is good to know that copying is lazy, but I
> don't think that fully solves my problems.  See below.
> On Thu, 2003-09-11 at 17:40, Thomas Lumley wrote:
> .....
>>you see that unpacking b from a didn't result in a copy, and that b must
>>just be a reference to a$m.  When b is modified it must be copied, but
>>this is true whether or not it is in a list. What matters is whether there
>>is another reference to it somewhere [actually, whether R thinks there
>>*might* be another reference: we try to be a bit conservative about this].
> I'm thinking of a situation like
> a <- array(0, dim=c(10000, 10))
> and then I modify a one row at a time.
> a[34,] <- newrow
> So if I write directly to a, I just overwrite the row.
> But if I make a copy, even a lazy one, when I change the row I have to
> make a copy of the whole array (unless the laziness is really clever,
> and your figures suggest that a single write causes the whole thing to
> be copied).
> Hmm, now that I think of it I suppose I could just return newrow from
> the inner function... except I have inner functions that produce several
> rows, with inner inner functions that do single rows...
>>Now, it is certainly possible that you could have a situation where
>>assigning with <<- was really faster than passing back a list, by enough
>>to matter.  I think this situation is unusual enough that there may not be
>>a firm idea of `good R style', since it assumes that the objects are small
>>enough to fit easily in memory but large enough that it's worth going to
>>some effort to reduce copying. You might get more useful input from the
>>Bioconductor list, where people tend to spend a lot of time doing
>>computationally expensive things to medium-sized data sets.
> Where and what is the Bioconductor list?
> I suppose optimization is one traditional reason to break style
> guidelines.
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