From ripley at stats.ox.ac.uk  Mon May 14 12:39:18 2007
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Mon, 14 May 2007 11:39:18 +0100 (BST)
Subject: [Rd] Native implementation of rowMedians()
In-Reply-To: <59d7961d0705140243qca73bdbr14234febed9ebc5d@mail.gmail.com>
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	<17992.7115.324752.778339@stat.math.ethz.ch>
	<Pine.LNX.4.64.0705140924420.31269@auk.stats>
	<59d7961d0705140243qca73bdbr14234febed9ebc5d@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0705141053240.5157@auk.stats>

On Mon, 14 May 2007, Henrik Bengtsson wrote:

> On 5/14/07, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
>> 
>> > Hi Henrik,
>> >>>>>> "HenrikB" == Henrik Bengtsson <hb at stat.berkeley.edu>
>> >>>>>>     on Sun, 13 May 2007 21:14:24 -0700 writes:
>> >
>> >    HenrikB> Hi,
>> >    HenrikB> I've got a version of rowMedians(x, na.rm=FALSE) for 
>> matrices that
>> >    HenrikB> handles missing values implemented in C.  It has been

[...]

>> Also, the 'a version of rowMedians' made me wonder what other version
>> there was, and it seems there is one in Biobase which looks a more
>> natural home.
>
> The rowMedians() in Biobase utilizes rowQ() in ditto.  I actually
> started of by adding support for missing values to rowQ() resulting in
> the method rowQuantiles(), for which there are also internal functions
> for both integer and double matrices.  rowQuantiles() is in R.native
> too, but since it has much less CPU milage I wanted to wait with that.
> The rowMedians() is developed from my rowQuantiles() optimized for
> the 50% quantile.
>
> Why do you think it is more natural to host rowMedians() in Biobase
> than in one of the core R packages?  Biobase comes with a lot of
> overhead for people not in the Bio-world.

Because that is where there seems to be a need for it, and having multiple 
functions of the same name in different packages is not ideal (and even 
with namespaces can cause confusion).

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] Native implementation of rowMedians()
Prof Brian Ripley