[R] possible bug in merge with duplicate blank names in 'by' field.

[Prof Brian Ripley]

What version of R is this (please do see the posting guide)?

In both 2.1.0 and 2.1.1 beta I get

> all
   Promoter ip.x ip.y ip
1            30   40 40
2            40   40 40
3        a   10   NA NA
4        c   20   20 20
5        b   NA   15 15
6        d   NA   30 30

so cannot reproduce your result. Are you sure that the `blanks' really are 
empty and not some character that is printing as empty on your unstated 
OS?

BTW ' ' is what is normally called `blank'.

BTW, these are not `names' but character strings: `names' has other 
meanings in R.

On Thu, 16 Jun 2005, Frank Gibbons wrote:

> Run this:
>
>> p <- c('a', 'c', '', ''); a <- c(10, 20, 30, 40); d1 <-
>> data.frame(Promoter=p, ip=a) # Note duplicate empty names in p.
>> p <- c('b', 'c', 'd', ''); a <- c(15, 20, 30, 40); d2 <-
>> data.frame(Promoter=p, ip=a)
>> all <- merge(x=d1, y=d2, by="Promoter", all=T)
>> all <- merge(x=all, y=d2, by="Promoter", all=T)
>> all
>
> Data is this:
>
>> d1
>>   Promoter ip
>> 1        a 10
>> 2        c 20
>> 3          30
>> 4          40
>>
>> d2
>>   Promoter ip
>> 1        b 15
>> 2        c 20
>> 3        d 30
>> 4          40
>
> Output looks like this:
>
>>   Promoter ip.x ip.y ip
>> 1            40   30 30
>> 2            40   40 30
>> 3            40   30 40
>> 4            40   40 40
>> 5        b   15   NA NA
>> 6        c   20   20 20
>> 7        d   30   NA NA
>> 8        a   NA   10 10
>
> The weird thing about this is (in my view) that each instance of '' is
> considered unique, so with each successive merge, all combinatorial
> possibilities are explored, like a SQL outer join (Cartesian product). For
> non-empty names, an inner join is performed.
>
> Dealing with genomic data (10^4 datapoints), it's easy to have a couple of
> blanks buried in the middle of things, and to combine several replicates
> with successive merges. I couldn't understand how my three replicates of
> 6000 points, in which I expected  substantial overlap in the labels, were
> taking so long to merge and ultimately generating 57000 labels. The culprit
> turned out to be a few hundred blanks buried in the middle.
>
> Why does the empty ("null") name merit special treatment? Perhaps I'm
> missing something. I hesitate to submit this as a bug, since technically I
> guess you could say that blank names, especially duplicates, are not
> kosher. But on the other hand, this combinatorial behaviour seems to occur
> only for blanks.
>
> -Frank
>
> PhD, Computational Biologist,
> Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
> Tel: 617-432-3555       Fax:
> 617-432-3557       http://llama.med.harvard.edu/~fgibbons
>
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>

-- 
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