From maechler at stat.math.ethz.ch  Thu Jan  5 10:02:21 2006
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Thu, 5 Jan 2006 10:02:21 +0100
Subject: [Rd] Pb with agrep()
In-Reply-To: <43BC767F.4060405@fhcrc.org>
References: <43BC767F.4060405@fhcrc.org>
Message-ID: <17340.57501.191566.727447@stat.math.ethz.ch>

>>>>> "Herve" == Herve Pages <hpages at fhcrc.org>
>>>>>     on Wed, 04 Jan 2006 17:29:35 -0800 writes:

    Herve> Happy new year everybody,
    Herve> I'm getting the following while trying to use the agrep() function:

    >> pattern <- "XXX"
    >> subject <- c("oooooo", "oooXooo", "oooXXooo", "oooXXXooo")
    >> max <- list(ins=0, del=0, sub=0) # I want exact matches only
    >> agrep(pattern, subject, max=max)
    Herve> [1] 4

    Herve> OK

    >> max$sub <- 1 # One allowed substitution
    >> agrep(pattern, subject, max=max)
    Herve> [1] 3 4

    Herve> OK

    >> max$sub <- 2 # Two allowed substitutions
    >> agrep(pattern, subject, max=max)
    Herve> [1] 3 4

    Herve> Wrong!

No. 
You have overlooked the fact that 'max.distance = 0.1' (10%) 
*remains* the default, even when 'max.distance' is specified as
a list as in your example [from  "?agrep" ] :

>> max.distance: Maximum distance allowed for a match.  Expressed either
>>           as integer, or as a fraction of the pattern length (will be
>>           replaced by the smallest integer not less than the
>>           corresponding fraction), or a list with possible components
>> 
>>           'all': maximal (overall) distance
>> 
>>           'insertions': maximum number/fraction of insertions
>> 
>>           'deletions': maximum number/fraction of deletions
>> 
>>           'substitutions': maximum number/fraction of substitutions
>> 
>>>>>>       If 'all' is missing, it is set to 10%, the other components
>>>>>>       default to 'all'.  The component names can be abbreviated. 

If you specify max$all as "100%", i.e, as 0.9999  ('< 1' !)  everything works
as you expect it:

agrep(pattern, subject, max = list(ins=0, del=0, sub= 2, all = 0.9999))
## --> 2 3 4


Martin Maechler, ETH Zurich



[Rd] Pb with agrep()
Martin Maechler