Pb with agrep()

"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

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
 

OK I got it! Thanks for the explanation.
Cheers,

Herv?

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Herv? Pag?s
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