From ggrothendieck at gmail.com  Thu Oct 23 02:35:34 2008
From: ggrothendieck at gmail.com (Gabor Grothendieck)
Date: Wed, 22 Oct 2008 20:35:34 -0400
Subject: [Rd] R 2.8.0 qqnorm produces error with object of class zoo?
In-Reply-To: <48FF952C.3040809@biostat.ku.dk>
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	<48FF215E.80807@biostat.ku.dk>
	<971536df0810220933l6be9989aie61bd69c7978bd17@mail.gmail.com>
	<48FF6256.8080702@biostat.ku.dk>
	<971536df0810221119k1709874fl309a83ad41e246c4@mail.gmail.com>
	<971536df0810221209x67e67bf2l1ed16e2a612db863@mail.gmail.com>
	<48FF952C.3040809@biostat.ku.dk>
Message-ID: <971536df0810221735r475f4b06s40354351ea4fae05@mail.gmail.com>

I don't think its hopeless.  order works ok provided the underlying class
defines an xtfrm method.  I think rank should follow that route too.  Its
arguably the inconsistency between rank and order (order but not the
rank uses xtfrm) that causes the inconsistent behavior between the two.
If rank were also built on top of xtfrm then it would work as desired as
well.

On Wed, Oct 22, 2008 at 5:03 PM, Peter Dalgaard
<p.dalgaard at biostat.ku.dk> wrote:
> Gabor Grothendieck wrote:
>>
>> And one other point.
>>
>> z <- zoo(1:4)
>> .gt(z, 1, 2)
>>
>> fails because z[1] and z[2] are at different time points so
>>
>>   z[1] == z[2]
>>
>> is logical(0) because when zoo compares objects it aligns them
>> first.
>
> Yes, that was the point that I was trying to make. Well, arguably it doesn't
> "fail", it just does what it is supposed to do. Things would "work" with [[
> or a preceding unclass(z), but that would break comparisons involving, say,
> POSIXlt objects. So you're sort of stuck between a rock and a hard place.
>
>>
>> On Wed, Oct 22, 2008 at 2:19 PM, Gabor Grothendieck
>> <ggrothendieck at gmail.com> wrote:
>>>
>>> Yes, I noticed that but rank is not generic.  An xtfrm.zoo
>>> method has been added to zoo on R-Forge but rank still
>>> fails:
>>>
>>>> R.version.string
>>>
>>> [1] "R version 2.8.0 Patched (2008-10-21 r46766)"
>>>>
>>>> packageDescription("zoo")$Version
>>>
>>> [1] "1.5-3"
>>>>
>>>> library(zoo)
>>>> # next line adds xtfrm zoo method
>>>> xtfrm.zoo <- coredata
>>>> z <- zoo(1:4)
>>>> order(z) # ok
>>>
>>> [1] 1 2 3 4
>>>>
>>>> qqnorm(z) # ok
>>>> rank(z) # error
>>>
>>> Error in if (xi == xj) 0L else if (xi > xj) 1L else -1L :
>>>  argument is of length zero
>>>
>>>
>>>>>> (If the MIME type is wrong, then that will happen.)
>>>>>>
>>>>>> Anyways, the root cause seems to be the new function .gt() which is
>>>>>> related to
>>>>>>
>>>>>>   o   New generic function xtfrm() as an auxiliary helper for
>>>>>>       sort(), order() and rank().  This should return a numeric
>>>>>>       vector that sorts in the same way as its input.  The default
>>>>>>       method supports any class with ==, > and is.na() methods but
>>>>>>       specific methods can be much faster.
>>>>>>
>>>>>>       As a side-effect, rank() will now work better on classed
>>>>>>       objects, although possibly rather slowly.
>>>>>>
>>>>>> Here, "better" may be in the eyes of the beholder, for
>>>>>>
>>>>>>
>>>>>>> dax[3]==dax[6]
>>>>>>>
>>>>>> Data:
>>>>>> logical(0)
>>>>>>
>>>>>> Index:
>>>>>> integer(0)
>>>>>>
>>>>>> and accordingly
>>>>>>
>>>>>>
>>>>>>> rank(dax)
>>>>>>>
>>>>>> Error in if (xi == xj) 0L else if (xi > xj) 1L else -1L :
>>>>>>  argument is of length zero
>>>>>>
>>>>>> which is the error that you are seeing.
>>>>>>
>>>>>> What to do about it is a bit dubious. Obviously, we don't want to
>>>>>> "fix"
>>>>>> .gt() so that it automatically unclasses objects, and I assume that
>>>>>> zoo
>>>>>> has its reasons for not wanting to compare series with different
>>>>>> indices. So I suppose that either the user must unclass, or zoo define
>>>>>> rank.zoo.
>>>>>>
>>>>> Actually qqnorm does not use rank but it does use order and with the
>>>>> xtfrm.zoo method I mentioned qqnorm works with zoo; however, I think
>>>>> rank needs to be fixed in R to make use of xtfrm as well since I would
>>>>> have
>>>>> expected that supplying an xtfrm method for zoo would be sufficient to
>>>>> get both order and rank to work without giving errors.  Also note that
>>>>> rank
>>>>> is not generic.
>>>>>
>>>> Notice that xtfrm.default() uses rank()....
>>>>
>>>> --
>>>>  O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
>>>>  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
>>>>  (*) \(*) -- University of Copenhagen   Denmark      Ph:  (+45) 35327918
>>>> ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)              FAX: (+45) 35327907
>>>>
>>>>
>>>>
>
>
> --
>   O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
>  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
>  (*) \(*) -- University of Copenhagen   Denmark      Ph:  (+45) 35327918
> ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)              FAX: (+45) 35327907
>



[Rd] R 2.8.0 qqnorm produces error with object of class zoo?
Gabor Grothendieck