Sklyar, Oleg (London) wrote:
> Ha, defined xtfrm for TimeDate, works instantly (xtfrm is already a
> method). However, it won't be taken up by order as it is not in the
> imported namespace, so order falls back to xtfrm.default.
>   
By "method" you mean "generic"?  xtfrm is an S3 generic.  I'm not clear 
what happens if you define an S3 method for it.  Yes, there is a problem 
defining an S4 generic & it would be good to deal with that.  
Nontrivial, however.
> Moreover, defining order (which is not a method unfortunately, *any
> chance of changing this*?):
>
> setGeneric("order")
> setMethod("order", "TimeDate", 
> 	function (..., na.last = TRUE, decreasing = FALSE) 
> 		order(list(...)[[1]]@.Data,na.last=na.last,
> decreasing=decreasing))
>
> does not help either as it won't be taken up, order still calls the
> default one, what am I doing wrong?
>   
I'm skeptical that this is true.  I did a simple example:

 > setClass("foo", contains = "numeric", representation(flag = "logical"))
[1] "foo"
 > xx = new("foo", rnorm(5))
 > setGeneric("order", sig = "...")
Creating a generic for "order" in package  ".GlobalEnv"
    (the supplied definition differs from and overrides the implicit 
generic in package "base": Signatures differ:  (...), (na.last, decreasing))
[1] "order"
 > setMethod("order", "foo", function (..., na.last = TRUE, decreasing = 
FALSE){message("Method called"); order(..1@.Data)})
[1] "order"
 > order(xx)
Method called
[1] 2 4 3 1 5

You do need to be calling order() directly from one of your functions, 
and have it in your namespace, if your package has one.
>
>
> Dr Oleg Sklyar
> Research Technologist
> AHL / Man Investments Ltd
> +44 (0)20 7144 3107
> osklyar@maninvestments.com 
>
>   
>> -----Original Message-----
>> From: John Chambers [mailto:jmc@r-project.org] 
>> Sent: 09 September 2008 15:11
>> To: Sklyar, Oleg (London)
>> Cc: R-devel@r-project.org
>> Subject: Re: [Rd] 'xtfrm' performance (influences 'order' 
>> performance) in R devel
>>
>> No definitive answers, but here are a few observations.
>>
>> In the call to order() code, I notice that you have dropped 
>> into the branch
>>     if (any(unlist(lapply(z, is.object))))
>> where the alternative in your case would seem to have been 
>> going directly to the internal code.
>>
>> You can consider a method for xtfrm(), which would help but 
>> won't get you completely back to a trivial computation.  
>> Alternatively,  order() should be eligible for the new 
>> mechanism of defining methods for "...".
>>
>> (Individual existing methods may not be the issue, and one 
>> can't infer anything definite from the evidence given,  but a 
>> plausible culprit is the "[" method.  Because [] expressions 
>> appear so often, it's always chancy to define a nontrivial 
>> method for this function.)
>>
>> John
>>
>> Sklyar, Oleg (London) wrote: 
>>
>> 	Hello everybody,
>> 	
>> 	it looks like the presense of some (do know know which) 
>> S4 methods for a
>> 	given S4 class degrades the performance of xtfrm (used 
>> in 'order' in new
>> 	R-devel) by a factor of millions. This is for classes 
>> that ARE derived
>> 	from numeric directly and thus should be quite trivial 
>> to convert to
>> 	numeric.
>> 	
>> 	Consider the following example:
>> 	
>> 	setClass("TimeDateBase", 
>> 	    representation("numeric", mode="character"),
>> 	    prototype(mode="posix")
>> 	)
>> 	setClass("TimeDate",
>> 	    representation("TimeDateBase", tzone="character"),
>> 	    prototype(tzone="London")
>> 	)
>> 	x = new("TimeDate", 1220966224 + runif(1e5))
>> 	
>> 	system.time({ z = order(x) })
>> 	## > system.time({ z = order(x) })
>> 	##   user  system elapsed 
>> 	##  0.048   0.000   0.048 
>> 	
>> 	getClass("TimeDate")
>> 	## Class "TimeDate"
>> 	
>> 	## Slots:
>> 	                                    
>> 	## Name:      .Data     tzone      mode
>> 	## Class:   numeric character character
>> 	
>> 	## Extends: 
>> 	## Class "TimeDateBase", directly
>> 	## Class "numeric", by class "TimeDateBase", distance 2
>> 	## Class "vector", by class "TimeDateBase", distance 3
>> 	
>> 	
>> 	Now, if I load a library that not only defines these 
>> same classes, but
>> 	also a bunch of methods for those, then I have the 
>> following result:
>> 	
>> 	library(AHLCalendar)
>> 	x = now() + runif(1e5) ## just random times in POSIXct format
>> 	x[1:5]
>> 	## TimeDate [posix] object in 'Europe/London' of length 5:
>> 	## [1] "2008-09-09 14:19:35.218" "2008-09-09 14:19:35.672"
>> 	## [3] "2008-09-09 14:19:35.515" "2008-09-09 14:19:35.721"
>> 	## [5] "2008-09-09 14:19:35.657"
>> 	
>> 	  
>>
>> 		system.time({ z = order(x) })
>> 		    
>>
>> 	
>> 	
>> 	Enter a frame number, or 0 to exit   
>> 	
>> 	 1: system.time({
>> 	 2: order(x)
>> 	 3: lapply(z, function(x) if (is.object(x)) xtfrm(x) else x)
>> 	 4: FUN(X[[1]], ...)
>> 	 5: xtfrm(x)
>> 	 6: xtfrm.default(x)
>> 	 7: as.vector(rank(x, ties.method = "min", na.last = "keep"))
>> 	 8: rank(x, ties.method = "min", na.last = "keep")
>> 	 9: switch(ties.method, average = , min = , max =
>> 	.Internal(rank(x[!nas], ties.
>> 	10: .gt(c(1220966375.21811, 1220966375.67217, 1220966375.51470,
>> 	1220966375.7211
>> 	11: x[j]
>> 	12: x[j]
>> 	
>> 	Selection: 0
>> 	Timing stopped at: 47.618 13.791 66.478 
>> 	
>> 	At the same time:
>> 	
>> 	system.time({ z = as.numeric(x) }) ## same as x@.Data
>> 	##   user  system elapsed 
>> 	##  0.001   0.000   0.001 
>> 	
>> 	The only difference between the two is that I have the 
>> following methods
>> 	defined for TimeDate (full listing below). 
>> 	
>> 	Any idea why this could be happenning. And yes, it is 
>> down to xtfrm
>> 	function, 'order' was just a place where the problem 
>> occured. Should
>> 	xtfrm function be smarter with respect to classes that 
>> are actually
>> 	derived from 'numeric'?
>> 	
>> 	  
>>
>> 		showMethods(class="TimeDate")
>> 		    
>>
>> 	Function: + (package base)
>> 	e1="TimeDate", e2="TimeDate"
>> 	e1="TimeDate", e2="numeric"
>> 	    (inherited from: e1="TimeDateBase", e2="numeric")
>> 	
>> 	Function: - (package base)
>> 	e1="TimeDate", e2="TimeDate"
>> 	
>> 	Function: Time (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: TimeDate (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: TimeDate<- (package AHLCalendar)
>> 	x="TimeSeries", value="TimeDate"
>> 	
>> 	Function: TimeSeries (package AHLCalendar)
>> 	x="data.frame", ts="TimeDate"
>> 	x="matrix", ts="TimeDate"
>> 	x="numeric", ts="TimeDate"
>> 	
>> 	Function: [ (package base)
>> 	x="TimeDate", i="POSIXt", j="missing"
>> 	x="TimeDate", i="Time", j="missing"
>> 	x="TimeDate", i="TimeDate", j="missing"
>> 	x="TimeDate", i="integer", j="missing"
>> 	    (inherited from: x="TimeDateBase", i="ANY", j="missing")
>> 	x="TimeDate", i="logical", j="missing"
>> 	    (inherited from: x="TimeDateBase", i="ANY", j="missing")
>> 	x="TimeSeries", i="TimeDate", j="missing"
>> 	x="TimeSeries", i="TimeDate", j="vector"
>> 	
>> 	Function: [<- (package base)
>> 	x="TimeDate", i="ANY", j="ANY", value="ANY"
>> 	x="TimeDate", i="ANY", j="ANY", value="numeric"
>> 	x="TimeDate", i="missing", j="ANY", value="ANY"
>> 	x="TimeDate", i="missing", j="ANY", value="numeric"
>> 	
>> 	Function: add (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: addMonths (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: addYears (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: align (package AHLCalendar)
>> 	x="TimeDate", to="character"
>> 	x="TimeDate", to="missing"
>> 	
>> 	Function: as.POSIXct (package base)
>> 	x="TimeDate"
>> 	
>> 	Function: as.POSIXlt (package base)
>> 	x="TimeDate"
>> 	
>> 	Function: coerce (package methods)
>> 	from="TimeDate", to="TimeDateBase"
>> 	
>> 	Function: coerce<- (package methods)
>> 	from="TimeDate", to="numeric"
>> 	
>> 	Function: dates (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: format (package base)
>> 	x="TimeDate"
>> 	
>> 	Function: fxFwdDate (package AHLCalendar)
>> 	x="TimeDate", country="character"
>> 	
>> 	Function: fxSettleDate (package AHLCalendar)
>> 	x="TimeDate", country="character"
>> 	
>> 	Function: holidays (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: index (package AHLCalendar)
>> 	x="TimeDate", y="POSIXt"
>> 	x="TimeDate", y="Time"
>> 	x="TimeDate", y="TimeDate"
>> 	
>> 	Function: initialize (package methods)
>> 	.Object="TimeDate"
>> 	    (inherited from: .Object="ANY")
>> 	
>> 	Function: leapYear (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: mday (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: mode (package base)
>> 	x="TimeDate"
>> 	    (inherited from: x="TimeDateBase")
>> 	
>> 	Function: mode<- (package base)
>> 	x="TimeDate", value="character"
>> 	    (inherited from: x="TimeDateBase", value="character")
>> 	
>> 	Function: month (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: pretty (package base)
>> 	x="TimeDate"
>> 	
>> 	Function: prettyFormat (package AHLCalendar)
>> 	x="TimeDate", munit="character"
>> 	x="TimeDate", munit="missing"
>> 	
>> 	Function: print (package base)
>> 	x="TimeDate"
>> 	
>> 	Function: show (package methods)
>> 	object="TimeDate"
>> 	    (inherited from: object="TimeDateBase")
>> 	
>> 	Function: summary (package base)
>> 	object="TimeDate"
>> 	
>> 	Function: td2tz (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: times (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: tojulian (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: toposix (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: tots (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: tzone (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: tzone<- (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: wday (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: yday (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	Function: year (package AHLCalendar)
>> 	x="TimeDate"
>> 	
>> 	
>> 	
>> 	Dr Oleg Sklyar
>> 	Research Technologist
>> 	AHL / Man Investments Ltd
>> 	+44 (0)20 7144 3107
>> 	osklyar@maninvestments.com
>> 	
>> 	
>> 	
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>> 	
>> 	  
>>
>>
>>     
>
>
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