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(...)[EMAIL PROTECTED],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([EMAIL PROTECTED])})
[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
> [EMAIL PROTECTED]
>
>
>> -----Original Message-----
>> From: John Chambers [mailto:[EMAIL PROTECTED]
>> 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 [EMAIL PROTECTED]
>> ## 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
>> [EMAIL PROTECTED]
>>
>>
>>
>> **********************************************************************
>> The contents of this email are for the named
>> addressee(s...{{dropped:22}}
>>
>> ______________________________________________
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>>
>>
>>
>
>
> **********************************************************************
> The contents of this email are for the named addressee(s...{{dropped:22}}
>
> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
[[alternative HTML version deleted]]
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
