From murdoch at stats.uwo.ca  Tue Apr 22 20:14:14 2008
From: murdoch at stats.uwo.ca (Duncan Murdoch)
Date: Tue, 22 Apr 2008 14:14:14 -0400
Subject: [Rd] graphics::Axis loosing S3/S4 class attributes of 'x' in
 2.7.0 RC
In-Reply-To: <971536df0804221029p55d19792s8bf49846ca2cf5de@mail.gmail.com>
References: <1A68FCB28DE72F4BA3B967E6506CCE430229487F@mildnpexmb01.maninvestments.ad.man.com>	
	<480DD38A.7090004@stats.uwo.ca>	
	<1A68FCB28DE72F4BA3B967E6506CCE4302294881@mildnpexmb01.maninvestments.ad.man.com>	
	<480DE708.3030104@stats.uwo.ca>	
	<1A68FCB28DE72F4BA3B967E6506CCE4302294884@mildnpexmb01.maninvestments.ad.man.com>	
	<480E1E00.8080409@stats.uwo.ca>
	<971536df0804221029p55d19792s8bf49846ca2cf5de@mail.gmail.com>
Message-ID: <480E2AF6.5000700@stats.uwo.ca>

On 4/22/2008 1:29 PM, Gabor Grothendieck wrote:
> Its not clear to me at this point what and where the proposed
> or already made change is but here
> is a test that should produce a year/month style rather than
> numeric style X axis:
> 
> library(zoo)
> z <- zoo(1:12, as.yearmon(2000 + 1:12/12))
> plot(z)

It does.

Duncan Murdoch

> 
> 
> On Tue, Apr 22, 2008 at 1:18 PM, Duncan Murdoch <murdoch at stats.uwo.ca> wrote:
>> There seem to be nonlinearities in the time-space continuum, so this
>> message arrived several hours after Martin's, even though both have the
>> same timestamp.  Please test his, and see if you can break it.  I'd
>> guess not, it looks simple enough, but not too simple.
>>
>> And for the future:
>>
>> Please test the alpha/beta/RC releases!  The change we're talking about
>> came fairly late in the process, but it was there for the last couple of
>> weeks.  It would be easier for everyone if it had been corrected before
>> release, rather than after.  It was announced on the RSS list, here:
>>
>> http://developer.r-project.org/blosxom.cgi/R-2-7-branch/NEWS/2008/04/08#n2008-04-08
>>
>> so it would really have helped if people who rely on special axis
>> handling by Axis had tested the change after they'd seen that notice.
>>
>> On 4/22/2008 10:26 AM, Sklyar, Oleg (MI London) wrote:
>>  > Ok, so what's wrong with the following fix for plot(x)
>>
>> The main thing that's wrong with it is that you don't explain what the
>> changes are.  I can't believe that the error is specific to the POSIXct
>> class, so it doesn't make sense that changes there would fix it in general.
>>
>> Duncan Murdoch
>>
>>
>>  > that would
>> > actually fix what needs to be fixed instead of changing plot.default?
>> > Fix means reverting plot.default in 2.7.0 to what it was (if testing in
>> > 2.7.0, copy and paste the OLD plot.default into the .GlobalEnv):
>> >
>> > plot.POSIXct <- function(x, y, xlab = "", ...) {
>> >     if (!missing(y)) {
>> >         side = 1
>> >         plotDef <- function(x, y, xaxt, xlab, ...) plot.default(x, y,
>> > xaxt="n", xlab=xlab, ...)
>> >         plotDef(x, y, xlab=xlab, ...)
>> >     } else {
>> >         side = 2
>> >         plotDef <- function(x, y, yaxt, xlab, ...) plot.default(x, y,
>> > yaxt="n", xlab=xlab, ...)
>> >         plotDef(seq_along(x), x, xlab=xlab, ...)
>> >     }
>> >     ## trick to remove arguments intended for title() or plot.default()
>> >     axisInt <- function(x, type, main, sub, xlab, ylab, col, lty, lwd,
>> >                         xlim, ylim, bg, pch, log, asp, axes, frame.plot,
>> > ...)
>> >         axis.POSIXct(side, x, ...)
>> >     dots <- list(...)
>> >     axes <- if("axes" %in% names(dots)) dots$axes else TRUE
>> >     xaxt <- if("xaxt" %in% names(dots)) dots$xaxt else par("xaxt")
>> >     if(axes && xaxt != "n") axisInt(x, ...)
>> > }
>> >
>> > plot.POSIXlt <- function(x, y, xlab = "", ...) {
>> >     if (missing(y)) plot.POSIXct(as.POSIXct(x), xlab=xlab, ...)
>> >     else plot.POSIXct(as.POSIXct(x), y=y, xlab=xlab, ...)
>> > }
>> >
>> > And try with:
>> > x = Sys.time() + runif(100,1,7200)
>> > plot(x)
>> > plot(x,1:100)
>> > plot(1:100,x)
>> >
>> > plot(as.POSIXlt(x))
>> > plot(as.POSIXlt(x),1:100)
>> > plot(1:100,as.POSIXlt(x))
>> >
>> >
>> > Dr Oleg Sklyar
>> > Technology Group
>> > Man Investments Ltd
>> > +44 (0)20 7144 3803
>> > osklyar at maninvestments.com
>> >
>> >> -----Original Message-----
>> >> From: Duncan Murdoch [mailto:murdoch at stats.uwo.ca]
>> >> Sent: 22 April 2008 14:24
>> >> To: Sklyar, Oleg (MI London)
>> >> Cc: R-devel at r-project.org
>> >> Subject: Re: [Rd] graphics::Axis loosing S3/S4 class
>> >> attributes of 'x' in 2.7.0 RC
>> >>
>> >> On 4/22/2008 9:08 AM, Sklyar, Oleg (MI London) wrote:
>> >> > Duncan,
>> >> >
>> >> > looking further, what has changed from 2.6.2 into 2.7.0 are the
>> >> > following two lines in plot.default, which I think were
>> >> logical before
>> >> > and are not really logical now:
>> >>
>> >> I believe it is behaving as documented now, so the behaviour
>> >> is "logical", even if it may not be convenient.  In your example
>> >>
>> >> x = Sys.time() + runif(100,1,7200) ## time over two hours,
>> >> POSIXct plot(x, 1:100) plot(1:100, x)
>> >>
>> >> the 1st works in 2.6.2 and 2.7.0 and the second only works in 2.6.2.
>> >> But the change below was designed to fix the case
>> >>
>> >> plot(x)
>> >>
>> >> which works in 2.7.0 and *not* in 2.6.2, so reverting the
>> >> change is not the way to address this.
>> >>
>> >> Duncan Murdoch
>> >>
>> >> >
>> >> > plot.R: plot.default (2.6.2):
>> >> > if (axes) {
>> >> >    localAxis(x, side=1, ...)
>> >> >    localAxis(y, side=2, ...)
>> >> > }
>> >> >
>> >> > plot.R: plot.default (2.7.0):
>> >> > ...
>> >> > if (axes) {
>> >> >    localAxis(xy$x, side=1, ...)
>> >> >    localAxis(xy$y, side=2, ...)
>> >> > }
>> >> >
>> >> > The fact that xy.coords is called does not really matter.
>> >> >
>> >> >
>> >> > Dr Oleg Sklyar
>> >> > Technology Group
>> >> > Man Investments Ltd
>> >> > +44 (0)20 7144 3803
>> >> > osklyar at maninvestments.com
>> >> >
>> >> >> -----Original Message-----
>> >> >> From: Duncan Murdoch [mailto:murdoch at stats.uwo.ca]
>> >> >> Sent: 22 April 2008 13:01
>> >> >> To: Sklyar, Oleg (MI London)
>> >> >> Cc: R-devel at r-project.org
>> >> >> Subject: Re: [Rd] graphics::Axis loosing S3/S4 class attributes of
>> >> >> 'x' in 2.7.0 RC
>> >> >>
>> >> >> On 22/04/2008 7:25 AM, Sklyar, Oleg (MI London) wrote:
>> >> >> > Following my previous post on S3 method despatch, I put
>> >> >> debug messages
>> >> >> > in the code of Axis, Axis.default and plot.default in
>> >> >> > graphics/R/axis.R and graphics/R/plot.R to print the
>> >> class of x, at
>> >> >> > and y on plot. After recompiling R, what I see is that x
>> >> *lost* its
>> >> >> > class attribute (at least for classes not known to
>> >> 'graphics') in
>> >> >> > Axis, called directly from plot.default and this could be
>> >> >> the reason
>> >> >> > why R did not despatch on Axis.MyClass from my previous
>> >> post. This
>> >> >> > happens for both S3 and S4 classes as in the code below!
>> >> >> Funny enough,
>> >> >> > even "integer" was reset to numeric in Axis...
>> >> >>
>> >> >> If you look at plot.default, you'll see it passes x and y through
>> >> >> xy.coords to get coordinates.  That function ends with
>> >> >>
>> >> >> return(list(x=as.double(x), y=as.double(y), xlab=xlab, ylab=ylab))
>> >> >>
>> >> >> so that's where classes get removed.  If you don't want this to
>> >> >> happen, shouldn't you be defining plot.MyClass, or calling the
>> >> >> default with axes=F, and then calling Axis on your object yourself?
>> >> >>
>> >> >> > Is this really an intended behaviour? It looks very wrong to me!
>> >> >>
>> >> >> This is documented:  ?plot.default tells you to look at ?xy.coords
>> >> >> for details of how x and y are handled, and xy.coords says "In any
>> >> >> other case, the 'x' argument is coerced to a vector and
>> >> >>       returned as *y* component where the resulting 'x' is just the
>> >> >>       index vector '1:n'.  In this case, the resulting 'xlab'
>> >> >> component
>> >> >>       is set to '"Index"'."
>> >> >>
>> >> >> Duncan Murdoch
>> >> >>
>> >> >> > Thanks,
>> >> >> > Oleg
>> >> >> >
>> >> >> > *** R version 2.7.0 RC (2008-04-20 r45403)
>> >> >> [/research/osklyar/R-devel]
>> >> >> > ***
>> >> >> >> Axis
>> >> >> > function (x = NULL, at = NULL, ..., side, labels = NULL) {
>> >> >> >     cat("In Axis() class(x)=", class(x), "; class(at)=",
>> >> class(at),
>> >> >> >         "\n", sep = "")
>> >> >> >     if (!is.null(x))
>> >> >> >         UseMethod("Axis", x)
>> >> >> >     else if (!is.null(at))
>> >> >> >         UseMethod("Axis", at)
>> >> >> >     else axis(side = side, at = at, labels = labels, ...) }
>> >> >> > <environment: namespace:graphics>
>> >> >> >> graphics:::Axis.default
>> >> >> > function (x = NULL, at = NULL, ..., side, labels = NULL) {
>> >> >> >     cat("In Axis.default() class(x)=", class(x), "; class(at)=",
>> >> >> >         class(at), "\n", sep = "")
>> >> >> >     if (is.null(at) && !is.null(x))
>> >> >> >         at = pretty(x)
>> >> >> >     axis(side = side, at = at, labels = labels, ...) }
>> >> >> > <environment: namespace:graphics>
>> >> >> >> setClass("MyClass", representation(smth="character"),
>> >> >> > contains="numeric")
>> >> >> > [1] "MyClass"
>> >> >> >> a = new("MyClass", runif(10))
>> >> >> >> a
>> >> >> > An object of class "MyClass"
>> >> >> >  [1] 0.773237167 0.548630205 0.987956687 0.212667925 0.337135151
>> >> >> > 0.112210501
>> >> >> >  [7] 0.007140895 0.972028903 0.443581963 0.536452424 Slot "smth":
>> >> >> > character(0)
>> >> >> >> plot(1:10,a)
>> >> >> > In plot.default() class(x)=integer; class(y)=MyClass In Axis()
>> >> >> > class(x)=numeric; class(at)=NULL In Axis.default()
>> >> >> class(x)=numeric;
>> >> >> > class(at)=NULL In Axis() class(x)=numeric; class(at)=NULL In
>> >> >> > Axis.default() class(x)=numeric; class(at)=NULL
>> >> >> >> plot(a,1:10)
>> >> >> > In plot.default() class(x)=MyClass; class(y)=integer In Axis()
>> >> >> > class(x)=numeric; class(at)=NULL In Axis.default()
>> >> >> class(x)=numeric;
>> >> >> > class(at)=NULL In Axis() class(x)=numeric; class(at)=NULL In
>> >> >> > Axis.default() class(x)=numeric; class(at)=NULL
>> >> >> >> b = runif(10)
>> >> >> >> class(b)="AnotherClass"
>> >> >> >> plot(b,1:10)
>> >> >> > In plot.default() class(x)=AnotherClass;
>> >> class(y)=integer In Axis()
>> >> >> > class(x)=numeric; class(at)=NULL In Axis.default()
>> >> >> class(x)=numeric;
>> >> >> > class(at)=NULL In Axis() class(x)=numeric; class(at)=NULL In
>> >> >> > Axis.default() class(x)=numeric; class(at)=NULL
>> >> >> >> plot(1:10)
>> >> >> > In plot.default() class(x)=integer; class(y)=NULL In Axis()
>> >> >> > class(x)=numeric; class(at)=NULL In Axis.default()
>> >> >> class(x)=numeric;
>> >> >> > class(at)=NULL In Axis() class(x)=numeric; class(at)=NULL In
>> >> >> > Axis.default() class(x)=numeric; class(at)=NULL>
>> >> >> >> sessionInfo()
>> >> >> > R version 2.7.0 RC (2008-04-20 r45403) x86_64-unknown-linux-gnu
>> >> >> >
>> >> >> > locale:
>> >> >> >
>> >> >>
>> >> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=C;LC
>> >> >> _
>> >> >> > MO
>> >> >> >
>> >> >>
>> >> NETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_AD
>> >> >> D
>> >> >> > RE
>> >> >> SS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
>> >> >> >
>> >> >> > attached base packages:
>> >> >> > [1] stats     graphics  grDevices utils     datasets
>> >> methods   base
>> >> >> >
>> >> >> >
>> >> >> > Dr Oleg Sklyar
>> >> >> > Technology Group
>> >> >> > Man Investments Ltd
>> >> >> > +44 (0)20 7144 3803
>> >> >> > osklyar at maninvestments.com
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >>
>> >> *********************************************************************
>> >> >> *
>> >> >> > The contents of this email are for the named addressee(s) only.
>> >> >> > It contains information which may be confidential and privileged.
>> >> >> > If you are not the intended recipient, please notify the sender
>> >> >> > immediately, destroy this email and any attachments and do not
>> >> >> > otherwise disclose or use them. Email transmission is
>> >> not a secure
>> >> >> > method of communication and Man Investments cannot accept
>> >> >> > responsibility for the completeness or accuracy of this
>> >> >> email or any
>> >> >> > attachments. Whilst Man Investments makes every effort
>> >> to keep its
>> >> >> > network free from viruses, it does not accept
>> >> >> responsibility for any
>> >> >> > computer virus which might be transferred by way of this
>> >> >> email or any
>> >> >> > attachments. This email does not constitute a request, offer,
>> >> >> > recommendation or solicitation of any kind to buy,
>> >> >> subscribe, sell or
>> >> >> > redeem any investment instruments or to perform other such
>> >> >> > transactions of any kind. Man Investments reserves the right to
>> >> >> > monitor, record and retain all electronic communications
>> >> >> through its
>> >> >> > network to ensure the integrity of its systems, for record
>> >> >> keeping and
>> >> >> > regulatory purposes.
>> >> >> >
>> >> >> > Visit us at: www.maninvestments.com
>> >> >> >
>> >> >> > ______________________________________________
>> >> >> > R-devel at r-project.org mailing list
>> >> >> > https://stat.ethz.ch/mailman/listinfo/r-devel
>> >> >>
>> >> >>
>> >>
>> >>
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>



[Rd] graphics::Axis loosing S3/S4 class attributes of 'x' in 2.7.0 RC
Duncan Murdoch