From ggrothendieck at gmail.com  Tue Apr 22 19:29:58 2008
From: ggrothendieck at gmail.com (Gabor Grothendieck)
Date: Tue, 22 Apr 2008 13:29:58 -0400
Subject: [Rd] graphics::Axis loosing S3/S4 class attributes of 'x' in
	2.7.0 RC
In-Reply-To: <480E1E00.8080409@stats.uwo.ca>
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>
Message-ID: <971536df0804221029p55d19792s8bf49846ca2cf5de@mail.gmail.com>

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)


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
> >> >> >
> >> >> >
> >> >> >
> >> >>
> >> *********************************************************************
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[Rd] graphics::Axis loosing S3/S4 class attributes of 'x' in 2.7.0 RC
Gabor Grothendieck