graphics::Axis loosing S3/S4 class attributes of 'x' in 2.7.0 RC

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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