Re: [Rd] prod(0, 1:1000) ; 0 * Inf etc
Interesting problem this.
My take on it would be that the true value depends
on how fast the 0 approaches 0 and how fast the n
approaches infinity.
Consider
f1 - function(n){prod(1/n , seq_len(n))}
f2 - function(n){prod(1/factorial(n) , seq_len(n))}
f3 - function(n){prod(n^(-n) , seq_len(n))}
All these are equal to prod( small number , 1:big number)
but applying these functions to an increasing sequence gives different
behaviour:
sapply(c(10,100,1000),f1)
[1] 3.628800e+05 9.332622e+155 Inf
sapply(c(10,100,1000),f2)
[1] 1 1 NaN
sapply(c(10,100,1000),f3)
[1] 3.628800e-04 9.332622e-43 NaN
f1() tends to infinity, f2() tends to 1, and f3() tends to zero.
Figuring out the appropriate limit in cases like this is a job
for a symbolic system.
I would say the original behaviour is desirable.
rksh
On 22 Apr 2008, at 02:43, Bill Dunlap wrote:
On Mon, 21 Apr 2008, Mathieu Ribatet wrote:
I definitely do agree with you.
Basically, I see two different ways to proceed:
1. one could first check if there are any 0 in the vector and then
return 0 without computing the product
That would fail for prod(0,Inf), which should return the same
thing as 0*Inf=NaN. Similarly for prod(0,NA) and prod(0,NaN).
Scanning for all these things might well be slower than just
doing the multiplications. Scanning also means that 0 is treated
more commutatively than other numbers.
2. or convert prod(x1, x2, x3) in prod(c(x1, x2, x3))
c() can convert values of classy objects in undesirable ways.
E.g.,
now-Sys.time()
min(now-file.info(.)$mtime, now-file.info(..)$mtime)
Time difference of 3787.759 secs
min(c(now-file.info(.)$mtime, now-file.info(..)$mtime))
[1] 1.052155
This may be considered a bug in c(), at least for class
timediff (and factor and ordered), but c() removes
attributes.
Martin Maechler a écrit :
I think most of us would expect prod(0:1000) to return 0, and ...
... it does.
However, many of us also expect
prod(x1, x2)to be equivalent to
prod(c(x1,x2))
the same as we can expect that for min(), max(), sum() and such
members of the Summary group.
Consequently, prod(0, 1:1000) should also return 0,
but as you see, it gives NaN which may be a bit puzzling...
The explanation is relatively simple:
1) The internal implementation uses
prod(x1, x2) := prod(x1) * prod(x2)
which in this case is
2) 0 * Infand that is not 0, but NaN;
not necessarily because we would want that, but I think just
because the underlying C math library does so.
I would personally like to change both behaviors,
but am currently only proposing to change prod() such as to
return 0 in such cases.
This would be S-plus compatible, in case that matters.
Opinions?
Martin Maechler, ETH Zurich R-core
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Re: [Rd] prod(0, 1:1000) ; 0 * Inf etc
I definitely do agree with you. Basically, I see two different ways to proceed: 1. one could first check if there are any 0 in the vector and then return 0 without computing the product That would fail for prod(0,Inf), which should return the same thing as 0*Inf=NaN. Similarly for prod(0,NA) and prod(0,NaN). Scanning for all these things might well be slower than just doing the multiplications. Scanning also means that 0 is treated more commutatively than other numbers. Yes you're right when vectors have special values - oupppsss. However, for the more commutatively behaviour of 0, to me this is not a problem - just a computational trick. We all know easily how to multiply by 11. This is just the same. What we want is that the operator is still commutative which (of course) is still the case. However, you're probably right with the time consuming approach of checking 0 (as well as special values) within the vector. The question is what is the main objective? Fast computations but could lead to miss-calculations - in rarely cases. Or run codes a little bit slower while returning the appropriate values - a little bit more often. I'm not sure users do so many times products of really huge length vectors though - but this is only my point of view. Best, Mathieu 2. or convert prod(x1, x2, x3) in prod(c(x1, x2, x3)) c() can convert values of classy objects in undesirable ways. E.g., now-Sys.time() min(now-file.info(.)$mtime, now-file.info(..)$mtime) Time difference of 3787.759 secs min(c(now-file.info(.)$mtime, now-file.info(..)$mtime)) [1] 1.052155 This may be considered a bug in c(), at least for class timediff (and factor and ordered), but c() removes attributes. Martin Maechler a ?crit : I think most of us would expect prod(0:1000) to return 0, and ... ... it does. However, many of us also expect prod(x1, x2)to be equivalent to prod(c(x1,x2)) the same as we can expect that for min(), max(), sum() and such members of the Summary group. Consequently, prod(0, 1:1000) should also return 0, but as you see, it gives NaN which may be a bit puzzling... The explanation is relatively simple: 1) The internal implementation uses prod(x1, x2) := prod(x1) * prod(x2) which in this case is 2) 0 * Infand that is not 0, but NaN; not necessarily because we would want that, but I think just because the underlying C math library does so. I would personally like to change both behaviors, but am currently only proposing to change prod() such as to return 0 in such cases. This would be S-plus compatible, in case that matters. Opinions? Martin Maechler, ETH Zurich R-core __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Institute of Mathematics Ecole Polytechnique F?d?rale de Lausanne STAT-IMA-FSB-EPFL, Station 8 CH-1015 Lausanne Switzerland http://stat.epfl.ch/ Tel: + 41 (0)21 693 7907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel Bill Dunlap Insightful Corporation bill at insightful dot com 360-428-8146 All statements in this message represent the opinions of the author and do not necessarily reflect Insightful Corporation policy or position. -- Institute of Mathematics Ecole Polytechnique Fédérale de Lausanne STAT-IMA-FSB-EPFL, Station 8 CH-1015 Lausanne Switzerland http://stat.epfl.ch/ Tel: + 41 (0)21 693 7907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] S3 method despatch (changed between 2.6.2 and 2.7.0 RC?)
Dear developers:
I have observed a change in the behaviour of S3 method despatch (as I
guess related to namespaces) between 2.6.2 and yesterday's 2.7.0 RC and
would be grateful if you could comment on that:
the 'Axis' function in the 'graphics' namespace calls
UseMethod(Axis,x), internally to despatch on the S3 Axis method
depending on the type of the argument. Both 2.6.2 and 2.7.0 define the
following Axis.* methods in 'graphics': Axis.Date, Axis.POSIXct
Axis.POSIXlt and Axis.default. Now, if one defines an Axis.MyClass
outside of the 'graphics' namespace, it is called automatically by 2.6.2
on objects of MyClass, i.e. R would search for further method definition
outside of the graphics namespace. Looks like this behaviour has changed
in 2.7.0 so that UseMethod called in a given namesspace (graphics) does
not despatch on methods defined in another namespace (global or another
package) as the example below shows.
Have I done something wrong?
Is it an intended behaviour, any idea how to go around it?
Thanks,
Oleg
PS: The difference in the code below is that 2.6.2 calls Axis.MyClass in
plot.default (and thus prints the message), while 2.7.0 does not.
x = 1:5
class(x) = c(MyClass,class(x))
Axis.MyClass = function (x, at, ..., side, labels=TRUE) {
print(running Axis.MyClass)
axis(side, at=if(!missing(x)) x else at, labels=labels, ...)
}
methods(Axis)
plot(x, 1:5)
== Output from 2.6.2 RC (2008-02-08)
===
methods(Axis)
[1] Axis.Date*Axis.MyClass Axis.POSIXct* Axis.POSIXlt*
Axis.default*
Non-visible functions are asterisked
plot(x, 1:5)
[1] running Axis.MyClass
sessionInfo()
R version 2.6.2 (2008-02-08)
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=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=
C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATI
ON=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17 tools_2.6.2
== Output from 2.7.0 RC (2008-04-20 r45403)
methods(Axis)
[1] Axis.Date*Axis.MyClass Axis.POSIXct* Axis.POSIXlt*
Axis.default*
Non-visible functions are asterisked
plot(x, 1:5)
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_ADDRE
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
loaded via a namespace (and not attached):
[1] tools_2.7.0
Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
[EMAIL PROTECTED]
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[Rd] Seqfault, Address 0, track X11() (PR#11231)
Full_Name: Liqun Xing Version: 2.6.2 OS: Solaris 9 Submission from: (NULL) (76.182.91.82) When first time launch X11(), it was fine. However, when closed the X11 windon by clicking the close button, or closed it off by command Dev.off() and launched the X11() again, got segfault, and asking for exiting R and other options. __ R-devel@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
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...
Is this really an intended behaviour? It looks very wrong to me!
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_ADDRE
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
[EMAIL PROTECTED]
**
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
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Visit us at: www.maninvestments.com
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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_ADDRE
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
[EMAIL PROTECTED]
**
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,
Re: [Rd] graphics::Axis loosing S3/S4 class attributes of 'x' in 2.7.0 RC
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:
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
[EMAIL PROTECTED]
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: 22 April 2008 13:01
To: Sklyar, Oleg (MI London)
Cc: R-devel@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_ADD
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
Re: [Rd] graphics::Axis loosing S3/S4 class attributes of 'x' in 2.7.0 RC
This also affects Axis.yearmon and Axis.yearqtr in the
zoo package which worked in R 2.6.2 and now don't work
properly. It seems more logical to define plot.whatever
to handle the object in question, i.e. we do define plot.zoo,
whereas only the Axis method ought to be required for the
X and Y coordinate axes.
On Tue, Apr 22, 2008 at 8:53 AM, Sklyar, Oleg (MI London)
[EMAIL PROTECTED] wrote:
Thanks Duncan,
this might explain why Axis.MyClass is never called.
However, it is really not only illogical to define plot.MyClass instead
of Axis.MyClass if the only thing I want is formatting of the axis, but
it is also broken in R 2.7.0 and here is why.
Let's forget about MyClass and take POSIXct, for which plot.POSIXct and
Axis.POSIXct are defined in graphics. First question would be, why
define Axis.POSIXct if it is logical to just define plot.POSIXct. But
then, try the following example in 2.7.0 and 2.6.2:
x = Sys.time() + runif(100,1,7200) ## time over two hours, POSIXct
plot(x,1:100)
plot(1:100,x)
The first plot will be correctly formatted in both R versions while the
second one will be *incorrectly* formatted in 2.7.0 (funny enough
xy.coords returns as.double in both, so that might not be the reason for
the problem).
What happens is that plot.POSIXct is called in the former case and thus
we get the correct formatting. However, plot.default is called in the
latter case. In 2.6.2 Axis.POSIXct was the reason why y axis was
correctly formatted here. In 2.7.0 Axis.default is called instead
because class of x is reset.
Now this perfectly indicates why it is logical to have Axis.MyClass
defined (as this two-liner would be called in all possible situations
producing correct axes independently where it is called from) and not
plot.MyClass (which would actually not cover the situation of only the
second argument being MyClass). Surely I can define S4 with multiple
signatures, but logically I would define Axis.MyClass.
Omitting axes completely is not a good options to enforce on users for
default plots, is it?
Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
[EMAIL PROTECTED]
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: 22 April 2008 13:01
To: Sklyar, Oleg (MI London)
Cc: R-devel@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
Re: [Rd] graphics::Axis loosing S3/S4 class attributes of 'x' in 2.7.0 RC
Lines 69/70 in plot.R of graphics:
xy$x and xy$y should have stayed as x and y
Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
[EMAIL PROTECTED]
-Original Message-
From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
Sent: 22 April 2008 14:12
To: Sklyar, Oleg (MI London)
Cc: Duncan Murdoch; R-devel@r-project.org
Subject: Re: [Rd] graphics::Axis loosing S3/S4 class
attributes of 'x' in 2.7.0 RC
This also affects Axis.yearmon and Axis.yearqtr in the zoo
package which worked in R 2.6.2 and now don't work
properly. It seems more logical to define plot.whatever
to handle the object in question, i.e. we do define plot.zoo,
whereas only the Axis method ought to be required for the X
and Y coordinate axes.
On Tue, Apr 22, 2008 at 8:53 AM, Sklyar, Oleg (MI London)
[EMAIL PROTECTED] wrote:
Thanks Duncan,
this might explain why Axis.MyClass is never called.
However, it is really not only illogical to define plot.MyClass
instead of Axis.MyClass if the only thing I want is
formatting of the
axis, but it is also broken in R 2.7.0 and here is why.
Let's forget about MyClass and take POSIXct, for which plot.POSIXct
and Axis.POSIXct are defined in graphics. First question
would be, why
define Axis.POSIXct if it is logical to just define
plot.POSIXct. But
then, try the following example in 2.7.0 and 2.6.2:
x = Sys.time() + runif(100,1,7200) ## time over two hours, POSIXct
plot(x,1:100)
plot(1:100,x)
The first plot will be correctly formatted in both R versions while
the second one will be *incorrectly* formatted in 2.7.0
(funny enough
xy.coords returns as.double in both, so that might not be
the reason
for the problem).
What happens is that plot.POSIXct is called in the former case and
thus we get the correct formatting. However, plot.default
is called in
the latter case. In 2.6.2 Axis.POSIXct was the reason why y
axis was
correctly formatted here. In 2.7.0 Axis.default is called instead
because class of x is reset.
Now this perfectly indicates why it is logical to have Axis.MyClass
defined (as this two-liner would be called in all possible
situations
producing correct axes independently where it is called
from) and not
plot.MyClass (which would actually not cover the situation
of only the
second argument being MyClass). Surely I can define S4 with
multiple
signatures, but logically I would define Axis.MyClass.
Omitting axes completely is not a good options to enforce
on users for
default plots, is it?
Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
[EMAIL PROTECTED]
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: 22 April 2008 13:01
To: Sklyar, Oleg (MI London)
Cc: R-devel@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,
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
[EMAIL PROTECTED]
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: 22 April 2008 13:01
To: Sklyar, Oleg (MI London)
Cc: R-devel@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;
Re: [Rd] graphics::Axis loosing S3/S4 class attributes of 'x' in 2.7.0 RC
So if plot(x) produced rubbish in 2.6.2 in sense of axis formatting
would not that mean that either plot.POSIXct or in fact Axis.POSIXct is
incorrectly defined? I will have a look at those to see if I can find a
fix.
Anyway, it does not seem to have any sense to argue any further, because
for me documented and logical are not the same things.
This fix effectively makes Axis.POSIXct and all other Axis.* methods
useless as there is now no despatch on Axis taking place in plot.default
and thus it is not clear why Axis and not Axis.default is actually used?
This would at least make the code cleaner. I was thinking that the idea
of methods is actually to have different implementations depending on
the argument class rather than coerce everything to double and use the
default instead.
Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
[EMAIL PROTECTED]
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: 22 April 2008 14:24
To: Sklyar, Oleg (MI London)
Cc: R-devel@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
[EMAIL PROTECTED]
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: 22 April 2008 13:01
To: Sklyar, Oleg (MI London)
Cc: R-devel@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)
Re: [Rd] graphics::Axis loosing S3/S4 class attributes of 'x' in 2.7.0 RC
On Tue, Apr 22, 2008 at 9:24 AM, Duncan Murdoch [EMAIL PROTECTED] wrote: 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) In what sense is plot(x) fixed? When I try it I get numbers on both axes -- times on neither. Clearly Axis should not behave in a way which effectively makes it useless and breaks reasonable old code. R.version.string [1] R version 2.7.0 RC (2008-04-17 r45367) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] graphics::Axis loosing S3/S4 class attributes of 'x' in 2.7.0 RC
OlegS == Sklyar, Oleg \(MI London\) [EMAIL PROTECTED]
on Tue, 22 Apr 2008 14:44:01 +0100 writes:
OlegS So if plot(x) produced rubbish in 2.6.2 in sense of axis formatting
OlegS would not that mean that either plot.POSIXct or in fact Axis.POSIXct
is
OlegS incorrectly defined? I will have a look at those to see if I can
find a
OlegS fix.
Me too.
OlegS Anyway, it does not seem to have any sense to argue any further,
because
OlegS for me documented and logical are not the same things.
It still makes much sense to discuss further.
I agree with you that the change 2.6.2 - 2.7.0 fixed one problem
but introduced another one.
2.7.1 (and before that 2.7.0 patched) should hopefully be
better than both 2.6.2 and 2.7.0
My current version is
if (axes) {
localAxis(if(is.null(y)) xy$x else x, side = 1, ...)
localAxis(if(is.null(y)) x else y, side = 2, ...)
}
which is I think better already than either predecessor;
it definitely is compatible with Rversion = 2.6.2 when both
(x,y) are specified,
and it produces the correct axes in these three cases:
## Axis() calls via plot()
x - as.Date(2008-04-22 09:45) + (i - 0:4)
plot(x)# not ok in 2.6.2, nor 2.7.0
plot(x, i)# ok in 2.6.2 and 2.7.0
plot(i, x)# ok in 2.6.2 and not in 2.7.0
I'm grateful for further examples, preferably not using code
from packages outside of standard R.
Martin Maechler, ETH Zurich
OlegS This fix effectively makes Axis.POSIXct and all other Axis.*
methods
OlegS useless as there is now no despatch on Axis taking place in
plot.default
OlegS and thus it is not clear why Axis and not Axis.default is actually
used?
OlegS This would at least make the code cleaner. I was thinking that the
idea
OlegS of methods is actually to have different implementations depending on
OlegS the argument class rather than coerce everything to double and use
the
OlegS default instead.
OlegS Dr Oleg Sklyar
OlegS Technology Group
OlegS Man Investments Ltd
OlegS +44 (0)20 7144 3803
OlegS [EMAIL PROTECTED]
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: 22 April 2008 14:24
To: Sklyar, Oleg (MI London)
Cc: R-devel@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$y, side=2, ...)
}
The fact that xy.coords is called does not really matter.
[..]
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] graphics::Axis loosing S3/S4 class attributes of 'x' in 2.7.0 RC
Ok, so what's wrong with the following fix for plot(x) that would
actually fix what needs to be fixed instead of changing plot.default?
Fix means reverting plot.default in 2.7.0 to what it was (if testing in
2.7.0, copy and paste the OLD plot.default into the .GlobalEnv):
plot.POSIXct - function(x, y, xlab = , ...) {
if (!missing(y)) {
side = 1
plotDef - function(x, y, xaxt, xlab, ...) plot.default(x, y,
xaxt=n, xlab=xlab, ...)
plotDef(x, y, xlab=xlab, ...)
} else {
side = 2
plotDef - function(x, y, yaxt, xlab, ...) plot.default(x, y,
yaxt=n, xlab=xlab, ...)
plotDef(seq_along(x), x, xlab=xlab, ...)
}
## trick to remove arguments intended for title() or plot.default()
axisInt - function(x, type, main, sub, xlab, ylab, col, lty, lwd,
xlim, ylim, bg, pch, log, asp, axes, frame.plot,
...)
axis.POSIXct(side, x, ...)
dots - list(...)
axes - if(axes %in% names(dots)) dots$axes else TRUE
xaxt - if(xaxt %in% names(dots)) dots$xaxt else par(xaxt)
if(axes xaxt != n) axisInt(x, ...)
}
plot.POSIXlt - function(x, y, xlab = , ...) {
if (missing(y)) plot.POSIXct(as.POSIXct(x), xlab=xlab, ...)
else plot.POSIXct(as.POSIXct(x), y=y, xlab=xlab, ...)
}
And try with:
x = Sys.time() + runif(100,1,7200)
plot(x)
plot(x,1:100)
plot(1:100,x)
plot(as.POSIXlt(x))
plot(as.POSIXlt(x),1:100)
plot(1:100,as.POSIXlt(x))
Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
[EMAIL PROTECTED]
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: 22 April 2008 14:24
To: Sklyar, Oleg (MI London)
Cc: R-devel@r-project.org
Subject: Re: [Rd] graphics::Axis loosing S3/S4 class
attributes of 'x' in 2.7.0 RC
On 4/22/2008 9:08 AM, Sklyar, Oleg (MI London) wrote:
Duncan,
looking further, what has changed from 2.6.2 into 2.7.0 are the
following two lines in plot.default, which I think were
logical before
and are not really logical now:
I believe it is behaving as documented now, so the behaviour
is logical, even if it may not be convenient. In your example
x = Sys.time() + runif(100,1,7200) ## time over two hours,
POSIXct plot(x, 1:100) plot(1:100, x)
the 1st works in 2.6.2 and 2.7.0 and the second only works in 2.6.2.
But the change below was designed to fix the case
plot(x)
which works in 2.7.0 and *not* in 2.6.2, so reverting the
change is not the way to address this.
Duncan Murdoch
plot.R: plot.default (2.6.2):
if (axes) {
localAxis(x, side=1, ...)
localAxis(y, side=2, ...)
}
plot.R: plot.default (2.7.0):
...
if (axes) {
localAxis(xy$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
[EMAIL PROTECTED]
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: 22 April 2008 13:01
To: Sklyar, Oleg (MI London)
Cc: R-devel@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),
[Rd] question about p-value implementation
Hello all, I hope I have found the right place for my question. There are different kinds of p-values for one-sided and two-sided tests, for example mid p-value [1], minimum-likelihood p-value [2] or conditional two-sided p-value [3]. I tried to find out what kind of p-value is implemented in R with regard to the two-sided chi-square (function chisq.test()) and Spearman rank test (function cor.test() with method=spearman), but I could not determine this from the documentation or the source. I would be thankful if someone with a better understanding could provide an explanation. [1] J. D. Gibbons, J. W. Pratt. P-Values: Interpretation and Methodology. 1975 [2] I. Rivals, L. Personnaz, L. Taing, M. C. Potier. Enrichment or depletion of a GO category within a class of genes: which test?. 2006 [3] E. Kulinskaya. One two-sided p-values for non-symmetrical distributions. 2007 Best regards, Vincent __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Bug in poly() (PR#11243)
Full_Name: Russell Lenth Version: 2.6.2 OS: Windows XP Pro Submission from: (NULL) (128.255.132.36) The poly() function allows a higher-degree polynomial than it should, when raw=FALSE. For example, consider 5 distinct 'x' values, each repeated twice. we can fit a polynomial of degree 8: = R x = rep(1:5, 2) R y = rnorm(10) R lm(y ~ poly(x, 8)) Call: lm(formula = y ~ poly(x, 8)) Coefficients: (Intercept) poly(x, 8)1 poly(x, 8)2 poly(x, 8)3 poly(x, 8)4 poly(x, 8)5 -0.07790 0.58768 0.30147 -0.18237 0.64779 -0.0 poly(x, 8)6 poly(x, 8)7 poly(x, 8)8 -0.22694 -0.07500 0.17235 = If we specify 'raw=TRUE' in the same example, we are limited (as we should) to a degree-4 polynomial: = R lm(y ~ poly(x, 8, raw=TRUE)) Call: lm(formula = y ~ poly(x, 8, raw = TRUE)) Coefficients: (Intercept) poly(x, 8, raw = TRUE)1 poly(x, 8, raw = TRUE)2 7.3958 -14.0150 8.2784 poly(x, 8, raw = TRUE)3 poly(x, 8, raw = TRUE)4 poly(x, 8, raw = TRUE)5 -1.9502 0.1597 NA poly(x, 8, raw = TRUE)6 poly(x, 8, raw = TRUE)7 poly(x, 8, raw = TRUE)8 NA NA NA = We do get an error with an even higher degree: = R lm(y ~ poly(x, 10)) Error in poly(x, 10) : 'degree' must be less than number of points = Looking at the code for poly(), I think the problem is that it should check the 'rank' result from its call to qr(). [The above results are using Windows XP Pro, but I verified this bug under Linux as well (x86_64, dual core). It seems pretty obvious to me that this bug is not platform-dependent.] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] plot(x) in 2.7.0 (with y=NULL) proposed code correction
OlegS == Sklyar, Oleg \(MI London\) [EMAIL PROTECTED]
on Tue, 22 Apr 2008 17:34:24 +0100 writes:
OlegS Hi all:
OlegS following the previous discussion, it looks like plot(x) with y=NULL
OlegS still does not work correctly. If one tries for example plot(1:5) it
OlegS works, but already for plot(runif(100)) it does not.
??? Not for me, with my propsal
{{maybe only in your too much modified version of R ??}
I've committed my proposal, and am interested in feedback,
notably additional relevant examples.
Martin
OlegS I posted the proposed correction for plot.POSIXct and
OlegS plot.POSIXlt before. Please voice your opinions
OlegS whether the following fix for plot.default could be
OlegS reasonable? I include the full function and the diff.
(And both suffered from wraparounds)
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] 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
[EMAIL PROTECTED]
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: 22 April 2008 14:24
To: Sklyar, Oleg (MI London)
Cc: R-devel@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
[EMAIL PROTECTED]
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: 22 April 2008 13:01
To: Sklyar, Oleg (MI London)
Cc: R-devel@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
Re: [Rd] graphics::Axis loosing S3/S4 class attributes of 'x' in 2.7.0 RC
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 [EMAIL PROTECTED] 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
[EMAIL PROTECTED]
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: 22 April 2008 14:24
To: Sklyar, Oleg (MI London)
Cc: R-devel@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
[EMAIL PROTECTED]
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: 22 April 2008 13:01
To: Sklyar, Oleg (MI London)
Cc: R-devel@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
Re: [Rd] plot(x) in 2.7.0 (with y=NULL) proposed code correction
To Martin:
sorry, you are right, my fault. Your SVN fix for axisLocal seems to
solve the problems for numerics.
However, the problem remains for POSIXct:
plot(Sys.time()+runif(100,1,7200))
(for me it plots time on y correctly, but labeling of index x axis and
xlab=Index are wrong/missing). I would assume that there is therefore
a problem in the current plot.POSIXct function.
In fact, if one simply sets: plot.POSIXct = plot.default the result IS
correct! This is probably because POSIXct is numeric internally and axis
handling is performed correctly by your fix, i.e. strictly there is no
need for plot.POSIXct. For plot.POSIXlt, one could simply convert x into
POSIXct and call the default.
I do not think there will be many more standard R examples because the
problem was about calling one of the Axis.* methods and those are
defined for POSIX and Date classes only.
To Duncan:
I would be happy if I could test it before, I have recently started at
the current position and even now cannot access the R SVN directly due
to the company's internet connection policy.
The above working correctly for POSIXct with plot.default and not
working with plot.POSIXct was exactly the reason, why for me it is
logical to define Axis.MyClass rather than plot.MyClass.
Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
[EMAIL PROTECTED]
-Original Message-
From: Martin Maechler [mailto:[EMAIL PROTECTED]
Sent: 22 April 2008 17:55
To: Sklyar, Oleg (MI London)
Cc: R-devel@r-project.org
Subject: Re: plot(x) in 2.7.0 (with y=NULL) proposed code correction
OlegS == Sklyar, Oleg \(MI London\)
[EMAIL PROTECTED]
on Tue, 22 Apr 2008 17:34:24 +0100 writes:
OlegS Hi all:
OlegS following the previous discussion, it looks like
plot(x) with y=NULL
OlegS still does not work correctly. If one tries for
example plot(1:5) it
OlegS works, but already for plot(runif(100)) it does not.
??? Not for me, with my propsal
{{maybe only in your too much modified version of R ??}
I've committed my proposal, and am interested in feedback,
notably additional relevant examples.
Martin
OlegS I posted the proposed correction for plot.POSIXct and
OlegS plot.POSIXlt before. Please voice your opinions
OlegS whether the following fix for plot.default could be
OlegS reasonable? I include the full function and the diff.
(And both suffered from wraparounds)
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Re: [Rd] plot(x) in 2.7.0 (with y=NULL) proposed code correction
On 4/22/2008 1:37 PM, Sklyar, Oleg (MI London) wrote:
To Martin:
sorry, you are right, my fault. Your SVN fix for axisLocal seems to
solve the problems for numerics.
However, the problem remains for POSIXct:
plot(Sys.time()+runif(100,1,7200))
(for me it plots time on y correctly, but labeling of index x axis and
xlab=Index are wrong/missing). I would assume that there is therefore
a problem in the current plot.POSIXct function.
In fact, if one simply sets: plot.POSIXct = plot.default the result IS
correct! This is probably because POSIXct is numeric internally and axis
handling is performed correctly by your fix, i.e. strictly there is no
need for plot.POSIXct. For plot.POSIXlt, one could simply convert x into
POSIXct and call the default.
I do not think there will be many more standard R examples because the
problem was about calling one of the Axis.* methods and those are
defined for POSIX and Date classes only.
To Duncan:
I would be happy if I could test it before, I have recently started at
the current position and even now cannot access the R SVN directly due
to the company's internet connection policy.
We do have daily binary builds, you don't need svn access. I don't know
if your company policy would allow you to download and install them, of
course. But if your company policy is not to allow you to test software
that matters to the company, then you may have bigger problems than bad
axis labels.
Duncan Murdoch
The above working correctly for POSIXct with plot.default and not
working with plot.POSIXct was exactly the reason, why for me it is
logical to define Axis.MyClass rather than plot.MyClass.
Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
[EMAIL PROTECTED]
-Original Message-
From: Martin Maechler [mailto:[EMAIL PROTECTED]
Sent: 22 April 2008 17:55
To: Sklyar, Oleg (MI London)
Cc: R-devel@r-project.org
Subject: Re: plot(x) in 2.7.0 (with y=NULL) proposed code correction
OlegS == Sklyar, Oleg \(MI London\)
[EMAIL PROTECTED]
on Tue, 22 Apr 2008 17:34:24 +0100 writes:
OlegS Hi all:
OlegS following the previous discussion, it looks like
plot(x) with y=NULL
OlegS still does not work correctly. If one tries for
example plot(1:5) it
OlegS works, but already for plot(runif(100)) it does not.
??? Not for me, with my propsal
{{maybe only in your too much modified version of R ??}
I've committed my proposal, and am interested in feedback,
notably additional relevant examples.
Martin
OlegS I posted the proposed correction for plot.POSIXct and
OlegS plot.POSIXlt before. Please voice your opinions
OlegS whether the following fix for plot.default could be
OlegS reasonable? I include the full function and the diff.
(And both suffered from wraparounds)
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Re: [Rd] plot(x) in 2.7.0 (with y=NULL) proposed code correction
On Tue, Apr 22, 2008 at 1:45 PM, Duncan Murdoch [EMAIL PROTECTED] wrote: defined for POSIX and Date classes only. zoo defines Axis methods for the yearmon and yearqtr classes and potentially other time/date classes will need Axis methods. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] graphics::Axis loosing S3/S4 class attributes of 'x' in 2.7.0 RC
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 [EMAIL PROTECTED] 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
[EMAIL PROTECTED]
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: 22 April 2008 14:24
To: Sklyar, Oleg (MI London)
Cc: R-devel@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
[EMAIL PROTECTED]
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: 22 April 2008 13:01
To: Sklyar, Oleg (MI London)
Cc: R-devel@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
Re: [Rd] plot(x) in 2.7.0 (with y=NULL) proposed code correction
On Tue, 22 Apr 2008, Martin Maechler wrote:
I've committed my proposal, and am interested in feedback,
notably additional relevant examples.
I tried the following test and the axes
looked right in 2.6.2 and the r45453
(right after your change to plot.R).
They looked bad (all were 2,4,6,8,10, not
1*pi,2*pi,3*pi) in r45390 (2008-04-19).
Axis.MyRadian - function(x = NULL, at = NULL, ...,
side, labels = NULL)
{
r - range(x)
npi - floor(r[1]/pi):ceiling(r[2]/pi)
at - npi * pi
labels - as.expression(lapply(
npi,function(i)substitute(i*pi, list(i=i
axis(side=side, at=at, labels=labels)
}
par(mfrow=c(2,2))
plot(structure(1:10, class=MyRadian), sin(1:10),
main=n pi radians on x axis)
plot(structure(1:10, class=MyRadian),
main=n pi radians on y axis)
plot(structure(1:10, class=MyRadian),
structure(10:1, class=MyRadian),
main=n pi radians on both axes)
plot(1:10, 1:10, main=no pi's on either axis)
par(mfrow=c(2,2))
Bill Dunlap
Insightful Corporation
bill at insightful dot com
360-428-8146
All statements in this message represent the opinions of the author and do
not necessarily reflect Insightful Corporation policy or position.
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