Re: [Rd] Problem with defining new method for residuals()
Dear Martin,
Thank you very much for your solution. It works fine.
Best regards,
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium
Research Institute for Nature and Forest
team Biometrics Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
thierry.onkel...@inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more than
asking him to perform a post-mortem examination: he may be able to say what the
experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not ensure
that a reasonable answer can be extracted from a given body of data.
~ John Tukey
-Oorspronkelijk bericht-
Van: Martin Morgan [mailto:mtmor...@fhcrc.org]
Verzonden: vrijdag 11 maart 2011 7:36
Aan: ONKELINX, Thierry
CC: r-devel@r-project.org; John Chambers
Onderwerp: Re: [Rd] Problem with defining new method for residuals()
On 03/10/2011 08:21 AM, ONKELINX, Thierry wrote:
Dear all,
I'm writing a package and I would like to reuse the residuals()
function. When I use a function which calls the redefined residuals
(for my custom class) I get an error (see below). It looks like the
wrong method is used. The strange this is, that when it execute the
code manually it get no error.
Hi Thierry --
I think this is a bug in the methods package.
Your package promotes stats::residuals to an S4 generic.
Normally this should work.
However, your package Depends: on lme4, which also promotes
stats::residuals to an S4 generic. Apparently, this
interferes with your own attempt to make a generic, even
though you do not import lme4 into your name space. As a
consequence of the (putative) bug, your package sees the
original stats::residuals.
A work-around seems to be to importFrom(lme4, residuals) and
do NOT import residuals from stats, so that your own method
is associated with the generic defined in lme4.
Martin
Any suggestions?
Best regards,
Thierry
The entire source code is at
svn://scm.r-forge.r-project.org/svnroot/aflp
The code with the error.
normalise(dummy)
Error in object$na.action : $ operator not defined for this S4 class
traceback()
5: naresid(object$na.action, object$residuals) at normalise.R#30 4:
residuals.default(outliers(data)) at normalise.R#30 3:
residuals(outliers(data)) at normalise.R#30 2:
nrow(residuals(outliers(data))) at normalise.R#30 1:
normalise(dummy) #This works fine
data - dummy nrow(residuals(outliers(data)))
[1] 0
NAMESPACE importFrom(stats, residuals, resid, hclust, princomp)
exportPattern(.)
METHODS setMethod(residuals, signature(object = AFLP.outlier),
function(object, ...){ object@Residual } )
setMethod(resid, signature(object = AFLP.outlier),
function(object, ...){ object@Residual } )
--
--
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek team Biometrie
Kwaliteitszorg
Gaverstraat 4 9500 Geraardsbergen Belgium
Research Institute for Nature and Forest team Biometrics Quality
Assurance Gaverstraat 4 9500 Geraardsbergen Belgium
tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be
To call in the statistician after the experiment is done may be no
more than asking him to perform a post-mortem examination:
he may be
able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an
answer does
not ensure that a reasonable answer can be extracted from a
given body
of data. ~ John Tukey
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[Rd] Using missing() in a S4 method with extra arguments
Hi all,
I have a function which makes use of missing() to determine which
arguments are provided in the call - basically, there are two sets of
arguments that map to different strategies the function uses to fulfill
its task. After conversion to an S4 generic I've run into the problem
that if a method uses extra arguments that are not in the signature of
the generic, usage of missing() fails. The following example exemplifies
this:
setGeneric(fun, function(x=0, y=0, ...) standardGeneric(fun))
# both methods should output if the second argument is missing
setMethod(fun, character, function(x=0, y=0, ...) missing(y))
setMethod(fun, numeric, function(x=0, y=0, z=0, ...) missing(y))
fun(a) # this works fine
fun(1) # this gives FALSE
I've understood so far that this is due to the fact that the numeric
method in this example is rewritten to:
function (x = 0, y = 0, ...)
{
.local - function (x = 0, y = 0, z = 0, ...)
missing(y)
.local(x, y, ...)
}
The call to .local evaluates y and it is no more missing.
Is there any alternative that works in this case? Or is there a chance
that missing() might be changed to work in this case in the near future?
Of course I know I could set NA or NULL as default values and check for
these, but there are reasons I want to have legal default values for all
arguments.
Best regards,
Andreas
Andreas Borg
Medizinische Informatik
UNIVERSITÄTSMEDIZIN
der Johannes Gutenberg-Universität
Institut für Medizinische Biometrie, Epidemiologie und Informatik
Obere Zahlbacher Straße 69, 55131 Mainz
www.imbei.uni-mainz.de
Telefon +49 (0) 6131 175062
E-Mail: b...@imbei.uni-mainz.de
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Re: [Rd] Using missing() in a S4 method with extra arguments
On 03/11/2011 02:07 AM, Andreas Borg wrote:
Hi all,
I have a function which makes use of missing() to determine which
arguments are provided in the call - basically, there are two sets of
arguments that map to different strategies the function uses to fulfill
its task. After conversion to an S4 generic I've run into the problem
that if a method uses extra arguments that are not in the signature of
the generic, usage of missing() fails. The following example exemplifies
this:
setGeneric(fun, function(x=0, y=0, ...) standardGeneric(fun))
# both methods should output if the second argument is missing
setMethod(fun, character, function(x=0, y=0, ...) missing(y))
setMethod(fun, numeric, function(x=0, y=0, z=0, ...) missing(y))
fun(a) # this works fine
fun(1) # this gives FALSE
Hi Andreas --
if you're testing for the missing-ness of y, and y is in the function
signature, then use that for dispatch
setMethod(fun, c(character, missing),
function(x=0, y=0, z=0, ...) missing)
setMethod(fun, c(character, ANY),
function(x=0, y=0, z=0, ...) not missing)
Since you're dispatching on x and y, it doesn't really make sense (to me
;) to assign default values to them. Testing for missing-ness of z would
I think have to rely on NA / NULL or other sentinel.
Martin
I've understood so far that this is due to the fact that the numeric
method in this example is rewritten to:
function (x = 0, y = 0, ...)
{
.local - function (x = 0, y = 0, z = 0, ...)
missing(y)
.local(x, y, ...)
}
The call to .local evaluates y and it is no more missing.
Is there any alternative that works in this case? Or is there a chance
that missing() might be changed to work in this case in the near future?
Of course I know I could set NA or NULL as default values and check for
these, but there are reasons I want to have legal default values for all
arguments.
Best regards,
Andreas
Andreas Borg
Medizinische Informatik
UNIVERSITÄTSMEDIZIN
der Johannes Gutenberg-Universität
Institut für Medizinische Biometrie, Epidemiologie und Informatik
Obere Zahlbacher Straße 69, 55131 Mainz
www.imbei.uni-mainz.de
Telefon +49 (0) 6131 175062
E-Mail: b...@imbei.uni-mainz.de
Diese E-Mail enthält vertrauliche und/oder rechtlich geschützte
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Re: [Rd] Using missing() in a S4 method with extra arguments
Hi Martin, in the real function, I am not dispatching on the argument for which I test missingness, but it might be a good idea to do so - this way I could make the function tidier by relocating different branches to seperate methods. Thanks for the suggestion! Andreas if you're testing for the missing-ness of y, and y is in the function signature, then use that for dispatch setMethod(fun, c(character, missing), function(x=0, y=0, z=0, ...) missing) setMethod(fun, c(character, ANY), function(x=0, y=0, z=0, ...) not missing) Since you're dispatching on x and y, it doesn't really make sense (to me ;) to assign default values to them. Testing for missing-ness of z would I think have to rely on NA / NULL or other sentinel. Martin -- Andreas Borg Medizinische Informatik UNIVERSITÄTSMEDIZIN der Johannes Gutenberg-Universität Institut für Medizinische Biometrie, Epidemiologie und Informatik Obere Zahlbacher Straße 69, 55131 Mainz www.imbei.uni-mainz.de Telefon +49 (0) 6131 175062 E-Mail: b...@imbei.uni-mainz.de Diese E-Mail enthält vertrauliche und/oder rechtlich geschützte Informationen. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtümlich erhalten haben, informieren Sie bitte sofort den Absender und löschen Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail und der darin enthaltenen Informationen ist nicht gestattet. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] hook for when R quits
Hi, Is there any way that a package can listen for when R quits? The Qt stuff is hooking into platform-specific event loops and when those die unexpectedly (from the perspective of Qt), it aborts, causing an annoying error dialog. If we could catch when R is killed, we could cleanup, like we do with .onUnload. Thanks, Michael [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] hook for when R quits
Take a look at reg.finalizer. You'd have to create an object internally that would persist until R exits - and a related function to handle cleanup of course. HTH Jeff On Fri, Mar 11, 2011 at 12:08 PM, Michael Lawrence lawrence.mich...@gene.com wrote: Hi, Is there any way that a package can listen for when R quits? The Qt stuff is hooking into platform-specific event loops and when those die unexpectedly (from the perspective of Qt), it aborts, causing an annoying error dialog. If we could catch when R is killed, we could cleanup, like we do with .onUnload. Thanks, Michael [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Jeffrey Ryan jeffrey.r...@lemnica.com www.lemnica.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] hook for when R quits
Thanks for the suggestion, but I don't think that R finalizes all of its objects when it quits. At least a simple test suggests that on Linux. Michael On Fri, Mar 11, 2011 at 10:19 AM, Jeffrey Ryan jeffrey.r...@lemnica.comwrote: Take a look at reg.finalizer. You'd have to create an object internally that would persist until R exits - and a related function to handle cleanup of course. HTH Jeff On Fri, Mar 11, 2011 at 12:08 PM, Michael Lawrence lawrence.mich...@gene.com wrote: Hi, Is there any way that a package can listen for when R quits? The Qt stuff is hooking into platform-specific event loops and when those die unexpectedly (from the perspective of Qt), it aborts, causing an annoying error dialog. If we could catch when R is killed, we could cleanup, like we do with .onUnload. Thanks, Michael [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Jeffrey Ryan jeffrey.r...@lemnica.com www.lemnica.com [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] hook for when R quits
See onSessionExit() in the R.utils package, e.g.
onSessionExit(function(...) {
cat(Bye bye world!\n);
})
quit();
Please pay attention to the Details section of help(onSessionExit);
there are ways that R can exit that will not be detected/handled.
/Henrik
On Fri, Mar 11, 2011 at 10:37 AM, Michael Lawrence
lawrence.mich...@gene.com wrote:
Thanks for the suggestion, but I don't think that R finalizes all of its
objects when it quits. At least a simple test suggests that on Linux.
Michael
On Fri, Mar 11, 2011 at 10:19 AM, Jeffrey Ryan
jeffrey.r...@lemnica.comwrote:
Take a look at reg.finalizer. You'd have to create an object
internally that would persist until R exits - and a related function
to handle cleanup of course.
HTH
Jeff
On Fri, Mar 11, 2011 at 12:08 PM, Michael Lawrence
lawrence.mich...@gene.com wrote:
Hi,
Is there any way that a package can listen for when R quits? The Qt stuff
is
hooking into platform-specific event loops and when those die
unexpectedly
(from the perspective of Qt), it aborts, causing an annoying error
dialog.
If we could catch when R is killed, we could cleanup, like we do with
.onUnload.
Thanks,
Michael
[[alternative HTML version deleted]]
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Re: [Rd] hook for when R quits
On 11/03/2011 1:37 PM, Michael Lawrence wrote: Thanks for the suggestion, but I don't think that R finalizes all of its objects when it quits. At least a simple test suggests that on Linux. Did you use onexit=TRUE? On Windows that appears to work... Duncan Murdoch Michael On Fri, Mar 11, 2011 at 10:19 AM, Jeffrey Ryanjeffrey.r...@lemnica.comwrote: Take a look at reg.finalizer. You'd have to create an object internally that would persist until R exits - and a related function to handle cleanup of course. HTH Jeff On Fri, Mar 11, 2011 at 12:08 PM, Michael Lawrence lawrence.mich...@gene.com wrote: Hi, Is there any way that a package can listen for when R quits? The Qt stuff is hooking into platform-specific event loops and when those die unexpectedly (from the perspective of Qt), it aborts, causing an annoying error dialog. If we could catch when R is killed, we could cleanup, like we do with .onUnload. Thanks, Michael [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Jeffrey Ryan jeffrey.r...@lemnica.com www.lemnica.com [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] hook for when R quits
On Fri, 11 Mar 2011, Duncan Murdoch wrote: On 11/03/2011 1:37 PM, Michael Lawrence wrote: Thanks for the suggestion, but I don't think that R finalizes all of its objects when it quits. At least a simple test suggests that on Linux. Did you use onexit=TRUE? On Windows that appears to work... It does work: RODBC makes extensive use of it, for exactly the purpose you describe (or rather, the C_level equivalent of 'it'). Duncan Murdoch Michael On Fri, Mar 11, 2011 at 10:19 AM, Jeffrey Ryanjeffrey.r...@lemnica.comwrote: Take a look at reg.finalizer. You'd have to create an object internally that would persist until R exits - and a related function to handle cleanup of course. HTH Jeff On Fri, Mar 11, 2011 at 12:08 PM, Michael Lawrence lawrence.mich...@gene.com wrote: Hi, Is there any way that a package can listen for when R quits? The Qt stuff is hooking into platform-specific event loops and when those die unexpectedly (from the perspective of Qt), it aborts, causing an annoying error dialog. If we could catch when R is killed, we could cleanup, like we do with .onUnload. Thanks, Michael [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Jeffrey Ryan jeffrey.r...@lemnica.com www.lemnica.com [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] hook for when R quits
On Fri, Mar 11, 2011 at 11:07 AM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On Fri, 11 Mar 2011, Duncan Murdoch wrote: On 11/03/2011 1:37 PM, Michael Lawrence wrote: Thanks for the suggestion, but I don't think that R finalizes all of its objects when it quits. At least a simple test suggests that on Linux. Did you use onexit=TRUE? On Windows that appears to work... Agree - here an object finalizer is more appropriate (different from an end-of-session hook). It does work: RODBC makes extensive use of it, for exactly the purpose you describe (or rather, the C_level equivalent of 'it'). In help(reg.finalizer) it says: 'onexit': logical: should the finalizer be run if the object is still uncollected at the end of the R session? What environments, objects, search path etc are available when the finalizer is called this way when R exits? Is safe to always add 'onexit=TRUE' (which now defaults to FALSE), or should I expect an exceptional R system that the finalizer needs to account for? Is there any further documentation on what happens when an R session shuts down and in which order? /Henrik Duncan Murdoch Michael On Fri, Mar 11, 2011 at 10:19 AM, Jeffrey Ryanjeffrey.r...@lemnica.comwrote: Take a look at reg.finalizer. You'd have to create an object internally that would persist until R exits - and a related function to handle cleanup of course. HTH Jeff On Fri, Mar 11, 2011 at 12:08 PM, Michael Lawrence lawrence.mich...@gene.com wrote: Hi, Is there any way that a package can listen for when R quits? The Qt stuff is hooking into platform-specific event loops and when those die unexpectedly (from the perspective of Qt), it aborts, causing an annoying error dialog. If we could catch when R is killed, we could cleanup, like we do with .onUnload. Thanks, Michael [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Jeffrey Ryan jeffrey.r...@lemnica.com www.lemnica.com [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] WARNING Undocumented S4 methods 'initialize' - why?
Dear all,
I am just writing the documentation file for S4 class 'QualTreeSet' and
get the following warning with R CMD check:
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'initialize' and siglist 'QualTreeSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
All my S4 classes have a method 'initialize' and R CMD check has never
complained. Thus, do you have any idea why I get suddenly this warning
for method 'initialize'?
Here is the code for 'QualTreeSet':
setClass(QualTreeSet,
representation(qualtype = character,
qualopt = character
),
contains=c(ProcesSet),
prototype(qualtype = rlm,
qualopt = raw
)
)#QualTreeSet
setMethod(initialize, QualTreeSet,
function(.Object,
qualtype = rlm,
qualopt = raw,
...)
{
if (qualtype == ) qualtype - rlm;
if (qualopt == ) qualopt - raw;
.Object - callNextMethod(.Object,
qualtype = qualtype,
qualopt = qualopt,
...);
.Object@qualtype = qualtype;
.Object@qualopt = qualopt;
.Object;
}
)#initialize
However, here is my code for a similar class 'ExprTreeSet' (which is the
class from where I have copied the code):
setClass(ExprTreeSet,
representation(exprtype = character,
normtype = character
),
contains=c(ProcesSet),
prototype(exprtype = none,
normtype = none
)
)#ExprTreeSet
setMethod(initialize, ExprTreeSet,
function(.Object,
exprtype = none,
normtype = none,
...)
{
if (exprtype == ) exprtype - none;
if (normtype == ) normtype - none;
.Object - callNextMethod(.Object,
exprtype = exprtype,
normtype = normtype,
...);
.Object@exprtype = exprtype;
.Object@normtype = normtype;
.Object;
}
)#initialize
In this case R CMD check does not complain, so why does it in the case
of 'QualTreeSet'?
Here is my:
sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] xps_1.11.4
Thank you in advance
Best regards
Christian
_._._._._._._._._._._._._._._._._._
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V.i.e.n.n.a A.u.s.t.r.i.a
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Re: [Rd] hook for when R quits
On 11/03/2011 3:11 PM, Henrik Bengtsson wrote: On Fri, Mar 11, 2011 at 11:07 AM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On Fri, 11 Mar 2011, Duncan Murdoch wrote: On 11/03/2011 1:37 PM, Michael Lawrence wrote: Thanks for the suggestion, but I don't think that R finalizes all of its objects when it quits. At least a simple test suggests that on Linux. Did you use onexit=TRUE? On Windows that appears to work... Agree - here an object finalizer is more appropriate (different from an end-of-session hook). It does work: RODBC makes extensive use of it, for exactly the purpose you describe (or rather, the C_level equivalent of 'it'). In help(reg.finalizer) it says: 'onexit': logical: should the finalizer be run if the object is still uncollected at the end of the R session? What environments, objects, search path etc are available when the finalizer is called this way when R exits? Is safe to always add 'onexit=TRUE' (which now defaults to FALSE), or should I expect an exceptional R system that the finalizer needs to account for? To be very conservative, I would assume that nothing in R is available other than things that are stored in that environment. That's probably not true, but it would be safe. This mechanism is for finalizing things that R doesn't know about. If you want to be less conservative, then you could look at the source code: currently R_RunExitFinalizers is the very first part of the cleanup. I don't know if we guarantee this though. Duncan Murdoch Is there any further documentation on what happens when an R session shuts down and in which order? /Henrik Duncan Murdoch Michael On Fri, Mar 11, 2011 at 10:19 AM, Jeffrey Ryanjeffrey.r...@lemnica.comwrote: Take a look at reg.finalizer. You'd have to create an object internally that would persist until R exits - and a related function to handle cleanup of course. HTH Jeff On Fri, Mar 11, 2011 at 12:08 PM, Michael Lawrence lawrence.mich...@gene.comwrote: Hi, Is there any way that a package can listen for when R quits? The Qt stuff is hooking into platform-specific event loops and when those die unexpectedly (from the perspective of Qt), it aborts, causing an annoying error dialog. If we could catch when R is killed, we could cleanup, like we do with .onUnload. Thanks, Michael [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Jeffrey Ryan jeffrey.r...@lemnica.com www.lemnica.com [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
