Re: [R] initalizing and checking validity of S4 classes
Martin Morgan [EMAIL PROTECTED] writes:
Hi Michal --
Add validObject to your initialize method:
Actually, a call to valid object is part of the default initialization
method which has been masked. A different solution, which might have
some other benefits is to delegate back to the default method using
callNextMethod. So you could do:
setMethod(initialize, someclass,
function(.Object, v=numeric(0), l=character(0))
{
# strip the vector names
cv - v
cl - l
names(cv) - NULL
names(cl) - NULL
callNextMethod(.Object=.Object, v=cv, l=cl)
} )
Here are two interpretations of this. (1) using 'initialize' means
that you are taking control of the initialization process, and hence
know when you need to call validObject.
Yes. Anytime you specialize a method you must take responsibility for
any less specific methods. In this case, the default 'initialize'
does object validation. So if you want validation, you either need to
do it directly or invoke the default method.
(2) Responsibility for object
validity is ambiguous -- does it belong with 'new', 'initialize', or a
'constructor' that the programmer might write? This is particularly
problematic with R's copy semantics, where creating transiently
invalid objects seems to be almost necessary (e.g., callNextMethod()
in 'initialize' might initialize the inherited slots of the object,
but the object itself is of the derived class and could well be
invalid 'invalid' after the base class has finished with initialize).
This is a good point. It suggests that, at least, one must initialize
all non-inherited slots to valid values _before_ calling the next
method.
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org
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[R] initalizing and checking validity of S4 classes
Dear Martin and Seth,
Thanks a million for explanations and suggestions. I find myself still in the
process of learning S4 system. Can you possibly suggest some material that I
could use in this process?
Anything apart from Programming with data book? I also know the notes written
by John Chambers and I also have Fritz Leisch's slides from the first UseR!,
all three available on the Web. Do you have any suggestions in that matter?
Thanks a lot in advance!
Best, Michal
Martin Morgan mtmorgan at fhcrc.org writes:
Hi Michal --
Add validObject to your initialize method:
Actually, a call to valid object is part of the default initialization
method which has been masked. A different solution, which might have
some other benefits is to delegate back to the default method using
callNextMethod. So you could do:
setMethod(initialize, someclass,
function(.Object, v=numeric(0), l=character(0))
{
# strip the vector names
cv - v
cl - l
names(cv) - NULL
names(cl) - NULL
callNextMethod(.Object=.Object, v=cv, l=cl)
} )
Here are two interpretations of this. (1) using 'initialize' means
that you are taking control of the initialization process, and hence
know when you need to call validObject.
Yes. Anytime you specialize a method you must take responsibility for
any less specific methods. In this case, the default 'initialize'
does object validation. So if you want validation, you either need to
do it directly or invoke the default method.
(2) Responsibility for object
validity is ambiguous -- does it belong with 'new', 'initialize', or a
'constructor' that the programmer might write? This is particularly
problematic with R's copy semantics, where creating transiently
invalid objects seems to be almost necessary (e.g., callNextMethod()
in 'initialize' might initialize the inherited slots of the object,
but the object itself is of the derived class and could well be
invalid 'invalid' after the base class has finished with initialize).
This is a good point. It suggests that, at least, one must initialize
all non-inherited slots to valid values _before_ calling the next
method.
+ seth
:
::
::: Note that my e-mail address has changed to m.j.bojanowski at uu dot nl
::: Please update you address books accordingly. Thank you!
::
:
Michal Bojanowski
ICS / Department of Sociology
Utrecht University
Heidelberglaan 2; 3584 CS Utrecht
The Netherlands
m.j.bojanowski at uu dot nl
http://www.fss.uu.nl/soc/bojanowski/
[[alternative HTML version deleted]]
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[R] initalizing and checking validity of S4 classes
Dear useRs and wizaRds,
I am currently developing a set of functions using S4 classes. On the way I
encountered the problem exemplified with the code below. For some reason the
'validity' method does not seem to work, i.e. does not check for errors in the
specification of the slots of the defined class. Any hints?
My understanding of the whole S4 system was that validity checks are made
*after* class initialization. Is that correct?
Thanks a lot in advance!
PS. Session info:
R version 2.5.1 (2007-06-27)
i386-pc-mingw32
locale:
LC_COLLATE=Polish_Poland.1250;LC_CTYPE=Polish_Poland.1250;LC_MONETARY=Polish_Poland.1250;LC_NUMERIC=C;LC_TIME=Polish_Poland.1250
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
-b-e-g-i-n--r--c-o-d-e-
setClass( someclass, representation(v=numeric, l=character),
prototype( v=numeric(0),
l=character(0) )
)
setMethod(initialize, someclass,
function(.Object, v=numeric(0), l=character(0))
{
# strip the vector names
cv - v
cl - l
names(cv) - NULL
names(cl) - NULL
rval - .Object
[EMAIL PROTECTED] - cv
[EMAIL PROTECTED] - cl
rval
} )
# at this point this should be OK
o - new(someclass, v=1:2, l=letters[1:3])
o
# check validity
f - function(object)
{
rval - NULL
if( length([EMAIL PROTECTED]) != length([EMAIL PROTECTED]) )
rval - c( rval, lengths dont match)
if( is.null(rval) ) return(TRUE)
else return(rval)
}
# this should return error description
f(o)
# define the validity method
setValidity( someclass, f)
# this should return an error
new(someclass, v=1:2, l=letters[1:3])
# but it doesn't...
-e-n-d--r--c-o-d-e-
Michal Bojanowski
ICS / Department of Sociology
Utrecht University
Heidelberglaan 2; 3584 CS Utrecht
Room 1428
m.j.bojanowski at uu dot nl
http://www.fss.uu.nl/soc/bojanowski/
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] initalizing and checking validity of S4 classes
Hi Michal --
Add validObject to your initialize method:
setMethod(initialize, someclass,
+ function(.Object, v=numeric(0), l=character(0))
+ {
+ # strip the vector names
+ cv - v
+ cl - l
+ names(cv) - NULL
+ names(cl) - NULL
+ rval - .Object
+ [EMAIL PROTECTED] - cv
+ [EMAIL PROTECTED] - cl
+ validObject(rval)
+ rval
+ } )
[1] initialize
new(someclass, v=1:2, l=letters[1:3])
Error in validObject(rval) :
invalid class someclass object: lengths dont match
Note that without initialize, we have:
setClass(A,
+ representation=representation(
+v=numeric, l=character))
[1] A
setValidity(A, f)
Slots:
Name: v l
Class: numeric character
new(A, v=1:2, l=letters[1:3])
Error in validObject(.Object) :
invalid class A object: lengths dont match
Here are two interpretations of this. (1) using 'initialize' means
that you are taking control of the initialization process, and hence
know when you need to call validObject. (2) Responsibility for object
validity is ambiguous -- does it belong with 'new', 'initialize', or a
'constructor' that the programmer might write? This is particularly
problematic with R's copy semantics, where creating transiently
invalid objects seems to be almost necessary (e.g., callNextMethod()
in 'initialize' might initialize the inherited slots of the object,
but the object itself is of the derived class and could well be
invalid 'invalid' after the base class has finished with initialize).
Martin
Bojanowski, M.J. (Michal) [EMAIL PROTECTED] writes:
Dear useRs and wizaRds,
I am currently developing a set of functions using S4 classes. On the way I
encountered the problem exemplified with the code below. For some reason the
'validity' method does not seem to work, i.e. does not check for errors in
the specification of the slots of the defined class. Any hints?
My understanding of the whole S4 system was that validity checks are made
*after* class initialization. Is that correct?
Thanks a lot in advance!
PS. Session info:
R version 2.5.1 (2007-06-27)
i386-pc-mingw32
locale:
LC_COLLATE=Polish_Poland.1250;LC_CTYPE=Polish_Poland.1250;LC_MONETARY=Polish_Poland.1250;LC_NUMERIC=C;LC_TIME=Polish_Poland.1250
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
-b-e-g-i-n--r--c-o-d-e-
setClass( someclass, representation(v=numeric, l=character),
prototype( v=numeric(0),
l=character(0) )
)
setMethod(initialize, someclass,
function(.Object, v=numeric(0), l=character(0))
{
# strip the vector names
cv - v
cl - l
names(cv) - NULL
names(cl) - NULL
rval - .Object
[EMAIL PROTECTED] - cv
[EMAIL PROTECTED] - cl
rval
} )
# at this point this should be OK
o - new(someclass, v=1:2, l=letters[1:3])
o
# check validity
f - function(object)
{
rval - NULL
if( length([EMAIL PROTECTED]) != length([EMAIL PROTECTED]) )
rval - c( rval, lengths dont match)
if( is.null(rval) ) return(TRUE)
else return(rval)
}
# this should return error description
f(o)
# define the validity method
setValidity( someclass, f)
# this should return an error
new(someclass, v=1:2, l=letters[1:3])
# but it doesn't...
-e-n-d--r--c-o-d-e-
Michal Bojanowski
ICS / Department of Sociology
Utrecht University
Heidelberglaan 2; 3584 CS Utrecht
Room 1428
m.j.bojanowski at uu dot nl
http://www.fss.uu.nl/soc/bojanowski/
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
