Re: [R] Extending a group of S4 classes by setClassUnion ?
Martin Morgan wrote
On 03/15/2012 09:51 AM, Alexander wrote:
Hi Martin,
thanks for your quick answer. I didn't know that '.' could be
missleading.
Is there any standard way to name function for S4 objects? get,set
etc..?
Hi Alexander -- it's usually better to include the original email in the
reply, to provide context especially for those joining the thread later.
I think 'get' and 'set' are implicit in the action of the 'getter'
fun(x) and 'setter' fun(x) - value function. I would have written (I
wouldn't have used par, which is an existing function unrelated to what
you're trying to do).
In fact, I have several getter and setter. For example gettermean and
gettervariance are less clear then getter.mean and getter.variance. The
names mean.getter, variance.getter have the disadvantage to have getter
and setter not in first place... (Ok, these are very minor problems...)
Martin Morgan wrote
setGeneric(parent,
function(object, ...) standardGeneric(parent'))
setMethod(parent, Father, function(object, ...) object@name)
setGeneric(parent-,
function(object, ..., value) standardGeneric(parent-))
setReplaceMethod(parent, c(Father, Son1),
function(object, ..., value) {
object@name - value
object
})
and used as
parent(obj)
parent(obj) - son
I realize I'm confused about Father / Son and 'parent' here, maybe you
meant something else by 'par'.
Yes indeed, par means parameter. But you're right, it is to close to
parent and very misleading in this example
Martin Morgan wrote
I saw your example, and I was wondering, why get.par(ext) put out Son1,
and not the same as get.par(new(Son1, name=Son1, par=3))
the setIs established a relationship between Extension and Father; you
could have established a relationship between Extension and Son1
setIs(Extension, Son1, ...)
and then you would get your expected result. I have to say that I have
rarely used setIs, so the complexity of inheritance may hold some
surprises, e.g., when there are setIs defined, from Extension to Father,
Son1, and Son2.
Martin
If I define a function just like setMethod(get.par, Father,
function(object) object@name) , for example
setMethod(get.par, Father, function(object) object@par)
then it would work, for all objects, which are either Son1 or Son2, but
not
all object, which are Father, contains also the variable par
get.par(new(Father))
Alexander
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I rewrote the example and I think if will have to write some setIs methods.
Do you know, how this is done? Here is a little example which shows, that
the order of initialization for setIs determins the results !!
setClass(Father,representation(name=character))
setClass(Son1,contains=Father,representation(parameter=numeric))
setClass(Son2,contains=Father,representation(parameter=logical))
Son1-new(Son1,name=Son1,parameter=3)
Son2-new(Son2,name=Son2,parameter=TRUE)
setGeneric(get.parameter,function(object){standardGeneric
(get.parameter)})
setMethod(get.parameter,Son1,function(object){return(object@parameter+3)})
setMethod(get.parameter,Son2,function(object){return(object@parameter==TRUE)})
get.parameter(Son1)
get.parameter(Son2)
setClass(Extension,representation(person=Father,text=character))
ext1 - new(Extension,person=Son1,text=new try)
ext2 - new(Extension,person=Son2,text=yesyes)
setIs(Extension, Son1,test=function(from){print(setIsSon1)
return(class(from@person)==Son1)
},
coerce=function(from) as(from@person,Son1,strict=FALSE),
replace=function(from, value) {from@person - value
from
}
)
setIs(Extension, Son2,test=function(from){print(setIsSon2)
return(class(from@person)==Son2)
},
coerce=function(from) as(from@person,Son2,strict=FALSE),
replace=function(from, value) {from@person - value
from
}
)
get.parameter(ext1) #setIsSon1, 6 correct result
get.parameter(ext2)# setIsSon1, Error in as(object, Son1, strict =
FALSE) :
Re: [R] Extending a group of S4 classes by setClassUnion ?
Hi Alexander --
On 03/15/2012 07:57 AM, Alexander wrote:
Hi,
I would like to create some S4 classes as follows
setClass(Father,representation(name=character))
setClass(Son1,contains=Father,representation(par=numeric))
setClass(Son2,contains=Father,representation(par=logical))
Son1-new(Son1)
Son1@name-Son1
Son1@par-3
it's more efficient to call new(Son1, name=Son1, par=3)
Son2-new(Son2)
Son2@name-Son2
Son2@par-TRUE
setGeneric(get.par,function(object){standardGeneric (get.par)})
functions with '.' in their names can be confusing, because it could
represent an S3 generic on 'get', for an S3 object of class 'par'.
setMethod(get.par,Son1,function(object){return(object@par+3)})
setMethod(get.par,Son2,function(object){return(!object@par)})
get.par(Son1)
get.par(Son2)
So far, so good. I would like now, to create a new class, which
extends/contains the subclasses of Father by some additional slots.
Is there any clean and simple possibility to inherite also the corresponding
function get.par ?
setClass(Extension,representation(person=Father,text=character))
Ext-new(Extension)
Ext@text-new try
Ext@person-Son1
get.par(Ext)
get.par(Ext@person)
Of course, get.par(Ext) returns an error. Is there any possibility to tell
R, that if now function exists for a Class, to transform the object to a
class, for which the function exists ? (I know, it is not very clear what I
am writing, but I am doing my best). I don't want to rewrite every method
for Extension like
setMethod(get.par,Extension,function(object){get.par(object@person)})
Is there any simpler solution by steClassUnion, setAs, setIs ?
You can provide an explicit relationship
setIs(Extension, Father,
coerce=function(from) from@person,
replace=function(from, value) {
from@person - value
from
})
and then define a method on 'Father' (since that's what you're asserting
equivalence to)
setMethod(get.par, Father, function(object) object@name)
and finally have success with
ext - new(Extension,
person=new(Son1, name=Son1, par=3),
text=new try)
get.par(ext)
[1] Son1
Neat, eh? But it really pays to ask whether the complexity of the class
structure you're creating is appropriate for the solution that you need
to implement -- imagine, for instance, writing a method that dispatches
on two arguments, and as a programmer you need to implement appropriate
methods for the tangle of dispatch that you have created.
Martin
Thanks a lot in advance
Alexander
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Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
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R-help@r-project.org mailing list
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Extending a group of S4 classes by setClassUnion ?
Hi Martin, thanks for your quick answer. I didn't know that '.' could be missleading. Is there any standard way to name function for S4 objects? get,set etc..? I saw your example, and I was wondering, why get.par(ext) put out Son1, and not the same as get.par(new(Son1, name=Son1, par=3)) If I define a function just like setMethod(get.par, Father, function(object) object@name) , for example setMethod(get.par, Father, function(object) object@par) then it would work, for all objects, which are either Son1 or Son2, but not all object, which are Father, contains also the variable par get.par(new(Father)) Alexander -- View this message in context: http://r.789695.n4.nabble.com/Extending-a-group-of-S4-classes-by-setClassUnion-tp4475251p4475650.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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] Extending a group of S4 classes by setClassUnion ?
On 03/15/2012 09:51 AM, Alexander wrote:
Hi Martin,
thanks for your quick answer. I didn't know that '.' could be missleading.
Is there any standard way to name function for S4 objects? get,set
etc..?
Hi Alexander -- it's usually better to include the original email in the
reply, to provide context especially for those joining the thread later.
I think 'get' and 'set' are implicit in the action of the 'getter'
fun(x) and 'setter' fun(x) - value function. I would have written (I
wouldn't have used par, which is an existing function unrelated to what
you're trying to do).
setGeneric(parent,
function(object, ...) standardGeneric(parent'))
setMethod(parent, Father, function(object, ...) object@name)
setGeneric(parent-,
function(object, ..., value) standardGeneric(parent-))
setReplaceMethod(parent, c(Father, Son1),
function(object, ..., value) {
object@name - value
object
})
and used as
parent(obj)
parent(obj) - son
I realize I'm confused about Father / Son and 'parent' here, maybe you
meant something else by 'par'.
I saw your example, and I was wondering, why get.par(ext) put out Son1,
and not the same as get.par(new(Son1, name=Son1, par=3))
the setIs established a relationship between Extension and Father; you
could have established a relationship between Extension and Son1
setIs(Extension, Son1, ...)
and then you would get your expected result. I have to say that I have
rarely used setIs, so the complexity of inheritance may hold some
surprises, e.g., when there are setIs defined, from Extension to Father,
Son1, and Son2.
Martin
If I define a function just like setMethod(get.par, Father,
function(object) object@name) , for example
setMethod(get.par, Father, function(object) object@par)
then it would work, for all objects, which are either Son1 or Son2, but not
all object, which are Father, contains also the variable par
get.par(new(Father))
Alexander
--
View this message in context:
http://r.789695.n4.nabble.com/Extending-a-group-of-S4-classes-by-setClassUnion-tp4475251p4475650.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
