Hi!
First of all thanks a lot to John Chambers. I think S4 makes some tasks really
easier.
This mail tries to summarise the mail exchange concerning contains="list" in S4.
I do not know all the R "internals" so instead of talking I try to use and to play
around with S4. People like I learn by example. But I would like to use all features
of S4. I dont say that anything is good or bad. I just ask on which parts and features
can I rely on? About which parts of methods I be sure that there are not going to
change in the nearest future? And making a search on several hundred packages in the
lib directory, and finding that setAs is used only in the file methods/R-ex/as.R its
not reassuring.
I like to use S4 and i like to use lists.
I like to use lists like maps or multimaps with key value pairs. I believe that I am
not the only one who uses lists to store different types of objects and to access them
using mylist[["key"]]. So in my opinion list had have and should have names. (I am not
a phyton user yet but I know that phyton has also a data structure to store key value
pairs and it is a quite important one.)
R provides a lot of powerfull functions which are operating on "lists" like sapply,
lapply, mapply, [[]] [] etc....
And all the list methods lapply, [], etc preserve the list names. So if they "return a
type" are "list" then list have names. But as I said i understand examples and so
probably nothing new to what you have already said. And I think that my examples will
show that even in S4 except for the function as(object,"list") old style "list" have
names attribute.
If I write a new class, and this class is a mainly a container class, I would like
rather inherit from a list (contains="list") with names rather then include it
(include means representation(list="list") like e.g. class Biobase:container does). I
like to inherit because I would not like to wrap every possible list function which is
available for lists. Its just because I even not know all of them. And if I have
inheritance as a tool this is not neceassary. Any function working on lists can be
used on a class inheriting from list.
The following code summarizes, by example, how names are treated when "list" is
"contained" by a class.
I show 3 versions how to inherit from "list" showing the problems with the 'naive'
inheritance.
And I think that the example shows also that in S4 the old styl "list" class are with
"names"!
There are also some inconsistencies, bugs which I am going to show on occasion?
#NAIVE inheritance from list.
#define cass
setClass("ListWithNames","list")
setClass("Mlist"
,representation(info="character") #uniq names have to be unique?
,contains="ListWithNames"
,prototype(uniq=FALSE)
)
tmp <- as.list(1:4)
names(tmp) <- letters[1:4]
mylist<-new("Mlist" , tmp , info="numeric" )
#Example of manipulating the list part of the object.
as(mylist,"list")<-lapply(mylist,"+",3)
as(mylist,"list") <- mylist[2:4]
as(mylist,"list") <- as(mylist,"ListWithNames")[2:4]
#what does not work is assigning shorter lists without names. Seems like a bug. Or is
there an explanation.
as(mylist,"list")<-as.list(1:5)
as(mylist,"list")<-as.list(1:4)
class(Mlist)
#I have not defined in class Representation
# a names attribute but there is the name attribute anyway inherited by from list.
[EMAIL PROTECTED]
# But this does not work. Of course.
[EMAIL PROTECTED] <- letters[5:9]
#Slots are implemented using attributes?
attributes([EMAIL PROTECTED])$names #this is what is expected.
attributes(mylist)$names #But whats this?
attributes(mylist)$names <- letters[2:11]
attributes([EMAIL PROTECTED])$names #are they the same? synchronized?
# So if @names are there why not make it official ?
# I make it official with a new class definition.
# REFINED version of "list" inheritance.
setClass("MlistN"
,representation(info="character",names="character") #uniq names have to be
unique?
,contains="ListWithNames"
)
mylistNam<-new("MlistN" , tmp , info="numeric")
[EMAIL PROTECTED]<-letters[4:7]
mylistNam["d"]
mylistNam[["d"]]
as(mylistNam,"list")<-tmp[1:3]
as(mylistNam,"list")<-as.list(1:4)
as(mylistNam,"list")<-as.list(1:3) #<- the same error as before.
as(mylistNam,"list")<-list(a=1,b=2,c=3,d=4)
#to get it more complicated
as(mylistNam,"ListWithNames") # Is without names??
## MORE REFINED version of list inheritance.
setClass("MlistN"
,representation(info="character",names="character") #uniq names have to be
unique?
,contains="list"
)
# I dont like the as(o,"list")
# My Solution. Now it does not mether wheter the list has or has not names is longer
or shorter.
setAs("MlistN","list"
,def=function(from){
print("test")
to<[EMAIL PROTECTED]
names(to)<[EMAIL PROTECTED]
to
}
,replace=function(from,value)
{
[EMAIL PROTECTED]<-value
[EMAIL PROTECTED]<-names(value)
from
}
)
bublegum <- list(b=1, u=3, b=4, l=4, e=2, g=1, u=4, m=2)
mylistNam <- bublegum
bubl<-bublegum[1:4]
names(bubl)<-NULL
as(mylistNam,"list") <- bubl
I have just one question: Can I rely that this is not going to change in further
versions of R?
/E
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