[Rd] S4 class, passing argument names to function, modify original
Hello, an S4 class "Foo" is defined with a setter, $. For several reasons, the
setter calls a function, .foo.update(). However, bypassing the argument names
of the setter does not work. Question 1: Why not and how can I fix this?
Question 2: What is the way to define either the function or the setter to
modify the original object (not returning the modified copy of it an overwrite
the original by assignment)? Thanks, Sören
setClass("Foo",
representation(
N = "numeric"
),
prototype(
N = 1
)
)
.foo.update <- function(object, ...) {
args <- list(...)
for (i in slotNames("Foo")[pmatch(names(args), slotNames("Foo"), nomatch=0)])
{
slot(object, i) <- args[[i]]
# indeed more to do here
return(object)
}
}
setReplaceMethod("$", "Foo",
function(x, name, value) {
x <- .foo.update(x, name=value)
x
}
)
x <- new("Foo")
x
x$N <- 99
x # NULL
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[Rd] S4 Slot assignment within function
Is there a simple way to assign values to S4 slots from within a function?
Doing this doesn't work:
> assign_slot<-function(x){
assign("OBJECT@slot",x,envir=parent.env(environment())
}
>assign_slot(x)
All I get from this is a new object with the name OBJECT@slot, the slot
assignment of OBJECT doesn't change.
I have thought about solutions such as eval(parse()) to pull this off, but
would prefer not to ugly up the code.
Thoughts??
I have searched rather thoroughly, but it is possible I overlooked
something. If I did, apologies.
-Brian
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Re: [Rd] C-Side: Applying a function (given as param) to data (given as param)
On Fri, Jun 03, 2011 at 11:14:39AM -0500, Douglas Bates wrote:
> On Fri, Jun 3, 2011 at 5:17 AM, oliver wrote:
> > Hello,
> >
> > I'm implementing a package (C-extension),
> > where one function gets data and a function
> > that needs to be applied to the data.
> >
> > I want to apply the function to (parts of)
> > the data on the C-side.
> >
> > 1) how do I apply a function (given via SEXP) to data
> > 2) how do I select parts of the data (also provided via SEXP)?
>
> Not to be facetious but you begin by reading the "Writing R Extensions"
> manual.
I already read inside it.
If there would be no question open i would not have registered to this mailing
list
and woulod not have asked that question.
Obviously my question was not answered in the "Writing R Extensions",
so if you can give me a hint this would be nice.
>
> An alternative is to read the vignette Rcpp-Introduction available as
> http://dirk.eddelbuettel.com/code/rcpp/Rcpp-introduction.pdf and soon
I use C, not C++.
But maybe it helps too.
I already created my own package with R and C successfully some days ago.
But so far I did not used fucntion pointers coming in via SEXP parameters.
And that was my specific question.
> to be in The R Journal. They show an explicit example of apply in
> compiled code (C++ using the Rcpp structures, in their case).
As just mentioned: I already created successfully a C-extension for R.
But I would like to know, how to call a function that I get via
SEXP as parameter. How can I find out the function definition,
for example the arity of the function and which arguments
a function uses.
The problem is, that the C-standard (at least the first ANSI-C standard)
does not guarantee portability for C-pointers.
To be portable, for example the function pointer you use must
definitely be of same type as the function you use.
So I need to know how I can use the SEXP-function pointers.
To be more concrete, this is how my function's API looks like
at the moment:
SEXP movapply( SEXP data, SEXP width, SEXP func )
{
/* some code */
return ( result );
}
data will be vector or list or matrix
width will be int value (I think vector of length 1)
func will be a function pointer of the type that is given as argument
I don't know on which kind of pointer to cast.
I think I will cast to a pure C-type, but then all data also must
match to the function definition.
What if the function wants to work on integer, but the data is double?
Somehow this must be handled, and I think the experts here can just point me
directly to some kind of docs or maybe older postinmgs here, which explain this?
Ciao,
Oliver
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Re: [Rd] S4 Slot assignment within function
On 11-06-03 5:03 PM, mcguirebc wrote:
Is there a simple way to assign values to S4 slots from within a function?
Doing this doesn't work:
assign_slot<-function(x){
assign("OBJECT@slot",x,envir=parent.env(environment())
}
assign_slot(x)
All I get from this is a new object with the name OBJECT@slot, the slot
assignment of OBJECT doesn't change.
I have thought about solutions such as eval(parse()) to pull this off, but
would prefer not to ugly up the code.
Thoughts??
I have searched rather thoroughly, but it is possible I overlooked
something. If I did, apologies.
I haven't tried this, but I would expect
OBJECT@slot <<- x
to work, assuming OBJECT already exists somewhere outside the function
but in its environment.
Duncan Murdoch
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Re: [Rd] C-Side: Applying a function (given as param) to data (given as param)
On 11-06-03 4:19 PM, oliver wrote:
On Fri, Jun 03, 2011 at 11:14:39AM -0500, Douglas Bates wrote:
On Fri, Jun 3, 2011 at 5:17 AM, oliver wrote:
Hello,
I'm implementing a package (C-extension),
where one function gets data and a function
that needs to be applied to the data.
I want to apply the function to (parts of)
the data on the C-side.
1) how do I apply a function (given via SEXP) to data
2) how do I select parts of the data (also provided via SEXP)?
Not to be facetious but you begin by reading the "Writing R Extensions" manual.
I already read inside it.
If there would be no question open i would not have registered to this mailing
list
and woulod not have asked that question.
Obviously my question was not answered in the "Writing R Extensions",
so if you can give me a hint this would be nice.
An alternative is to read the vignette Rcpp-Introduction available as
http://dirk.eddelbuettel.com/code/rcpp/Rcpp-introduction.pdf and soon
I use C, not C++.
But maybe it helps too.
I already created my own package with R and C successfully some days ago.
But so far I did not used fucntion pointers coming in via SEXP parameters.
And that was my specific question.
to be in The R Journal. They show an explicit example of apply in
compiled code (C++ using the Rcpp structures, in their case).
As just mentioned: I already created successfully a C-extension for R.
But I would like to know, how to call a function that I get via
SEXP as parameter. How can I find out the function definition,
for example the arity of the function and which arguments
a function uses.
You should almost certainly do this in R, not in C. If you are doing it
in C code you'll just be duplicating the implementation from R, and your
code will break if that implementation ever changes.
In R you use formals(fn) to extract the function header.
The problem is, that the C-standard (at least the first ANSI-C standard)
does not guarantee portability for C-pointers.
To be portable, for example the function pointer you use must
definitely be of same type as the function you use.
So I need to know how I can use the SEXP-function pointers.
They are not function pointers, they are pointers to R objects.
Duncan Murdoch
To be more concrete, this is how my function's API looks like
at the moment:
SEXP movapply( SEXP data, SEXP width, SEXP func )
{
/* some code */
return ( result );
}
data will be vector or list or matrix
width will be int value (I think vector of length 1)
func will be a function pointer of the type that is given as argument
I don't know on which kind of pointer to cast.
I think I will cast to a pure C-type, but then all data also must
match to the function definition.
What if the function wants to work on integer, but the data is double?
Somehow this must be handled, and I think the experts here can just point me
directly to some kind of docs or maybe older postinmgs here, which explain this?
Ciao,
Oliver
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Re: [Rd] C-Side: Applying a function (given as param) to data (given as param)
Oliver,
For an example of moving averages, take a look at the C source of the xts and
TTR packages. The sources are browsable on R-forge.
In short, REAL etc are functions to extract the data of an SEXP. They need to
match the types coming in. So your C needs to check the type and branch
accordingly.
It is all in the guide as well as in working example code in R sources as well
as many hundreds of package sources. You have access to it all, so spend the
time just reading the sources is my recommendation.
Best,
Jeff
Jeffrey Ryan|Founder|jeffrey.r...@lemnica.com
www.lemnica.com
On Jun 3, 2011, at 3:19 PM, oliver wrote:
> On Fri, Jun 03, 2011 at 11:14:39AM -0500, Douglas Bates wrote:
>> On Fri, Jun 3, 2011 at 5:17 AM, oliver wrote:
>>> Hello,
>>>
>>> I'm implementing a package (C-extension),
>>> where one function gets data and a function
>>> that needs to be applied to the data.
>>>
>>> I want to apply the function to (parts of)
>>> the data on the C-side.
>>>
>>> 1) how do I apply a function (given via SEXP) to data
>>> 2) how do I select parts of the data (also provided via SEXP)?
>>
>> Not to be facetious but you begin by reading the "Writing R Extensions"
>> manual.
>
> I already read inside it.
> If there would be no question open i would not have registered to this
> mailing list
> and woulod not have asked that question.
> Obviously my question was not answered in the "Writing R Extensions",
> so if you can give me a hint this would be nice.
>
>
>>
>> An alternative is to read the vignette Rcpp-Introduction available as
>> http://dirk.eddelbuettel.com/code/rcpp/Rcpp-introduction.pdf and soon
>
> I use C, not C++.
>
> But maybe it helps too.
>
> I already created my own package with R and C successfully some days ago.
>
> But so far I did not used fucntion pointers coming in via SEXP parameters.
>
> And that was my specific question.
>
>
>
>
>> to be in The R Journal. They show an explicit example of apply in
>> compiled code (C++ using the Rcpp structures, in their case).
>
>
> As just mentioned: I already created successfully a C-extension for R.
>
> But I would like to know, how to call a function that I get via
> SEXP as parameter. How can I find out the function definition,
> for example the arity of the function and which arguments
> a function uses.
>
> The problem is, that the C-standard (at least the first ANSI-C standard)
> does not guarantee portability for C-pointers.
> To be portable, for example the function pointer you use must
> definitely be of same type as the function you use.
>
> So I need to know how I can use the SEXP-function pointers.
>
>
> To be more concrete, this is how my function's API looks like
> at the moment:
>
> SEXP movapply( SEXP data, SEXP width, SEXP func )
> {
> /* some code */
>
> return ( result );
> }
>
>
>
> data will be vector or list or matrix
> width will be int value (I think vector of length 1)
> func will be a function pointer of the type that is given as argument
>
> I don't know on which kind of pointer to cast.
> I think I will cast to a pure C-type, but then all data also must
> match to the function definition.
>
> What if the function wants to work on integer, but the data is double?
>
> Somehow this must be handled, and I think the experts here can just point me
> directly to some kind of docs or maybe older postinmgs here, which explain
> this?
>
>
> Ciao,
> Oliver
>
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Re: [Rd] S4 Slot assignment within function
On 06/03/2011 02:03 PM, mcguirebc wrote:
Is there a simple way to assign values to S4 slots from within a function?
Doing this doesn't work:
assign_slot<-function(x){
assign("OBJECT@slot",x,envir=parent.env(environment())
}
assign_slot(x)
All I get from this is a new object with the name OBJECT@slot, the slot
assignment of OBJECT doesn't change.
I have thought about solutions such as eval(parse()) to pull this off, but
would prefer not to ugly up the code.
Thoughts??
I have searched rather thoroughly, but it is possible I overlooked
something. If I did, apologies.
Maybe you're looking for ?ReferenceClasses rather then S4 classes?
Martin
-Brian
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Re: [Rd] S4 class, passing argument names to function, modify original
On 06/04/2011 03:07 AM, soeren.vo...@uzh.ch wrote:
Hello, an S4 class "Foo" is defined with a setter, $. For several reasons, the
setter calls a function, .foo.update(). However, bypassing the argument names of the
setter does not work. Question 1: Why not and how can I fix this? Question 2: What is the
way to define either the function or the setter to modify the original object (not
returning the modified copy of it an overwrite the original by assignment)? Thanks, Sören
setClass("Foo",
representation(
N = "numeric"
),
prototype(
N = 1
)
)
.foo.update<- function(object, ...) {
args<- list(...)
for (i in slotNames("Foo")[pmatch(names(args), slotNames("Foo"),
nomatch=0)]) {
slot(object, i)<- args[[i]]
# indeed more to do here
return(object)
}
}
Since names(args) is 'name', and 'name' is not a slot of 'Foo', the
return of pmatch is 0 and .foo.update returns NULL. Put return(object)
outside the for loop.
setReplaceMethod("$", "Foo",
function(x, name, value) {
x<- .foo.update(x, name=value)
here your intention is that name=value to be substituted with N=99, but
you end up with name=99. You could arrange to parse this correctly, but
this isn't usually what you _want_ to do and I don't really understand
what you're trying to accomplish. Maybe
.foo.update <- function(object, name, value, ...)
{
slot(object, name) <- value
## some other stuff
object
}
Hope that helps a bit.
Martin
x
}
)
x<- new("Foo")
x
x$N<- 99
x # NULL
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[Rd] Interfacing a C++ class
Hello
Apologies for cross-posting, the discussion should (if) go to R-devel, but I
also want to reach the rcpp-devel people.
My C++ class FOO is a module available through Rcpp, and it works fine and is
-- so far -- bug free. With trying to further develop my R package, I thought
it was a good idea to interface my C++ workhorse FOO with an S4 class Foo.
After some long and not always insightful trip through S4 classes and methods,
I am not sure if I am on the right way of thinking and designing. Since there
is no local assistance available, could you help to make things clearer?
Just a brief outline:
FOO is the C++ object, and Foo should be the S4 class. If the user creates an
object, say bar, from class Foo, the creation process automatically makes a new
FOO object relating to bar in that a unique name of the FOO instance is stored
in a slot of bar. All the user then has to do is modify bar by simple
assignments. The getters and setters ("$", "[") are set up and work. Each
modification goes in hand with assigning new values to bar as well as updating
the FOO object through available setters from FOO.
So far, this way has brought me to about 100 lines, but now I read about
ReferenceClasses and was wondering, if there is a much easier way of achieving
my goals. Moreover, I was not sure any longer if my goals make sense or if a
more advanced programmer would do it totally different (and could share some
structural thinking on their approach).
The idea behind my way of doing was based upon several considerations. First, a
"classical" R object would not confuse users, as I assume users of my package
to be rather non-skilled (and not willing to change that). Second, I want to
create a properly programmed package for distribution on CRAN and publication,
eventually. Third, I want to save objects across sessions. So if a user
restores a session, a simple command, say, restore(), would do the trick to
build all the related C++ objects again. However, I admit that I still have not
figured out how to automatically clean up the workspace correctly before
leaving a session, wanted or unwanted, that is, clean up memory before leaving
home. Fourth, pure arithmetic check is done in C++, however, semantic check
*should* be left to R, and the validity and class routines seem to be perfect
for this. Fifth, some work should be done in R, such as the passing of data
frames or samples from distributions.
I hope to get some structured ideas and hints how to start and/or proceed.
Thank you in advance,
Sören
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Re: [Rd] S4 class, passing argument names to function, modify original
On 04.06.2011, at 15:41, Martin Morgan wrote:
> On 06/04/2011 03:07 AM, soeren.vo...@uzh.ch wrote:
>
>> Hello, an S4 class "Foo" is defined with a setter, $. For several reasons,
>> the setter calls a function, .foo.update(). However, bypassing the argument
>> names of the setter does not work. Question 1: Why not and how can I fix
>> this? Question 2: What is the way to define either the function or the
>> setter to modify the original object (not returning the modified copy of it
>> an overwrite the original by assignment)? Thanks, Sören
>>
>> setClass("Foo",
>> representation(
>> N = "numeric"
>> ),
>> prototype(
>> N = 1
>> )
>> )
>>
>> .foo.update<- function(object, ...) {
>> args<- list(...)
>> for (i in slotNames("Foo")[pmatch(names(args), slotNames("Foo"),
>> nomatch=0)]) {
>> slot(object, i)<- args[[i]]
>> # indeed more to do here
>> return(object)
>> }
>> }
>
> Since names(args) is 'name', and 'name' is not a slot of 'Foo', the return of
> pmatch is 0 and .foo.update returns NULL. Put return(object) outside the for
> loop.
>
>> setReplaceMethod("$", "Foo",
>> function(x, name, value) {
>> x<- .foo.update(x, name=value)
>> x
>> }
>> )
>>
>> x<- new("Foo")
>> x
>> x$N<- 99
>> x # NULL
>
> here your intention is that name=value to be substituted with N=99, but you
> end up with name=99. You could arrange to parse this correctly, but this
> isn't usually what you _want_ to do and I don't really understand what you're
> trying to accomplish.
Exactly, what I want to parse is "N"=99. To clarify, .foo.update should be the
"one" workhorse to do a couple of things depending on arguments on more than
one object (see my post on interfacing a C++ class, just some minutes ago).
Thus, assigning x@N = 10 (x$N, x["N"]) should not only end up in x (object of
class Foo) with value 10, but also should invoke FOO$setN(10) (a setter for the
C++ object, not shown here). So far, .foo.update works perfectly and indeed
alters the object x, but the setter does not parse the argument name. I tried
with quote, substitute, deparse ..., but got none working ...
> Maybe
>
> .foo.update <- function(object, name, value, ...)
> {
>slot(object, name) <- value
>## some other stuff
>object
> }
>
> Hope that helps a bit.
>
> Martin
Thanks, Sören
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Re: [Rd] Interfacing a C++ class
On Jun 4, 2011, at 10:31 AM, soeren.vo...@uzh.ch wrote:
> Hello
>
> Apologies for cross-posting, the discussion should (if) go to R-devel, but I
> also want to reach the rcpp-devel people.
>
> My C++ class FOO is a module available through Rcpp, and it works fine and is
> -- so far -- bug free. With trying to further develop my R package, I thought
> it was a good idea to interface my C++ workhorse FOO with an S4 class Foo.
> After some long and not always insightful trip through S4 classes and
> methods, I am not sure if I am on the right way of thinking and designing.
> Since there is no local assistance available, could you help to make things
> clearer?
>
> Just a brief outline:
>
> FOO is the C++ object, and Foo should be the S4 class. If the user creates an
> object, say bar, from class Foo, the creation process automatically makes a
> new FOO object relating to bar in that a unique name of the FOO instance is
> stored in a slot of bar. All the user then has to do is modify bar by simple
> assignments. The getters and setters ("$", "[") are set up and work. Each
> modification goes in hand with assigning new values to bar as well as
> updating the FOO object through available setters from FOO.
>
It's fairly simple, you just create an external pointer for your object,
register "delete obj;" as its finalizer and put it in a slot of your S4 object
. Have a look, for example, at rJava. It uses S4 objects with one slot being an
external pointer to the object in Java (in your case C++). For a C++ package
with external pointers see Acinonyx (aka iPlots eXtreme) - from RCalls.cpp:
static void AObjFinalizer(SEXP ref) {
if (TYPEOF(ref) == EXTPTRSXP) {
AObject *o = static_cast (R_ExternalPtrAddr(ref));
if (o) o->release(); // NOTE: you would probably use delete o;
instead
}
}
SEXP A2SEXP(AObject *o) {
SEXP xp = R_MakeExternalPtr(o, R_NilValue, R_NilValue);
R_RegisterCFinalizerEx(xp, AObjFinalizer, TRUE);
return xp;
}
AObject *SEXP2A(SEXP o) {
if (TYPEOF(o) != EXTPTRSXP)
Rf_error("invalid object");
return (AObject*) R_ExternalPtrAddr(o);
}
> So far, this way has brought me to about 100 lines, but now I read about
> ReferenceClasses and was wondering, if there is a much easier way of
> achieving my goals. Moreover, I was not sure any longer if my goals make
> sense or if a more advanced programmer would do it totally different (and
> could share some structural thinking on their approach).
>
ReferenceClasses are very similar - they differ from the approach I described
only in that they use an environment for the reference semantics where your
would use external pointer to your object. Technically, you could put your
external pointer in a reference class object - what you would gain is the
ability to store other R objects alongside if you need them.
> The idea behind my way of doing was based upon several considerations. First,
> a "classical" R object would not confuse users, as I assume users of my
> package to be rather non-skilled (and not willing to change that). Second, I
> want to create a properly programmed package for distribution on CRAN and
> publication, eventually. Third, I want to save objects across sessions. So if
> a user restores a session, a simple command, say, restore(), would do the
> trick to build all the related C++ objects again. However, I admit that I
> still have not figured out how to automatically clean up the workspace
> correctly before leaving a session, wanted or unwanted, that is, clean up
> memory before leaving home.
Again, have a look at rJava (see ?.jcache) - it uses Java object serialization
to cache serialized versions of objects (as raw vectors) in the protection part
of the pointer which gets serialized by R on save(). Then restoration is
automatic: when rJava sees a NULL pointer (that's what the are deserialized
too) in the S4 object, it checks whether there is a serialized cache and
restores the Java object.
Cheers,
Simon
> Fourth, pure arithmetic check is done in C++, however, semantic check
> *should* be left to R, and the validity and class routines seem to be perfect
> for this. Fifth, some work should be done in R, such as the passing of data
> frames or samples from distributions.
>
> I hope to get some structured ideas and hints how to start and/or proceed.
>
> Thank you in advance,
> Sören
>
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>
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[Rd] Does anybody successfully built latest R on AIX 5.3?
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[Rd] call / do.call expression too big
I am designing a remote procedure protocol for R, which basically performs a
do.call on data and arguments supplied by a client. However, I am
experiencing unfortunate behavior of the do.call function. The function
do.call seems to serialize all objects in the args list, resulting in an
enormous expression, that is then in some way or another returned by many
functions. A short example:
args <- list(data=cars, formula=dist~speed);
do.call("lm",args);
One can see that for this small example, the returned 'call' attribute is
already huge. Another example:
eval(call("cor.test", x=rnorm(100), y=rnorm(100)))
I completely understand why this happens, yet I was wondering if there is an
alternative to call/do.call that constructs the call in an different way so
that the actual call object is somewhat more compact and does not contain
all the data that was involved in the function. For example one that
attaches the args list in an environment and constructs a call that refers
to these objects or something similar.
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Re: [Rd] call / do.call expression too big
Try this:
args <- list(data=quote(cars), formula=dist~speed)
On Sat, Jun 4, 2011 at 7:49 PM, Jeroen Ooms wrote:
> I am designing a remote procedure protocol for R, which basically performs a
> do.call on data and arguments supplied by a client. However, I am
> experiencing unfortunate behavior of the do.call function. The function
> do.call seems to serialize all objects in the args list, resulting in an
> enormous expression, that is then in some way or another returned by many
> functions. A short example:
>
> args <- list(data=cars, formula=dist~speed);
> do.call("lm",args);
>
> One can see that for this small example, the returned 'call' attribute is
> already huge. Another example:
>
> eval(call("cor.test", x=rnorm(100), y=rnorm(100)))
>
> I completely understand why this happens, yet I was wondering if there is an
> alternative to call/do.call that constructs the call in an different way so
> that the actual call object is somewhat more compact and does not contain
> all the data that was involved in the function. For example one that
> attaches the args list in an environment and constructs a call that refers
> to these objects or something similar.
>
>
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> View this message in context:
> http://r.789695.n4.nabble.com/call-do-call-expression-too-big-tp3574335p3574335.html
> Sent from the R devel mailing list archive at Nabble.com.
>
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Henrique Dallazuanna
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Re: [Rd] call / do.call expression too big
> I completely understand why this happens, yet I was wondering if there is an
> alternative to call/do.call that constructs the call in an different way so
> that the actual call object is somewhat more compact and does not contain
> all the data that was involved in the function. For example one that
> attaches the args list in an environment and constructs a call that refers
> to these objects or something similar.
Like this?
argn <- lapply(names(args), as.name)
names(argn) <- names(args)
call <- as.call(c(list(as.name("lm")), argn))
eval(call, args)
Hadley
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Department of Statistics / Rice University
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