Hi,
On Aug 14, 2012, at 10:07 AM, Bert Gunter wrote:
> (Offlist, as my comments are not worth bothering the list about).
>
Almost off list!
> I don't understand the purpose of this tirade (whose reasonableness I
> make no judgment of). R is what it is. If you don't like it for
> whatever reason, don't use it.
>
> As a point of order, there are several packages that "automate" pass
> by reference/pointers in R to some extent: packages ref, R.oo, and
> proto are 3 that I know of, but I think there are others. My
> understanding is that this tends to be computationally inefficient in
> R, but I have no direct knowledge.
>
I wonder why Reference Classes are not mentioned - I think they maybe be
informally called R5 and RefClass, too. You can learn about them with
?setRefClass.
I have tried using this approach quite recently as I was working with very
large data frames. I'm no software engineer, so I am not sure if using R5
style was a significant help to my problem, but with one exception it was
pretty painless to give it a shake.* In fact, inside the methods (and
therefore the object instance environment?) I probably was working in the
pass-by-value paradigm.
I'm hoping that those in the know could shed some light on the pros and cons of
using Reference Classes.
Cheers,
Ben
* There are two ways to add methods to a reference class: (1) in the call to
setRefClass() which generates the object definition, and (2) using the
MyRefClass$methods() function after the generator object is created. After some
puzzle-filled afternoons I settled on the latter as being waaaaay better. I
have pasted below an example.
##### START
# generator
MyRefClassR5 <- setRefClass("MyRefClassR5",
# here are the field properties
fields = list(
x = "numeric",
y = "numeric",
color = "character",
flavor = "character"),
# here we can add methods - but there is a handier way
# see the length() method added below
methods = list(
plot = function(color = .self$color, flavor = .self$flavor, pch = 15,
...){
graphics::plot(.self$x, .self$y, col = color, main = flavor, pch =
pch, ...)
speak("plotting")
},
speak = function(message = paste(.self$flavor, "is the color",
.self$color)){
cat("MyRefClass:", message, "\n")
})
)
MyRefClass <- function(x = seq(from = 0, to = 10), y = x^2,
color = "brown", flavor = "chocolate"){
X <- MyRefClassR5$new(x = x, y = y,
color = color, flavor = flavor)
return(X)
}
# create an instance, a
a <- MyRefClass()
a$speak()
a$plot()
# So, now I have an instance, a, of MyRefClassR5.
# But suppose I want to add a new method called length.
# this is a handier way to add methods as it adds them to existing
# instances of the class - if this new method is added above in the
# setRefClass() generator, then subsequent instances of the object would
# have a length() method, but object a would be orphaned without it.
MyRefClassR5$methods(
length = function(){
len <- c(x = base::length(.self$x), y = base::length(.self$y))
s <- paste("length x =", len["x"], " length y =", len["y"])
speak(s)
return(len)
})
# can I use this method on instance a? Yup!
a$length()
#### END
> As you presumably already know, you can also implement this manually
> through the use of environments and S3 or S4 semantics. You might also
> be interested in Luke Tierney's comments on references in R:
>
> http://homepage.stat.uiowa.edu/~luke/R/references.html
>
> Cheers,
> Bert
>
> On Tue, Aug 14, 2012 at 2:07 AM, Jan T Kim <jtt...@googlemail.com> wrote:
>> On Mon, Aug 13, 2012 at 11:20:26PM -0300, Alexandre Aguiar wrote:
>>> Sachinthaka Abeywardana <sachin.abeyward...@gmail.com> escreveu:
>>>> Think you are missing the point,
>>>
>>> As lover of C-style pointers, I must admit that hiding complexities
>>> (and associated problems) of pointers is a great feature of all successful
>>> high level languages (HLLs). As much as they spare time and can be easily
>>> learned by non-programmers, they impose penalties in performance and
>>> memory consumption.
>>>
>>> Most drawbacks of HLLs have been effectively and efficiently addressed
>>> by a number of strategies in such a way that currently we have a wide
>>> variety of options. Languages have become tools to solve problems and,
>>> as such, we must pick the proper tool for each problem. That means the
>>> very first step is properly assessing the problem.
>>
>> yes, I quite agree. In my experience, the root of the trouble leading
>> to "how can I pass things by reference in R" requests is that many problems
>> involve objects that retain their identity while their attributes change in
>> a dynamic way. These are represented more adequately by having multiple
>> functions changing state of the same (identical!) object, rather than
>> approximating this by repeatedly replacing an object with an updated
>> copy of itself, or by using other "hacks".
>>
>> The overheads / inefficiencies that come with such hacks are really just
>> a consequence of an inadequate representation of the problem (i.e. "as
>> though one had not assessed it properly", if you will). As a further
>> indication that this is a design issue rather than one of optimisation
>> at the implementation level, notice that from a database perspective,
>> holding multiple copies that represent the same thing in memory amounts
>> to a denormalised design.
>>
>> Personally, I understand functional programming evangelists who object
>> to state and side effects because this "purism" is adequate (and also
>> often very elegant) for enabling parallel and distributed computing. But
>> noticing that this is not much of an issue for R (which e.g. doesn't
>> support multithreading much), I do think on a regular basis that
>> providing a mechanism enabling multiple references to one instance
>> would be an improvement that would not do too much damage.
>>
>> As it is, I've resigned to using other languages where I need an object
>> graph, and producing a first normal form type of table where I want to
>> do something in R. But I do get the feeling that I'm doing something
>> not quite right, and I frequently reiterate the problem analysis outlined
>> above to myself in order to put that funny feeling behind me.
>>
>> Just my 2 pence, Jan
>>
>>>
>>> My 2 cents.
>>>
>>>
>>> --
>>>
>>> Alexandre Aguiar, MD SCT
>>> SPS Consultoria
>>>
>>> --
>>> Sent from my tablet. Please, excuse my brevity.
>>> Enviado do tablet. Por favor, perdoe a brevidade.
>>> Publi?? de le tablet. S'il vous pla??t pardonnez la bri??vet??.
>>> Ver??ffentlicht aus dem Tablet. Bitte verzeihen Sie die K??rze.
>>> Enviado desde mi tablet. Por favor, disculpen mi brevedad.
>>> Inviato dal mio tablet. Per favore, scusate la mia brevit??.
>>>
>>> ______________________________________________
>>> 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.
>>
>> --
>> +- Jan T. Kim -------------------------------------------------------+
>> | email: jtt...@gmail.com |
>> | WWW: http://www.jtkim.dreamhosters.com/ |
>> *-----=< hierarchical systems are for files, not for humans >=-----*
>>
>> ______________________________________________
>> 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.
>
>
>
> --
>
> Bert Gunter
> Genentech Nonclinical Biostatistics
>
> Internal Contact Info:
> Phone: 467-7374
> Website:
> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
>
> ______________________________________________
> 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.
Ben Tupper
Bigelow Laboratory for Ocean Sciences
180 McKown Point Rd. P.O. Box 475
West Boothbay Harbor, Maine 04575-0475
http://www.bigelow.org
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