Re: [R] Google's R Style Guide (has become S3 vs S4, in part)
Martin Morgan mtmor...@fhcrc.org on Tue, 01 Sep 2009 09:07:05 -0700 writes: spencerg wrote: Bryan Hanson wrote: Looks like the discussion is no longer about R Style, but S3 vs S4? yes nice topic rename! To that end, I asked more or less the same question a few weeks ago, arising from the much the same motivations. The discussion was helpful, here's the link: http://www.nabble.com/Need-Advice%3A-Considering-Converting-a-Package-from-S 3-to-S4-tc24901482.html#a24904049 For what it's worth, I decided, but with some ambivalence, to stay with S3 for now and possibly move to S4 later. In the spirit of S4, I did write a function that is nearly the equivalent of validObject for my S3 object of interest. Overall, it looked like I would have to spend a lot of time moving to S4, while staying with S3 would allow me to get the project done and get results going much faster (see Frank Harrell's comment in the thread above). Bryan's original post started me thinking about this, but I didn't respond. I'd classify myself as an 'S4' 'expert', with my ignorance of S3 obvious from Duncan's corrections to my earlier post. It's hard for me to make a comparative statement about S3 vs. S4, and hard really to know what is 'hard' for someone new to S4, to R, to programming, ... I would have classified most of the responses in that thread as coming from 'S3' 'experts'. As a concrete example (concrete for us non-programmers, non-statisticians), I recently decided that I wanted to add a descriptive piece of text to a number of my plots, and it made sense to include the text with the object. So I just added a list element to the existing S3 object, e.g. Myobject$descrip No further work was necessary, I could use it right away. If instead, if I had made Myobject an S4 object, then I would have to go back, redefine the object, update validObject, and possibly write some new accessor and definitely constructor functions. At least, that's how I understand the way one uses S4 classes. This is a variant of Gabor's comment, I guess, that it's easy to modify S3 on an as-needed basis. In S3, forgoing any pretext of 'best practices', one might s3 - structure(list(x=1:10, y=10:1), class=MyS3Object) ## some lines of code... if (aTest) s3$descraption - A description (either 'description' or 'discraption' is a typo, uncaught by S3). In S4 I'd have to change my class definition from setClass(MyS4Object, representation(x=numeric, y=numeric)) to setClass(MyS4Object, representation(x=numeric, y=numeric, description=character)) but the body of the code would look surprising similar s4 - new(MyS4Object, x=1:10, y=10:1) ## some lines of code... if (aTest) s...@description - A description (no typo, because I'd have been told that the slot 'discraption' didn't exist). In the S3 case the (implicit) class definition is a single line, perhaps nested deep inside a function. In S4 the class definition is in a single location. Best practices might make me want to have a validity method (x and y the same dimensions? 'description' of length 1?), to use a constructor and accessors (to provide an abstraction to separate the interface from its implementation), etc., but those issues are about best practices. A downstream consequence is that s4 always has a 'description' slot (perhaps initialized with an appropriate default in the 'prototype' argument of setClass, but that's more advanced), whereas s3 only sometimes has 'description'. So I'm forced to check is.null(s3$description) whenever I'm expecting a character vector. It doesn't stop there: If you keep the same name for your redefined S4 class, I don't know what happens when you try to access stored objects of that class created before the change, but it might not be pretty. If you give your redefined S4 class a different name, then Actually, the old object is loaded in R. It is not valid (validObject(originalS4) would complain about 'slots in class definition not in object'). One might write an 'updateObject' generic and method that detects and corrects this. This contrasts with S3, where there is no knowing whether the object is consistent with the current (implicit) class definition. you have a lot more code to change before you can use the redefined class like you want. For slot addition, this is not true -- old code works fine. For slot removal / renaming, this is analogous to S3 -- code needs reworking; use of accessors might help isolate code using the class from the implementation of the class. A couple of
Re: [R] Google's R Style Guide (has become S3 vs S4, in part)
Looks like the discussion is no longer about R Style, but S3 vs S4? To that end, I asked more or less the same question a few weeks ago, arising from the much the same motivations. The discussion was helpful, here's the link: http://www.nabble.com/Need-Advice%3A-Considering-Converting-a-Package-from-S 3-to-S4-tc24901482.html#a24904049 For what it's worth, I decided, but with some ambivalence, to stay with S3 for now and possibly move to S4 later. In the spirit of S4, I did write a function that is nearly the equivalent of validObject for my S3 object of interest. Overall, it looked like I would have to spend a lot of time moving to S4, while staying with S3 would allow me to get the project done and get results going much faster (see Frank Harrell's comment in the thread above). As a concrete example (concrete for us non-programmers, non-statisticians), I recently decided that I wanted to add a descriptive piece of text to a number of my plots, and it made sense to include the text with the object. So I just added a list element to the existing S3 object, e.g. Myobject$descrip No further work was necessary, I could use it right away. If instead, if I had made Myobject an S4 object, then I would have to go back, redefine the object, update validObject, and possibly write some new accessor and definitely constructor functions. At least, that's how I understand the way one uses S4 classes. Back to trying to get something done! Bryan * Bryan Hanson Professor of Chemistry Biochemistry DePauw University, Greencastle IN USA On 9/1/09 6:16 AM, Duncan Murdoch murd...@stats.uwo.ca wrote: Corrado wrote: Thanks Duncan, Spencer, To clarify, the situation is: 1) I have no reasons to choose S3 on S4 or vice versa, or any other coding convention 2) Our group has not done any OO developing in R and I would be the first, so I can set up the standards 3) I am starting from scratch with a new package, so I do not have any code I need to re-use. 4) I am an R OO newbie, so whatever I can learn from the beginning what is better and good for me. So the questions would be two: 1) What coding style guide should we / I follow? Is the google style guide good, or is there something better / more prescriptive which makes our research group life easier? I don't think I can answer that. I'd recommend planning to spend some serious time on the decision, and then go by your personal impression. S4 is definitely harder to learn but richer, so don't make the decision too quickly. Take a look at John Chamber's new book, try small projects in each style, etc. 2) What class type should I use? From what you two say, I should use S3 because is easier to use what are the disadvantages? Is there an advantages / disadvantages table for S3 and S4 classes? S3 is much more limited than S4. It dispatches on just one argument, S4 can dispatch on several. S3 allows you to declare things to be of a certain class with no checks that anything will actually work; S4 makes it easier to be sure that if you say something is of a certain class, it really is. S4 hides more under the hood: if you understand how regular R functions work, learning S3 is easy, but there's still a lot to learn before you'll be able to use S4 properly. Duncan Murdoch __ 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. __ 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] Google's R Style Guide (has become S3 vs S4, in part)
Bryan Hanson wrote: Looks like the discussion is no longer about R Style, but S3 vs S4? To that end, I asked more or less the same question a few weeks ago, arising from the much the same motivations. The discussion was helpful, here's the link: http://www.nabble.com/Need-Advice%3A-Considering-Converting-a-Package-from-S 3-to-S4-tc24901482.html#a24904049 For what it's worth, I decided, but with some ambivalence, to stay with S3 for now and possibly move to S4 later. In the spirit of S4, I did write a function that is nearly the equivalent of validObject for my S3 object of interest. Overall, it looked like I would have to spend a lot of time moving to S4, while staying with S3 would allow me to get the project done and get results going much faster (see Frank Harrell's comment in the thread above). As a concrete example (concrete for us non-programmers, non-statisticians), I recently decided that I wanted to add a descriptive piece of text to a number of my plots, and it made sense to include the text with the object. So I just added a list element to the existing S3 object, e.g. Myobject$descrip No further work was necessary, I could use it right away. If instead, if I had made Myobject an S4 object, then I would have to go back, redefine the object, update validObject, and possibly write some new accessor and definitely constructor functions. At least, that's how I understand the way one uses S4 classes. It doesn't stop there: If you keep the same name for your redefined S4 class, I don't know what happens when you try to access stored objects of that class created before the change, but it might not be pretty. If you give your redefined S4 class a different name, then you have a lot more code to change before you can use the redefined class like you want. By contrast, with S3, if you have any code that tests the number of components in a list, that will have to be changed. Spencer Back to trying to get something done! Bryan * Bryan Hanson Professor of Chemistry Biochemistry DePauw University, Greencastle IN USA On 9/1/09 6:16 AM, Duncan Murdoch murd...@stats.uwo.ca wrote: Corrado wrote: Thanks Duncan, Spencer, To clarify, the situation is: 1) I have no reasons to choose S3 on S4 or vice versa, or any other coding convention 2) Our group has not done any OO developing in R and I would be the first, so I can set up the standards 3) I am starting from scratch with a new package, so I do not have any code I need to re-use. 4) I am an R OO newbie, so whatever I can learn from the beginning what is better and good for me. So the questions would be two: 1) What coding style guide should we / I follow? Is the google style guide good, or is there something better / more prescriptive which makes our research group life easier? I don't think I can answer that. I'd recommend planning to spend some serious time on the decision, and then go by your personal impression. S4 is definitely harder to learn but richer, so don't make the decision too quickly. Take a look at John Chamber's new book, try small projects in each style, etc. 2) What class type should I use? From what you two say, I should use S3 because is easier to use what are the disadvantages? Is there an advantages / disadvantages table for S3 and S4 classes? S3 is much more limited than S4. It dispatches on just one argument, S4 can dispatch on several. S3 allows you to declare things to be of a certain class with no checks that anything will actually work; S4 makes it easier to be sure that if you say something is of a certain class, it really is. S4 hides more under the hood: if you understand how regular R functions work, learning S3 is easy, but there's still a lot to learn before you'll be able to use S4 properly. Duncan Murdoch __ 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. __ 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. -- Spencer Graves, PE, PhD President and Chief Operating Officer Structure Inspection and Monitoring, Inc. 751 Emerson Ct. San José, CA 95126 ph: 408-655-4567 __ 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] Google's R Style Guide (has become S3 vs S4, in part)
spencerg wrote:
Bryan Hanson wrote:
Looks like the discussion is no longer about R Style, but S3 vs S4?
yes nice topic rename!
To that end, I asked more or less the same question a few weeks ago,
arising
from the much the same motivations. The discussion was helpful,
here's the
link:
http://www.nabble.com/Need-Advice%3A-Considering-Converting-a-Package-from-S
3-to-S4-tc24901482.html#a24904049
For what it's worth, I decided, but with some ambivalence, to stay
with S3
for now and possibly move to S4 later. In the spirit of S4, I did
write a
function that is nearly the equivalent of validObject for my S3 object of
interest.
Overall, it looked like I would have to spend a lot of time moving to S4,
while staying with S3 would allow me to get the project done and get
results
going much faster (see Frank Harrell's comment in the thread above).
Bryan's original post started me thinking about this, but I didn't
respond. I'd classify myself as an 'S4' 'expert', with my ignorance of
S3 obvious from Duncan's corrections to my earlier post. It's hard for
me to make a comparative statement about S3 vs. S4, and hard really to
know what is 'hard' for someone new to S4, to R, to programming, ... I
would have classified most of the responses in that thread as coming
from 'S3' 'experts'.
As a concrete example (concrete for us non-programmers,
non-statisticians),
I recently decided that I wanted to add a descriptive piece of text to a
number of my plots, and it made sense to include the text with the
object.
So I just added a list element to the existing S3 object, e.g.
Myobject$descrip No further work was necessary, I could use it right
away.
If instead, if I had made Myobject an S4 object, then I would have to go
back, redefine the object, update validObject, and possibly write some
new
accessor and definitely constructor functions. At least, that's how I
understand the way one uses S4 classes.
This is a variant of Gabor's comment, I guess, that it's easy to modify
S3 on an as-needed basis. In S3, forgoing any pretext of 'best
practices', one might
s3 - structure(list(x=1:10, y=10:1), class=MyS3Object)
## some lines of code...
if (aTest)
s3$descraption - A description
(either 'description' or 'discraption' is a typo, uncaught by S3).
In S4 I'd have to change my class definition from
setClass(MyS4Object, representation(x=numeric, y=numeric))
to
setClass(MyS4Object, representation(x=numeric, y=numeric,
description=character))
but the body of the code would look surprising similar
s4 - new(MyS4Object, x=1:10, y=10:1)
## some lines of code...
if (aTest)
s...@description - A description
(no typo, because I'd have been told that the slot 'discraption' didn't
exist). In the S3 case the (implicit) class definition is a single line,
perhaps nested deep inside a function. In S4 the class definition is in
a single location.
Best practices might make me want to have a validity method (x and y the
same dimensions? 'description' of length 1?), to use a constructor and
accessors (to provide an abstraction to separate the interface from its
implementation), etc., but those issues are about best practices.
A downstream consequence is that s4 always has a 'description' slot
(perhaps initialized with an appropriate default in the 'prototype'
argument of setClass, but that's more advanced), whereas s3 only
sometimes has 'description'. So I'm forced to check
is.null(s3$description) whenever I'm expecting a character vector.
It doesn't stop there: If you keep the same name for your
redefined S4 class, I don't know what happens when you try to access
stored objects of that class created before the change, but it might not
be pretty. If you give your redefined S4 class a different name, then
Actually, the old object is loaded in R. It is not valid
(validObject(originalS4) would complain about 'slots in class definition
not in object'). One might write an 'updateObject' generic and method
that detects and corrects this. This contrasts with S3, where there is
no knowing whether the object is consistent with the current (implicit)
class definition.
you have a lot more code to change before you can use the redefined
class like you want.
For slot addition, this is not true -- old code works fine. For slot
removal / renaming, this is analogous to S3 -- code needs reworking; use
of accessors might help isolate code using the class from the
implementation of the class.
A couple of comments on Duncan's
S3Foo - function(x=numeric(), y=numeric()) {
structure(list(x=as.numeric(x), y=as.numeric(y)), class=S3Foo)
}
I used makeS3Foo to emphasize that it was a constructor, but in my own
code I use S3Foo(). Realizing that, as Henrik has now also pointed out,
I'm far from perfect, the use of as.numeric() combines validity checking
and coercion, which I think is not usually a good thing (even when
efficient). In particular this
as.numeric(factor(c(one, two, three)))
