Re: [R] Overriding predict based on newdata...
David: Thanks! Is it generally frowned upon (if I'm Incorporating this into a package) to override a generic function like predict, even if I plan on making it a pass-through function (same parameters, and if the data type doesn't match my weird data type, it will simply pass the parameters through to the generic S3 predict)? --j On Mon, Mar 17, 2014 at 4:08 AM, David Winsemius dwinsem...@comcast.net wrote: S3 classes only dispatch on the basis of the first parameter class. That was one of the reasons for the development of S4-classed objects. You say you have the expectation that the object is of a class that has an ordinary `predict` method presumably S3 in character, so you probably need to write a function that will mask the existing method. You would rewrite the existing test for the existence of 'newdata' and the the definition of the new function would persist through the rest of the session and could be source()-ed in further sessions. -- David. On Mar 16, 2014, at 2:09 PM, Jonathan Greenberg wrote: R-helpers: I'm having some trouble with this one -- I figure because I'm a bit of a noob with S3 classes... Here's my challenge: I want to write a custom predict statement that is triggered based on the presence and class of a *newdata* parameter (not the object parameter). The reason is I am trying to write a custom function based on an oddly formatted dataset that has been assigned an R class. If the predict function detects it (class(newdata) == myweirdformat) it does a conversion of the newdata to what most predict statements expect (e.g. a dataframe) and then passes the converted dataset along to the generic predict statement. If newdata is missing or is not of the odd class it should just pass everything along to the generic predict as usual. What would be the best way to approach this problem? Since (my understanding) is that predict is dispatched based on the object parameter, this is causing me confusion -- my object should still remain the model, I'm just allowing a new data type to be fed into the predict model(s). Cheers! --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ 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. David Winsemius Alameda, CA, USA -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ 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] Overriding predict based on newdata...
On Mon, Mar 17, 2014 at 4:08 AM, David Winsemius dwinsem...@comcast.netwrote: S3 classes only dispatch on the basis of the first parameter class. A minor distinction: S3 classes only dispatch on the basis on *one* of the parameters. The person who writes the generic gets to choose, and for predict() it is the first parameter, but it doesn't have to be for other generics. In model-fitting functions you often have formula= as the first argument and data= as the second, and it makes much more sense to dispatch on data= than on formula=. The first well-known example is probably MASS::loglm, used in S Programming to illustrate this issue but most of the methods in my survey package also dispatch based on the second argument. That was one of the reasons for the development of S4-classed objects. You say you have the expectation that the object is of a class that has an ordinary `predict` method presumably S3 in character, so you probably need to write a function that will mask the existing method. Or write an S4 method for predict and use setGeneric(). That's also not perfect: if everyone did it there would be lots of competing S4 generics with the same name, and too many people would have to understand how they are scoped. -thomas -- Thomas Lumley Professor of Biostatistics University of Auckland [[alternative HTML version deleted]] __ 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] Overriding predict based on newdata...
Jonathan:
As David said, this is a key aspect of S4 (there are others, of
course). But it can be simulated in S3, I think, albeit inelegantly.
You merely have to extend the class of object, the fitted object you
dispatch on, and then write an appropriate method for this extended
class. e.g.
## wholly untested!
class(obj)- c(mySpecial,class(obj)) ## extend class of fitted object
predict.mySpecial- function(object,newdata,...){
if(inherits(newdata,weirdClasss)){
... ## do something
}
else NextMethod() ## pass through to standard predict method
}
## Now this will work as desired:
predict(obj)
If this is obviously stupid -- or even not so obviously -- I would
appreciate someone pointing it out.
Best,
Bert
Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374
Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom.
H. Gilbert Welch
On Tue, Mar 18, 2014 at 7:28 AM, Jonathan Greenberg j...@illinois.edu wrote:
David:
Thanks! Is it generally frowned upon (if I'm Incorporating this into
a package) to override a generic function like predict, even if I
plan on making it a pass-through function (same parameters, and if the
data type doesn't match my weird data type, it will simply pass the
parameters through to the generic S3 predict)?
--j
On Mon, Mar 17, 2014 at 4:08 AM, David Winsemius dwinsem...@comcast.net
wrote:
S3 classes only dispatch on the basis of the first parameter class. That was
one of the reasons for the development of S4-classed objects. You say you
have the expectation that the object is of a class that has an ordinary
`predict` method presumably S3 in character, so you probably need to write
a function that will mask the existing method. You would rewrite the
existing test for the existence of 'newdata' and the the definition of the
new function would persist through the rest of the session and could be
source()-ed in further sessions.
--
David.
On Mar 16, 2014, at 2:09 PM, Jonathan Greenberg wrote:
R-helpers:
I'm having some trouble with this one -- I figure because I'm a bit of
a noob with S3 classes... Here's my challenge: I want to write a
custom predict statement that is triggered based on the presence and
class of a *newdata* parameter (not the object parameter). The
reason is I am trying to write a custom function based on an oddly
formatted dataset that has been assigned an R class. If the predict
function detects it (class(newdata) == myweirdformat) it does a
conversion of the newdata to what most predict statements expect (e.g.
a dataframe) and then passes the converted dataset along to the
generic predict statement. If newdata is missing or is not of the odd
class it should just pass everything along to the generic predict as
usual.
What would be the best way to approach this problem? Since (my
understanding) is that predict is dispatched based on the object
parameter, this is causing me confusion -- my object should still
remain the model, I'm just allowing a new data type to be fed into the
predict model(s).
Cheers!
--j
--
Jonathan A. Greenberg, PhD
Assistant Professor
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
259 Computing Applications Building, MC-150
605 East Springfield Avenue
Champaign, IL 61820-6371
Phone: 217-300-1924
http://www.geog.illinois.edu/~jgrn/
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007
__
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.
David Winsemius
Alameda, CA, USA
--
Jonathan A. Greenberg, PhD
Assistant Professor
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
259 Computing Applications Building, MC-150
605 East Springfield Avenue
Champaign, IL 61820-6371
Phone: 217-300-1924
http://www.geog.illinois.edu/~jgrn/
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007
__
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] Overriding predict based on newdata...
S3 classes only dispatch on the basis of the first parameter class. That was one of the reasons for the development of S4-classed objects. You say you have the expectation that the object is of a class that has an ordinary `predict` method presumably S3 in character, so you probably need to write a function that will mask the existing method. You would rewrite the existing test for the existence of 'newdata' and the the definition of the new function would persist through the rest of the session and could be source()-ed in further sessions. -- David. On Mar 16, 2014, at 2:09 PM, Jonathan Greenberg wrote: R-helpers: I'm having some trouble with this one -- I figure because I'm a bit of a noob with S3 classes... Here's my challenge: I want to write a custom predict statement that is triggered based on the presence and class of a *newdata* parameter (not the object parameter). The reason is I am trying to write a custom function based on an oddly formatted dataset that has been assigned an R class. If the predict function detects it (class(newdata) == myweirdformat) it does a conversion of the newdata to what most predict statements expect (e.g. a dataframe) and then passes the converted dataset along to the generic predict statement. If newdata is missing or is not of the odd class it should just pass everything along to the generic predict as usual. What would be the best way to approach this problem? Since (my understanding) is that predict is dispatched based on the object parameter, this is causing me confusion -- my object should still remain the model, I'm just allowing a new data type to be fed into the predict model(s). Cheers! --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ 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. David Winsemius Alameda, CA, USA __ 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] Overriding predict based on newdata...
R-helpers: I'm having some trouble with this one -- I figure because I'm a bit of a noob with S3 classes... Here's my challenge: I want to write a custom predict statement that is triggered based on the presence and class of a *newdata* parameter (not the object parameter). The reason is I am trying to write a custom function based on an oddly formatted dataset that has been assigned an R class. If the predict function detects it (class(newdata) == myweirdformat) it does a conversion of the newdata to what most predict statements expect (e.g. a dataframe) and then passes the converted dataset along to the generic predict statement. If newdata is missing or is not of the odd class it should just pass everything along to the generic predict as usual. What would be the best way to approach this problem? Since (my understanding) is that predict is dispatched based on the object parameter, this is causing me confusion -- my object should still remain the model, I'm just allowing a new data type to be fed into the predict model(s). Cheers! --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ 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.
