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Parlamis Franklin

2005-Dec-29 05:52 UTC

[R] trouble with S4 methods for group "Summary"

Hello.  This question concerns the Methods package.  I have created a  
new class and am trying to set a method for it for S4 group generic  
"Summary".  I have run into some signature problems.  An example:

	> setClass("track", representation(x="numeric",
y="character"))
	[1] "track"
	> setGeneric("max", group="Summary")
	[1] "max"
	> setMethod("Summary", signature(x="track"), function(x,
..., na.rm)
callGeneric(x at x, ..., na.rm))
	[1] "Summary"
	> dd<-new("track", x=c(1,2), y="abc")
	> max(dd)
	[1] -Inf
	Warning message:
	no finite arguments to max; returning -Inf
	> showMethods("max")
	
	Function "max":
	na.rm = "ANY"
	na.rm = "track"
	na.rm = "missing"
	    (inherited from na.rm = "ANY")

As you can see from the above, the method I tried to set for  
"max" (via "Summary") was defined for the formal argument
"na.rm" not
"x".  This makes sense because the standardGeneric created for max  
only allows methods to be defined for argument "na.rm"

	> max
	standardGeneric for "max" defined from package "base"
   	belonging to group(s): Summary
	
	function (..., na.rm = FALSE)
	standardGeneric("max")
	<environment: 0x19447a28>
	Methods may be defined for arguments: na.rm

However, group "Summary" purports to allow you to define methods for  
arguments "x" and "na.rm".

	> Summary
	groupGenericFunction for "Summary" defined from package
"base"
	
	function (x, ..., na.rm = FALSE)
	stop("function 'Summary' is a group generic; do not call it
directly",
	    domain = NA)
	<environment: 0x16aef098>
	Methods may be defined for arguments: x, na.rm

How does this work?  Can someone point me to where I am going wrong,  
and explain how to define S4 methods for group "Summary" for argument
"x"?  Perhaps I need to do more in my "setGeneric" call? 
Thanks in
advance.

Martin Maechler

2005-Dec-29 21:22 UTC

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[R] trouble with S4 methods for group "Summary"

Yes, setting 'Summary'  S4 group methods is a bit painful,
because the S3 generic starts with "...".

In the 'Matrix' CRAN package,
we do the following  {thanks to hints by John Chambers IIRC}:

Our AllGeneric.R file
(https://svn.R-project.org/R-packages/trunk/Matrix/R/AllGeneric.R)
ends with

###---- Group Generics ----
## The following are **WORKAROUND** s currently needed for all non-Primitives:

##  "Math"
setGeneric("log", group="Math")
setGeneric("gamma", group="Math")
setGeneric("lgamma", group="Math")

## "Math2"
setGeneric("round",  group="Math2")
setGeneric("signif", group="Math2")

## "Summary" --- this needs some hoop jumping that may become
unnecessary
##               in a future version of R (>= 2.3.x):

.max_def <- function(x, ..., na.rm = FALSE) base::max(x, ..., na.rm = na.rm)
.min_def <- function(x, ..., na.rm = FALSE) base::min(x, ..., na.rm = na.rm)
.range_def <- function(x, ..., na.rm = FALSE) base::range(x, ..., na.rm =
na.rm)
.prod_def <- function(x, ..., na.rm = FALSE) base::prod(x, ..., na.rm =
na.rm)
.sum_def <- function(x, ..., na.rm = FALSE) base::sum(x, ..., na.rm = na.rm)
.any_def <- function(x, ..., na.rm = FALSE) base::any(x, ..., na.rm = na.rm)
.all_def <- function(x, ..., na.rm = FALSE) base::all(x, ..., na.rm = na.rm)

setGeneric("max", function(x, ..., na.rm = FALSE)
standardGeneric("max"),
           useAsDefault = .max_def, group = "Summary")
setGeneric("min", function(x, ..., na.rm = FALSE)
standardGeneric("min"),
           useAsDefault = .min_def, group="Summary")
setGeneric("range", function(x, ..., na.rm = FALSE)
standardGeneric("range"),
           useAsDefault = .range_def, group="Summary")
setGeneric("prod", function(x, ..., na.rm = FALSE)
standardGeneric("prod"),
           useAsDefault = .prod_def, group="Summary")
setGeneric("sum", function(x, ..., na.rm = FALSE)
standardGeneric("sum"),
           useAsDefault = .sum_def, group="Summary")
setGeneric("any", function(x, ..., na.rm = FALSE)
standardGeneric("any"),
           useAsDefault = .any_def, group="Summary")
setGeneric("all", function(x, ..., na.rm = FALSE)
standardGeneric("all"),
           useAsDefault = .all_def, group="Summary")

##-------------------------

and then in dMatrix.R we have

## This needs extra work in ./AllGeneric.R :
setMethod("Summary", signature(x = "dMatrix", na.rm =
"ANY"),
          function(x, ..., na.rm) callGeneric(x at x, ..., na.rm = na.rm))


I think you can safely follow this recipe;

Regards,
Martin Maechler, ETH Zurich

>>>>> "Parlamis" == Parlamis Franklin <fparlamis at
mac.com>
>>>>>     on Wed, 28 Dec 2005 19:52:00 -1000 writes:
    Parlamis> Hello.  This question concerns the Methods
    Parlamis> package.  I have created a new class and am trying
    Parlamis> to set a method for it for S4 group generic
    Parlamis> "Summary".  I have run into some signature
    Parlamis> problems.  An example:

    >> setClass("track", representation(x="numeric",
    >> y="character"))
    Parlamis> 	[1] "track"
    >> setGeneric("max", group="Summary")
    Parlamis> 	[1] "max"
    >> setMethod("Summary", signature(x="track"),
function(x,
    >> ..., na.rm)
    Parlamis> callGeneric(x at x, ..., na.rm)) [1] "Summary"
    >> dd<-new("track", x=c(1,2), y="abc") max(dd)
    Parlamis> 	[1] -Inf Warning message: no finite arguments to
    Parlamis> max; returning -Inf
    >> showMethods("max")
	
    Parlamis> 	Function "max": na.rm = "ANY" na.rm =
"track"
    Parlamis> na.rm = "missing" (inherited from na.rm =
"ANY")

    Parlamis> As you can see from the above, the method I tried
    Parlamis> to set for "max" (via "Summary") was
defined for
    Parlamis> the formal argument "na.rm" not "x".  This
makes
    Parlamis> sense because the standardGeneric created for max
    Parlamis> only allows methods to be defined for argument
    Parlamis> "na.rm"

    >> max
    Parlamis> 	standardGeneric for "max" defined from package
    Parlamis> "base" belonging to group(s): Summary
	
    Parlamis> 	function (..., na.rm = FALSE)
    Parlamis> standardGeneric("max") <environment:
0x19447a28>
    Parlamis> Methods may be defined for arguments: na.rm

    Parlamis> However, group "Summary" purports to allow you to
    Parlamis> define methods for arguments "x" and
"na.rm".

    >> Summary
    Parlamis> 	groupGenericFunction for "Summary" defined from
    Parlamis> package "base"
	
    Parlamis> 	function (x, ..., na.rm = FALSE) stop("function
    Parlamis> 'Summary' is a group generic; do not call it
    Parlamis> directly", domain = NA) <environment: 0x16aef098>
    Parlamis> Methods may be defined for arguments: x, na.rm

    Parlamis> How does this work?  Can someone point me to where
    Parlamis> I am going wrong, and explain how to define S4
    Parlamis> methods for group "Summary" for argument
"x"?
    Parlamis> Perhaps I need to do more in my "setGeneric" call?
    Parlamis> Thanks in advance.

    Parlamis> ______________________________________________
    Parlamis> R-help at stat.math.ethz.ch mailing list
    Parlamis> https://stat.ethz.ch/mailman/listinfo/r-help
    Parlamis> PLEASE do read the posting guide!
    Parlamis> http://www.R-project.org/posting-guide.html

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