R version 2.7.0 Under development (unstable) (2008-01-31 r44280)
Copyright (C) 2008 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ##--- S4 Methods (and Classes)
> options(useFancyQuotes=FALSE)
> library(methods)
> ##too fragile: showMethods(where = "package:methods")
> 
> ##-- S4 classes with S3 slots [moved from ./reg-tests-1.R]
> setClass("test1", representation(date="POSIXct"))
[1] "test1"
> x <- new("test1", date=as.POSIXct("2003-10-09"))
> stopifnot(format(x @ date) == "2003-10-09")
> ## line 2 failed in 1.8.0 because of an extraneous space in "%in%"
> 
> stopifnot(all.equal(3:3, 3.), all.equal(1., 1:1))
> 
> ## trace (requiring methods):
> f <- function(x, y) { c(x,y)}
> xy <- 0
> trace(f, quote(x <- c(1, x)), exit = quote(xy <<- x), print = FALSE)
[1] "f"
> fxy <- f(2,3)
> stopifnot(identical(fxy, c(1,2,3)))
> stopifnot(identical(xy, c(1,2)))
> untrace(f)
> 
> ## a generic and its methods
> 
> setGeneric("f")
[1] "f"
> setMethod("f", c("character", "character"), function(x,	 y) paste(x,y))
[1] "f"
> 
> ## trace the generic
> trace("f", quote(x <- c("A", x)), exit = quote(xy <<- c(x, "Z")), print = FALSE)
[1] "f"
> 
> ## should work for any method
> 
> stopifnot(identical(f(4,5), c("A",4,5)),
+           identical(xy, c("A", 4, "Z")))
> 
> stopifnot(identical(f("B", "C"), paste(c("A","B"), "C")),
+           identical(xy, c("A", "B", "Z")))
> 
> ## trace a method
> trace("f", sig = c("character", "character"), quote(x <- c(x, "D")),
+       exit = quote(xy <<- xyy <<- c(x, "W")), print = FALSE)
[1] "f"
> 
> stopifnot(identical(f("B", "C"), paste(c("A","B","D"), "C")))
> # These two got broken by Luke's lexical scoping fix
> #stopifnot(identical(xy, c("A", "B", "D", "W")))
> #stopifnot(identical(xy, xyy))
> 
> ## but the default method is unchanged
> stopifnot(identical(f(4,5), c("A",4,5)),
+           identical(xy, c("A", 4, "Z")))
> 
> removeGeneric("f")
[1] TRUE
> ## end of moved from trace.Rd
> 
> 
> ## print/show dispatch  [moved from  ./reg-tests-2.R ]
> ## The results  have waffled back and forth.
> ## Currently (R 2.4.0) the intent is that automatic printing of S4
> ## objects should correspond to a call to show(), as per the green
> ## book, p. 332.  Therefore, the show() method is called, once defined,
> ## for auto-printing foo, regardless of the S3 or S4 print() method.
> setClass("bar", representation(a="numeric"))
[1] "bar"
> foo <- new("bar", a=pi)
> foo
An object of class "bar"
Slot "a":
[1] 3.141593

> show(foo)
An object of class "bar"
Slot "a":
[1] 3.141593

> print(foo)
An object of class "bar"
Slot "a":
[1] 3.141593

> 
> setMethod("show", "bar", function(object){cat("show method\n")})
[1] "show"
> show(foo)
show method
> foo
show method
> print(foo)
show method
> # suppressed because output depends on current choice of S4 type or
> # not.  Can reinstate when S4 type is obligatory
> # print(foo, digits = 4)
> 
> print.bar <- function(x, ...) cat("print method\n")
> foo
show method
> print(foo)
print method
> show(foo)
show method
> 
> setMethod("print", "bar", function(x, ...){cat("S4 print method\n")})
Creating a new generic function for "print" in ".GlobalEnv"
[1] "print"
> foo
show method
> print(foo)
S4 print method
> show(foo)
show method
> ## calling print() with more than one argument suppresses the show()
> ## method, largely to prevent an infinite loop if there is in fact no
> ## show() method for this class.  A better solution would be desirable.
> print(foo, digits = 4)
S4 print method
> 
> setClassUnion("integer or NULL", members = c("integer","NULL"))
[1] "integer or NULL"
> setClass("c1", representation(x = "integer", code = "integer or NULL"))
[1] "c1"
> nc <- new("c1", x = 1:2)
> str(nc)# gave ^ANULL^A in 2.0.0
Formal class 'c1' [package ".GlobalEnv"] with 2 slots
  ..@ x   : int [1:2] 1 2
  ..@ code: NULL
> ##
> 
> 
> library(stats4)
> showMethods("coerce", classes=c("matrix", "numeric"))
Function: coerce (package methods)
from="ANY", to="matrix"
from="ANY", to="numeric"

> ## {gave wrong result for a while in R 2.4.0}
> 
> ## the following showMethods() output tends to generate errors in the tests
> ## whenever the contents of the packages change. Searching in the
> ## diff's can easily mask real problems.  If there is a point
> ## to the printout, e.g., to verify that certain methods exist,
> ## hasMethod() would be a useful replacement
> 
> ## showMethods(where = "package:stats4")
> ## showMethods("show")
> ## showMethods("show")
> ## showMethods("plot") # (ANY,ANY) and (profile.mle, missing)
> ## showMethods(classes="mle")
> ## showMethods(classes="matrix")
> 
> 
> ##--- "[" fiasco before R 2.2.0 :
> d2 <- data.frame(b= I(matrix(1:6,3,2)))
> ## all is well:
> d2[2,]
     [,1] [,2]
[1,]    2    5
> stopifnot(identical(d2[-1,], d2[2:3,]))
> ## Now make "[" into S4 generic by defining a trivial method
> setClass("Mat", representation(Dim = "integer", "VIRTUAL"))
[1] "Mat"
> setMethod("[", signature(x = "Mat",
+ 			 i = "missing", j = "missing", drop = "ANY"),
+ 	  function (x, i, j, drop) x)
[1] "["
> ## Can even remove the method: it doesn't help
> removeMethod("[", signature(x = "Mat",
+                             i = "missing", j = "missing", drop = "ANY"))
[1] TRUE
> d2[1:2,] ## used to fail badly; now okay
     [,1] [,2]
[1,]    1    4
[2,]    2    5
> stopifnot(identical(d2[-1,], d2[2:3,]))
> ## failed in R <= 2.1.x
> 
> 
> ## Fritz' S4 "odditiy"
> setClass("X", representation(bar="numeric"))
[1] "X"
> setClass("Y", contains="X")
[1] "Y"
> ## Now we define a generic foo() and two different methods for "X" and
> ## "Y" objects for arg missing:
> setGeneric("foo", function(object, arg) standardGeneric("foo"))
[1] "foo"
> setMethod("foo", signature(object= "X", arg="missing"),
+           function(object, arg) cat("an X object with bar =", object@bar, "\n"))
[1] "foo"
> setMethod("foo", signature(object= "Y", arg="missing"),
+           function(object, arg) cat("a Y object with bar =", object@bar, "\n"))
[1] "foo"
> ## Finally we create a method where arg is "logical" only for class
> ## "X", hence class "Y" should inherit that:
> setMethod("foo", signature(object= "X", arg= "logical"),
+           function(object, arg) cat("Hello World!\n") )
[1] "foo"
> ## now create objects and call methods:
> y <- new("Y", bar=2)
> ## showMethods("foo")
> foo(y)
a Y object with bar = 2 
> foo(y, arg=TRUE)## Hello World!
Hello World!
> ## OK, inheritance worked, and we have
> ## showMethods("foo")
> foo(y)
a Y object with bar = 2 
> ## still 'Y' -- was 'X object' in R < 2.3
> 
> 
> ## Multiple inheritance
> setClass("A", representation(x = "numeric"))
[1] "A"
> setClass("B", representation(y = "character"))
[1] "B"
> setClass("C", contains = c("A", "B"), representation(z = "logical"))
[1] "C"
> new("C")
An object of class "C"
Slot "z":
logical(0)

Slot "x":
numeric(0)

Slot "y":
character(0)

> setClass("C", contains = c("A", "B"), representation(z = "logical"),
+          prototype = prototype(x = 1.5, y = "test", z = TRUE))
[1] "C"
> (cc <- new("C"))
An object of class "C"
Slot "z":
[1] TRUE

Slot "x":
[1] 1.5

Slot "y":
[1] "test"

> ## failed reconcilePropertiesAndPrototype(..) after svn r37018
> 
> 
> ## "Logic" group -- was missing in R <= 2.4.0
> stopifnot(all(getGroupMembers("Logic") %in% c("&", "|")),
+ 	  any(getGroupMembers("Ops") == "Logic"))
> setClass("brob", contains="numeric")
[1] "brob"
> b <- new("brob", 3.14)
> logic.brob.error <- function(nm)
+     stop("logic operator '", nm, "' not applicable to brobs")
> logic2 <- function(e1,e2) logic.brob.error(.Generic)
> setMethod("Logic", signature("brob", "ANY"), logic2)
[1] "Logic"
> setMethod("Logic", signature("ANY", "brob"), logic2)
[1] "Logic"
> ## Now ensure that using group members gives error:
> assertError <- function(expr)
+     stopifnot(inherits(try(expr, silent = TRUE), "try-error"))
> assertError(b & b)
Warning message:
Ambiguous method selection for "&", target "brob#brob" (the first of the signatures shown will be used)
    brob#ANY
    ANY#brob
 
> assertError(b | 1)
> assertError(TRUE & b)
> 
> 
> ## methods' hidden cbind() / rbind:
> cBind <- methods:::cbind
> setClass("myMat", representation(x = "numeric"))
[1] "myMat"
> setMethod("cbind2", signature(x = "myMat", y = "missing"), function(x,y) x)
[1] "cbind2"
> m <- new("myMat", x = c(1, pi))
> stopifnot(identical(m, cBind(m)))
> 
> 
> ## explicit print or show on a basic class with an S4 bit
> ## caused infinite recursion
> setClass("Foo", representation(name="character"), contains="matrix")
[1] "Foo"
> (f <- new("Foo", name="Sam", matrix()))
An object of class "Foo"
     [,1]
[1,]   NA
Slot "name":
[1] "Sam"

> (m <- as(f, "matrix"))
     [,1]
[1,]   NA
> show(m)
     [,1]
[1,]   NA
> print(m)
     [,1]
[1,]   NA
> ## fixed in 2.5.0 patched
> 
> ## callGeneric inside a method with new arguments {hence using .local()}:
> setGeneric("Gfun", function(x, ...) standardGeneric("Gfun"),
+ 	   useAsDefault = function(x, ...) sum(x, ...))
[1] "Gfun"
> setClass("myMat", contains="matrix")
[1] "myMat"
> setClass("mmat2", contains="matrix")
[1] "mmat2"
> setClass("mmat3", contains="mmat2")
[1] "mmat3"
> setMethod(Gfun, signature(x = "myMat"),
+ 	  function(x, extrarg = TRUE) {
+ 	      cat("in 'myMat' method for 'Gfun() : extrarg=", extrarg, "\n")
+ 	      Gfun(unclass(x))
+ 	  })
[1] "Gfun"
attr(,"package")
[1] ".GlobalEnv"
> setMethod(Gfun, signature(x = "mmat2"),
+ 	  function(x, extrarg = TRUE) {
+ 	      cat("in 'mmat2' method for 'Gfun() : extrarg=", extrarg, "\n")
+ 	      x <- unclass(x)
+ 	      callGeneric()
+ 	  })
[1] "Gfun"
attr(,"package")
[1] ".GlobalEnv"
> setMethod(Gfun, signature(x = "mmat3"),
+ 	  function(x, extrarg = TRUE) {
+ 	      cat("in 'mmat3' method for 'Gfun() : extrarg=", extrarg, "\n")
+ 	      x <- as(x, "mmat2")
+ 	      callGeneric()
+ 	  })
[1] "Gfun"
attr(,"package")
[1] ".GlobalEnv"
> wrapG <- function(x, a1, a2) {
+     myextra <- missing(a1) && missing(a2)
+     Gfun(x, extrarg = myextra)
+ }
> 
> (mm <- new("myMat", diag(3)))
An object of class "myMat"
     [,1] [,2] [,3]
[1,]    1    0    0
[2,]    0    1    0
[3,]    0    0    1
> Gfun(mm)
in 'myMat' method for 'Gfun() : extrarg= TRUE 
[1] 3
> stopifnot(identical(wrapG(mm),    Gfun(mm, TRUE)),
+           identical(wrapG(mm,,2), Gfun(mm, FALSE)))
in 'myMat' method for 'Gfun() : extrarg= TRUE 
in 'myMat' method for 'Gfun() : extrarg= TRUE 
in 'myMat' method for 'Gfun() : extrarg= FALSE 
in 'myMat' method for 'Gfun() : extrarg= FALSE 
> 
> Gfun(mm, extrarg = FALSE)
in 'myMat' method for 'Gfun() : extrarg= FALSE 
[1] 3
> m2 <- new("mmat2", diag(3))
> Gfun(m2)
in 'mmat2' method for 'Gfun() : extrarg= TRUE 
[1] 3
> Gfun(m2, extrarg = FALSE)
in 'mmat2' method for 'Gfun() : extrarg= FALSE 
[1] 3
> ## The last two gave Error ...... variable ".local" was not found
> (m3 <- new("mmat3", diag(3)))
An object of class "mmat3"
     [,1] [,2] [,3]
[1,]    1    0    0
[2,]    0    1    0
[3,]    0    0    1
> Gfun(m3)
in 'mmat3' method for 'Gfun() : extrarg= TRUE 
in 'mmat2' method for 'Gfun() : extrarg= TRUE 
[1] 3
> Gfun(m3, extrarg = FALSE) # used to not pass 'extrarg'
in 'mmat3' method for 'Gfun() : extrarg= FALSE 
in 'mmat2' method for 'Gfun() : extrarg= FALSE 
[1] 3
> 
> ## -- a variant of the above which failed in version <= 2.5.1 :
> setGeneric("Gf", function(x, ...) standardGeneric("Gf"))
[1] "Gf"
> setMethod(Gf, signature(x = "mmat2"),
+           function(x, ...) {
+               cat("in 'mmat2' method for 'Gf()\n")
+               x <- unclass(x)
+               callGeneric()
+           })
[1] "Gf"
attr(,"package")
[1] ".GlobalEnv"
> setMethod(Gf, signature(x = "mmat3"),
+           function(x, ...) {
+               cat("in 'mmat3' method for 'Gf()\n")
+               x <- as(x, "mmat2")
+               callGeneric()
+           })
[1] "Gf"
attr(,"package")
[1] ".GlobalEnv"
> setMethod(Gf, signature(x = "matrix"),
+ 	  function(x, a1, ...) {
+               cat(sprintf("matrix %d x %d ...\n", nrow(x), ncol(x)))
+               list(x=x, a1=a1, ...)
+           })
[1] "Gf"
attr(,"package")
[1] ".GlobalEnv"
> 
> wrap2 <- function(x, a1, ...) {
+     A1 <- if(missing(a1)) "A1" else as.character(a1)
+     Gf(x, ..., a1 = A1)
+ }
> ## Gave errors in R 2.5.1 :
> wrap2(m2, foo = 3.14)
in 'mmat2' method for 'Gf()
matrix 3 x 3 ...
$x
     [,1] [,2] [,3]
[1,]    1    0    0
[2,]    0    1    0
[3,]    0    0    1

$a1
[1] "A1"

$foo
[1] 3.14

> wrap2(m2, 10, answer.all = 42)
in 'mmat2' method for 'Gf()
matrix 3 x 3 ...
$x
     [,1] [,2] [,3]
[1,]    1    0    0
[2,]    0    1    0
[3,]    0    0    1

$a1
[1] "10"

$answer.all
[1] 42

> 
> 
> ## regression tests of dispatch: most of these became primitive in 2.6.0
> setClass("c1", "numeric")
[1] "c1"
> setClass("c2", "numeric")
[1] "c2"
> x_c1 <- new("c1")
> # the next failed < 2.5.0 as the signature in .BasicFunsList was wrong
> setMethod("as.character", "c1", function(x, ...) "fn test")
[1] "as.character"
> as.character(x_c1)
[1] "fn test"
> 
> setMethod("as.integer", "c1", function(x, ...) 42)
[1] "as.integer"
> as.integer(x_c1)
[1] 42
> 
> setMethod("as.logical", "c1", function(x, ...) NA)
[1] "as.logical"
> as.logical(x_c1)
[1] NA
> 
> setMethod("as.complex", "c1", function(x, ...) pi+0i)
[1] "as.complex"
> as.complex(x_c1)
[1] 3.141593+0i
> 
> setMethod("as.raw", "c1", function(x) as.raw(10))
[1] "as.raw"
> as.raw(x_c1)
[1] 0a
> 
> # as.numeric sets methods on all the equivalent functions
> setMethod("as.numeric", "c1", function(x, ...) 42+pi)
[1] "as.numeric"
> as.numeric(x_c1)
[1] 45.14159
> as.double(x_c1)
[1] 45.14159
> as.real(x_c1)
[1] 45.14159
> showMethods(as.numeric)
Function: as.numeric (package base)
x="c1"

> showMethods(as.double)
Function: as.numeric (package base)
x="c1"

> showMethods(as.real)
Function: as.numeric (package base)
x="c1"

> 
> setMethod(as.double, "c2", function(x, ...) x@.Data+pi)
[1] "as.numeric"
> x_c2 <- new("c2", pi)
> as.numeric(x_c2)
[1] 6.283185
> showMethods(as.numeric)
Function: as.numeric (package base)
x="c1"
x="c2"

> 
> promptClass("c1", stdout())# want all methods
\name{c1-class}
\docType{class}
\alias{c1-class}
\alias{as.character,c1-method}
\alias{as.complex,c1-method}
\alias{as.integer,c1-method}
\alias{as.logical,c1-method}
\alias{as.numeric,c1-method}
\alias{as.raw,c1-method}

\title{Class "c1" ~~~ }
\description{	 ~~ A concise (1-5 lines) description of what the class is.  ~~}
\section{Objects from the Class}{
Objects can be created by calls of the form \code{new("c1", ...)}.
	 ~~ describe objects here ~~ 
}
\section{Slots}{
	 \describe{
    \item{\code{.Data}:}{Object of class \code{"numeric"} ~~ }
  }
}
\section{Extends}{
Class \code{"\linkS4class{numeric}"}, from data part.
Class \code{"\linkS4class{vector}"}, by class "numeric", distance 2.
}
\section{Methods}{
  \describe{
    \item{as.character}{\code{signature(x = "c1")}: ... }
    \item{as.complex}{\code{signature(x = "c1")}: ... }
    \item{as.integer}{\code{signature(x = "c1")}: ... }
    \item{as.logical}{\code{signature(x = "c1")}: ... }
    \item{as.numeric}{\code{signature(x = "c1")}: ... }
    \item{as.raw}{\code{signature(x = "c1")}: ... }
	 }
}
\references{ ~put references to the literature/web site here ~ }
\author{ ~~who you are~~ }
\note{ ~~further notes~~ }

 ~Make other sections like Warning with \section{Warning }{....} ~

\seealso{
	~~objects to See Also as \code{\link{~~fun~~}}, ~~~
	or \code{\linkS4class{CLASSNAME}} for links to other classes
}
\examples{
showClass("c1")
}
\keyword{classes}
A shell of class documentation has been written to the 
connection 'stdout'.
 
> 
> ## '!' changed signature from 'e1' to 'x' in 2.6.0
> setClass("foo", "logical")
[1] "foo"
> setMethod("!", "foo", function(e1) e1+NA)
[1] "!"
Warning message:
argument in method definition changed from (e1) to (x) 
> selectMethod("!", "foo")
Method Definition:

function (x) 
x + NA

Signatures:
        x    
target  "foo"
defined "foo"
> xx <- new("foo", FALSE)
> !xx
An object of class "foo"
[1] NA
> 
> ## This failed for about one day -- as.vector(x, mode) :
> setMethod("as.vector", signature(x = "foo", mode = "missing"),
+           function(x) unclass(x))
Creating a new generic function for "as.vector" in ".GlobalEnv"
[1] "as.vector"
> ## whereas this fails in R versions earlier than 2.6.0:
> setMethod("as.vector", "foo", function(x) unclass(x))# gives message
In method for function "as.vector": expanding the signature 
to include omitted arguments in definition: mode = "missing" 
[1] "as.vector"
> 
> ## stats4::AIC in R < 2.7.0 used to clobber stats::AIC
> pfit <- function(data) {
+     m <- mean(data)
+     loglik <- sum(dpois(data, m))
+     ans <- list(par = m, loglik = loglik)
+     class(ans) <- "pfit"
+     ans
+ }
> AIC.pfit <- function(object, ..., k = 2) -2*object$loglik + k
> AIC(pfit(1:10))
[1] 0.05867604
> library(stats4)
> AIC(pfit(1:10)) # failed in R < 2.7.0
[1] 0.05867604
> 
> ## For a few days (~ 2008-01-30), this failed to work without any notice:
> setClass("Mat",  representation(Dim = "integer","VIRTUAL"))
[1] "Mat"
> setClass("dMat", representation(x = "numeric",  "VIRTUAL"), contains = "Mat")
[1] "dMat"
> setClass("CMat", representation(dnames = "list","VIRTUAL"), contains = "Mat")
[1] "CMat"
> setClass("dCMat", contains = c("dMat", "CMat"))
[1] "dCMat"
> stopifnot(!isVirtualClass("dCMat"),
+ 	  length(slotNames(new("dCMat"))) == 3)
> 
>