similar to: Suppressing "creating new generic" and "expanding the signature" messages

I noticed this oddity about [ and setMethod. First, I define testFunc, which sorts a data frame by the first column and returns the entries that aren't NAs, and testIt, which runs testFunc repeatedly on a random large data frame, each time saving the return into a dummy placeholder (for demonstration's sake). > require(methods) Loading required package: methods [1] TRUE > testFunc

I noticed this oddity about [ and setMethod. First, I define testFunc, which sorts a data frame by the first column and returns the entries that aren't NAs, and testIt, which runs testFunc repeatedly on a random large data frame, each time saving the return into a dummy placeholder (for demonstration's sake). > require(methods) Loading required package: methods [1] TRUE > testFunc

My question has two parts. The first is with regard to the frame or environment in which generic functions are defined in packages. It seems as though they are defined (i.e. exist as objects) in frame 1, even when defined in a package. The following is a short example: setClass("track",representation(x="numeric",y="numeric")) plotTrack <- function(x,y,...)

This seemed too advanced for r-help and is related to the recent discussion of character vectors in dataframes. Following Brian Ripley's most excellent advice, we are moving to a world in which character vectors in dataframes are always of class AsIs. The cool way of doing this seemed to be the following: > cat(c("x", "y", "z"), file = "test.txt",

Full_Name: Tim Keitt Version: 1.5 OS: Linux Submission from: (NULL) (128.227.201.237) The function "setMethod" makes the following call to "insertMethod": allMethods <- insertMethod(allMethods, signature, fnames[1:length(signature)], asMethodDefinition(definition, signature)) If I understand insertMethod correctly, the third argument should be the names of the

I'm trying to create a package for working on orientation data, i.e. data where the observations are 3D rotations. There are several different representations of orientations in common use: SO(3) matrices, Euler angles, unit quaternions, etc. One thing I'd like is to make it convenient to work in any representation, and have conversions to others done as needed. I'm trying to do

I noticed this oddity about R profiling and setMethod. First, I "test out" Rprof. > require(methods) Loading required package: methods [1] TRUE > > Rprof("test.out") > data.frame("a") X.a. 1 a > Rprof(NULL) So far, so good. Next, I define myClass. > setClass("myClass", representation(mySlot = "numeric")) [1]

Hello, Thomas Stabla (statho3@web.de) has already sent this question to R-help, Wed, 12 Nov 2003 21:21:31 +0100, but we are not sure whether we should better post this mail to this audience than to R-help: --------------------------------------------------------------------- We are using S4-classes and want to force a validity check when an object is created. How can this be done, when an

Hi, I don't understand why this code doesn't work (f(b2)): ///////////////// setClass("B0", representation(b0 = "numeric")) setClass("B1", representation("B0", b1 = "character")) setClass("B2", representation("B1", b2 = "logical")) f <- function(x) class(x) setMethod("f", "B0",

Hi, while playing with the `methods' package I was not able to find what the recommended way of dealing with the following problem is. Suppose there is a generic function `foo' and two functions `foo.default' and `foo.formula', in the classical way: foo <- function(y, ...) UseMethod("foo") foo.default <- function(y, ...) {} foo.formula <- function(formula,

Hi! Trying to reproduce some examples from "Programming with Data" page 341. Can not reproduce it neither on R1.8.1. nor R1.9.0devel? library(methods) setClass("track",representation(x="numeric",y="numeric")) setMethod("[" ,"track" ,function(x,...,drop=T){ track(x at x[...],y at y[...]) }

Hello, I have defined a new class > setClass("myclass", representation(min = "numeric", max = "numeric")) and want to write accessor functions, so that for > foo = new("myclass", min = 0, max = 1) > min(foo) # prints 0 > max(foo) # prints 1 At first i created a generic function for "min" > setGeneric("min",

I have some questions about S4 style methods and generics. First of all, is there any way of using default values for arguments in the generics/methods? My own experiments show that such arguments are always ignored. The green book seems to be silent on this matter. The second question is about using a non-trivial function body for generics. Page 351 of the green book gives an example of this

Full_Name: Henrik Bengtsson Version: R v1.4.1 OS: WinMe Submission from: (NULL) (217.208.14.137) Doing the following library(methods) setGeneric("foo", function(x) standardGeneric("foo")) setMethod("foo", "ANY", function(x) cat(x)) fails with Error in while (value[n] == "ANY") n <- n - 1 : missing value where logical needed It

Full_Name: Colin A. Smith Version: 1.8.0 OS: Mac OS X 10.2.6 Submission from: (NULL) (216.102.90.18) Both Biobase and my package annaffy use S4 classes to define methods for "[". Both packages use the save image method of installation. (See annaffy 1.0.3 in BioC CVS.) Depending on how both packages are loaded, the Biobase definitions seem to be getting masked out: >

I have been writing some S4 classes and have a problem about how I might pass a signature to "c()". Take the following example: setClass("collection", representation("list", date="POSIXt")) x <- new("collection", list(1,2,3), date=Sys.time()) y <- new("collection", list(4,5,6), date=Sys.time()) obviously, I can do c(x,y), but

Hi, we have some questions concerning the definition of new arithmetic methods. In our package "distr" (on CRAN) we define some new arithmetic methods for "+", "-", "*", "/". After loading "distr" the corresponding arithmetic methods work. Now, if we define a new class and also a new method for one of the arithmetic methods

1. I'm putting together my first package that uses S4 classes and objects. I'd like to document them, but I'm not sure what the documentation should look like, and package.skeleton doesn't produce any at all for the classes or methods. Are there any good examples to follow? 2. How do I do the equivalent of debug(foo), when foo is an anonymous function being used as a method?

I'm trying to write a package which uses classes/methods as defined in the `methods' package. I have a single .R file which defines the class and various methods for that class. At the top of the file I have require(methods) and then setClass("myclass", ...) setGeneric("intersect") setMethod("intersect", "myclass", function(x,y) ...) I noticed

Hello, I've stumbled upon following problem, when trying to overload the methods for group Math for an S4-class which contains functions as slots. setClass("NumFunction", representation = list(fun = "function")) NumFunction <- function(f) new("NumFunction", fun = f) square <- function(x) x^2 NF <- NumFunction(square)