s4

I want to create a class in R, should I use S3 or S4 class? I read a lot of different things about them, is there one superior to the other one? S3 can only dispatch on it's first argument, whereas S4 can dispatch on multiple arguments. If you want to be able to write methods for function foo that should do different things if given an object of class "bar" or given objects of class "bar" and "foobar" , or given objects of class "barfoo" and "foobar" , then S4 provides a far better way to handle such complexities. S3 is very simple and easy to implement, but isn't really a formal object

How would a person dput() an S4 object? I tried this require(sp) require(splancs) plot(0, 0, xlim = c(-100, 100), ylim = c(-100, 100)) poly.d <- getpoly() #draw a pretty polygon - PRETTY! poly.d <- rbind(poly.d, poly.d[1,]) # close the polygon because of Polygons() and its kin poly.d <- SpatialPolygons(list(Polygons(list(Polygon(poly.d)), ID = 1))) poly.d dput(poly.d) Notice that if I dput() an S4 object, I cannot reconstruct it again. Your thoughts? As it currently stands, you cannot dput this object. The code of dput contains the following loop: if (isS4(x)) { cat("new(\"", class(x), "\"\n",

Possible Duplicate: R: show source code of an S4 function in a package I downloaded a package ( GEOquery ) and was playing with some of the functions. One of them is called Table , which, to my understanding, is able to tabulate an S4 dataset. E.g. > summary(GDS2853) # GDS2853 is a dataset I downloaded from NCBI Length Class Mode 1 GDS S4 getAnywhere(Table) shows > getAnywhere(Table) A single object matching ‘Table’ was found It was found in the following places package:GEOquery namespace:GEOquery with value function (object) standardGeneric("Table") <environment: 0x06ad5268> attr(,"generic")

I'm working with wavelets on a program and I'm used the package wavelets to create the DWT of a time series using the function dwt . This function returns an object of class dwt , which is a S4 object with many slots: W , V , levels , filter , and so on. How can I access the W 's as a vector? Ari B. Friedman @ will let you access the slots of an S4 object. So if your object is called wave , then wave@W should get you your vector. Note that often the best way to do this is to not access the slot directly but rather through an accessor function (e.g. coefs() rather than digging out the

I am trying to add a spatial method to merge which needs to be S4 (since it dispatches on the types of two different objects). I have tried using an earlier solution as follows: #' Merge a SpatialPolygonsDataFrame with a data.frame #' @param SPDF A SpatialPolygonsDataFrame #' @param df A data.frame #' @param \dots Parameters to pass to merge.data.frame #' #' @export #' @docType methods #' @rdname merge-methods setGeneric("merge", function(SPDF, df, ...){ cat("generic dispatch\n") standardGeneric("merge") }) #' @rdname merge-methods #' @aliases merge,SpatialPolygonsDataFrame,data.frame-method

Is it possible to create an S4 class, where one or more of the slots can be of multiple classes? For example. Let's say that you had a situation where data could be either a vector, or a data.frame. exampleClass <- setClass("exampleClass", representation(raw=c("data.frame","numeric","character"), anotherSlot=c("data.frame","numeric")) Or, is this the type of situation where defining a sub-class / super-class becomes necessary? PS: Searching for a useful tutorial on S4 classes produces limited results. Links to a good tutorial on S4 class creation/usage/documentation would be greatly

Below I posted a mini example in which I want do write documentation for an “[“ method for a S4 class. Does someone know how to properly document a method for the generic "[" using roxygen and S4? I get a warning when checking the package after building (see below). #' An S4 class that stores a string. #' @slot a contains a string #' @export setClass("testClass", representation(a="character")) #' extract method for testClass #' #' @docType methods #' @rdname extract-methods setMethod("[", signature(x = "testClass", i = "ANY", j="ANY"), function (x, i, j, ..., drop){ print("void function") } )