similar to: Documenting generic S4 replacement method for package building

I do lots of analyses on large microarray data sets so memory use and speed and both important issues for me. I have been trying to estimate the overheads associated with using formal S4 data objects instead of ordinary lists for large data objects. In some simple experiments (using R 1.7.1 in Windows 2000) with large but simple objects it seems that giving a data object a formal class

I feel tedious when I define a S4 class and the methods. For each method, I have to call both setMethod and setGeneric (or both setReplaceMethod and setGeneric). I would like a more compact grammar so that I can reduce the key strokes. I'm wondering if there is a better way available. setClass( Class='A', representation=representation( x='numeric' )

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Hi R friends,   I'm still studying S4 classes and I have a question about slot assignment. Why would I have to use a special setter method [example 2 below] if I can assign data to a slot directly when I call new() [example 1 below]?   ## first way to do it (the idiosyncratic way?) setClass(Class = "TestClass", representation = representation(myDf = "data.frame"))

For documentation we use a system that generates Rd files from special comments in the code. (inlinedocs). It is crucial to be able to get the defining source code for objects like methods to extract the comments from it. Here is an R session that shows how this works for several kinds of methods and (at the end of the session) how if fails for methods of "initialize" >

Hi all, I'm trying to come to grips with how to document S4 methods using ROxygen - mostly following posts such as this: http://tinyurl.com/ae3kdno I just can't get it to work (this is roxygen2_2.2.2). I attach an example below which seems parsed properly, but "R CMD check" keeps complaining > ... > Undocumented S4 methods: > ... > generic 'set<-' and

Dear all, Assume that I have an S4 class "MyClass" with a slot "myname", which is initialized to: myname="" in method("initialize"): myclass <- new("MyClass", myname="") Assume that class "MyClass" has a method "mymethod": "mymethod.MyClass" <- function(object, myname=character(0), ...) {

Hi all, I'm trying to implement the matrix multiplication operator, which is S4 generic, for an old-style S3 class. The following works as expected: x <- 1:10 class(x) <- "myClass" setOldClass("myClass") setGeneric("myMethod", function(x, y) standardGeneric("myMethod")) setMethod("myMethod", c("myClass", "myClass"),

Hi I have the code like I show below. The problem here is that I have a setReplacementMethod to set the value of my class slot. However, this function doesn't work when I call it within another function definition (declared by setMethod) of the same class. I do not understand this behavior that much. I'm wondering how to make this work? Any help would be really appreciated. Thank you.

The %*% function is a primitive. As it says in the documentation under ?Methods_Details Methods may be defined for most primitives, and corresponding metadata objects will be created to store them. Calls to the primitive still go directly to the C code, which will sometimes check for applicable methods. The definition of ?sometimes? is that methods must have been detected

Hi, I recognized that the function 'setReplaceMethod' is creating a character vector in the user workspace having the name (e.g. "newClass") of the class used as value. If you can sort out a mistake by myself, I would like you to file a bug report. BBFN, Jonathan setClass("newClass", representation(value="numeric")) setMethod(f = "initialize",

Hi, I recognized that the function 'setReplaceMethod' is creating a character vector in the user workspace having the name (e.g. "newClass") of the class used as value. If you can sort out a mistake by myself, I would like you to file a bug report. BBFN, Jonathan setClass("newClass", representation(value="numeric")) setMethod(f = "initialize",

>>>>> Jonathan Fritzemeier <clausjonathan.fritzemeier at uni-duesseldorf.de> >>>>> on Fri, 23 Jun 2017 16:15:30 +0200 writes: > Hi, > I recognized that the function 'setReplaceMethod' is creating a > character vector in the user workspace having the name (e.g. "newClass") > of the class used as value. If you can

List, In order to get rid of some old, unreadable S3 code in package sp, I'm trying to rewrite things using S4 methods. Somewhere I fail, and I cannot sort out why. In order to isolate the problem, I created two functions, doNothing<- and dosth, and both should do nothing. The issue is that in most cases they do nothing, but in some cases dosth(obj) changes the class of obj and breaks with

Dear all Below is the code for "scriptPreFilter.R" which gives the following result: > source("scriptPreFilter.R") > prefltr <- new("PreFilter", mad=c(0.5,0.01)) [1] "------initialize:PreFilter------" [1] "------initialize:Filter------" > str(prefltr) Formal class 'PreFilter' [package ".GlobalEnv"] with 2 slots

Hello, promptMethods generate a macro for signatures, but the macro does not exist in the Rd parser. > setClass("track", + representation(x="numeric", y="numeric")) [1] "track" > setGeneric("foo", function(x){ standardGeneric("foo") } ) [1] "foo" > setMethod( "foo", "track",

Hi, I'm new to this mailing list and to R-programming so if the question is stupid I apologize. I have to create a package, which includes an S4-class called "BList". For objects of this class I implemented a method "show", which displays the first 15 data-lines of the object. I further implemented a method "showall", which displays the whole data in the object.

Hi, I'm developing in S4 and I wanted to see the methods for a specific class using showMethods but I didn't succed. Can someone help ? See the example below. setClass("myclass", representation( name ="character" ) ) setGeneric("mymeth", function(obj, ...){ standardGeneric("mymeth") } ) setMethod("mymeth",

Dear R users, I am writing my first R package and it finally past the R CMD check. Before sending it to CRAN, I would like to check a few issues. 1. I created s4 classes and methods in the package but I want only 1 function (foo) to be available to users and documented in the manual that goes with the package. I put foo in 1 file and the rest (internal functions, classes and methods) in a

Hi- I used to use "<<-" to do assignment inside a class method, and just found that now it is broken in R 2.0. For example, the following code ----------------------------------------------------------------------- setClass( "myclass", representation(x="numeric") ) setGeneric("incrXByOne", function(obj) standardGeneric("incrXByOne"))