s4

A simple example is that I have created an extension to show , which is a S4 base method. I don't want to cause a disambiguation fork by re-documenting show in my package, and I also want to consolidate the documentation of my extension to show in the documentation for the new class, myPkgSpClass , by adding an alias for show,myPkgSpClass-method . #' @export #' @aliases show,myPkgSpClass-method #' @rdname myPkgSpClass-class setMethod("show", "myPkgSpClass", function(object){ show(NA) }) The problem I'm having, is that this results in an serious warning during documentation-build by roxygen2,

I generate a plot using the package hexbin : # install.packages("hexbin", dependencies=T) library(hexbin) set.seed(1234) x <- rnorm(1e6) y <- rnorm(1e6) hbin <- hexbin( x = x , y = y , xbin = 50 , xlab = expression(alpha) , ylab = expression(beta) ) ## Using plot method for hexbin objects: plot(hbin, style = "nested.lattice") abline(h=0) This seems to generate an S4 object ( hbin ), which I then plot using plot . Now I'd like to add a horizontal line to that plot using abline , but unfortunately this gives the error: plot.new has not yet been called I have also no idea, how I can manipulate e

I am currently writing a package using reference classes. I have come across an issue which from reading various sources: Method initialisation in R reference classes Can't reliably use RefClass methods in Snowfall I gather is caused because reference methods are not all copied to every object in the class rather they are copied when first accessed. https://stat.ethz.ch/pipermail/r-devel/2011-June/061261.html As an example define: test <- setRefClass("TEST", fields = list( a = "numeric"), methods = list( addone = function(){ a <<- a+1 }, initialize = function(){ a <<- 1 } ) ) example <- test

Actual question How do I avoid Rd file name conflicts when a S4 generic and its method(s) are not necessarily all defined in the same package (package containing (some of) the custom method(s) depends on the package containing the generic) and using roxygenize() from package roxygen2 to generate the actual Rd files? I'm not sure if this is a roxygen2 problem or a common problem when the generic and its method(s) are scattered across packages (which IMHO in general definitely is a realistic use-case scenario if you follow a modular programming style). What's the recommended way to handle these

I have a S4 class and I would like to define the linear combination of these objects. Is it possible to dispatch * and + functions on this specific class? here is an example: setClass("yyy", representation(v="numeric")) setMethod("+", signature(e1 = "yyy", e2 = "yyy"), function (e1, e2) e1@v + e2@v) setMethod("+", signature(e1 = "yyy", e2 = "numeric"), function (e1, e2) e1@v + e2) then, > y1 <- new("yyy", v = 1) > y2 <- new("yyy", v = 2) > > y1 + y2 [1] 3 > y1 + 3 [1] 4 The + operator is part of the Arith group generic (see ?GroupGenericFunctions ) so one can implement all functions in the

While my question is related to this recent one , I suspect its answer(s) will have to do with the detailed workings of R's S4 object system. What I would expect: ( TLDR; -- All indications are that as(4L, "numeric") should dispatch to a function whose body uses as.numeric(4L) to convert it to a "numeric" vector.) Whenever one uses as(object, Class) to convert an object to the desired Class , one is really triggering a behind-the-scenes call to coerce() . coerce() , in turn, has a bunch of methods that are dispatched to based on the signature of the function call -- here the class of its first

My S4 class has a method that is called many times. I noticed that the execution time is much slower than it would be if a similar function was called independently. So I added a slot with type "function" to my class and used that function instead of the method. The example below shows two ways of doing this, and both of them run much faster than the corresponding method. Also, the example suggests that the lower speed of the method is not due to method having to retrieve data from the class, since the functions are faster even when they also do that. Of course, this way of doing things is not