Question

I am making a package where I want to define a new method for plot. I am using roxygen in-source documentation. This question seems very similar to:
How to properly document a S3 method of a generic from a different package, using Roxygen?
and
Roxygen2 – how to properly document S3 methods
but I still cannot get it to work.

The relevant parts that are causing me trouble are:

#' Generic plot method
#'
#' @param x \dots
#' @param ... \dots
#' @export
plot <- function(x, ...) UseMethod("plot")

#' Default plot method
#'
#' @param x \dots
#' @param ... \dots
#' @importFrom graphics plot
#' @method plot default
#' @S3method plot default
plot.default <- function(x, ...) graphics::plot(x, ...)

#' Plotting function for ABI object
#'
#' Description.
#' 
#' @param x ABI object as generated by newABI.
#' @param base Character. Bases to look at.
#' @param ... Other options passed to plot().
#' @return Nothing. Side-effect: plots graphs.
#' @method plot ABI
#' @S3method plot ABI
plot.ABI <- function(x, base, ...) {
#Overly simplified
plot(1, 1, main = base)
}

When I run this and investigate methods(plot), there is no method defined for ABI objects. Accessing the function by ABI:::plot (ABI is the name of the package) does work. Using :: does not.

During the package build check, there is a warning:

* checking S3 generic/method consistency ... WARNING
plot:
  function(x)
plot.ABI:
  function(x, base, ...)
See section ‘Generic functions and methods’ of the ‘Writing R
Extensions’ manual.

It seems that there is a disagreement in arguments. But I don’t understand this, since the generic has arguments x and … and so does my ABI method (in addition to base).

So there are two problems, which I hope stem from the same issue: The plot.ABI method is not exported and the package check throws a warning.

How do I solve this?

Answer 1

A few problems:

1. Don’t include a generic that is already defined elsewhere. Just add your method.

2. The signatures of every method must at least include every element in the generic, in the same order. It’s annoying sometimes, but it’s incontrovertible.

Update

I had said, “Your @export needs to list the function name,” but apparently this is not correct. See the comments. Note also that listing the method should export it. I seem to recall needing an explicit export in cases where you aren’t including the generic in your package’s namespace, but I could be wrong (so often am!).