Why your S3 method isn’t working

June 15, 2018
By

(This article was first published on That’s so Random, and kindly contributed to R-bloggers)

Throughout the last years I noticed the following happening with a number of people. One of those people was actually yours truely a few years back. Person is aware of S3 methods in R through regular use of print, plot and summary functions and decides to give it a go in own work. Creates a function that assigns a class to its output and then implements a bunch of methods to work on the class. Strangely, some of these methods appear to be working as expected, while others throw an error. After a confusing and painful debugging session, person throws hands in the air and continues working without S3 methods. Which was working fine in the first place. This is a real pity, because all the person is overlooking is a very small step in the S3 chain: the generic function.

A nonworking method

So we have a function doing all kinds of complicated stuff. It outputs a list with several elements. We assign a S3 class to it before returning, so we can subsequently implement a number of methods1. Lets just make something up here.

my_func <- function(x) {
  ret <- list(dataset = x, 
              d = 42, 
              y = rnorm(10), 
              z = c('a', 'b', 'a', 'c'))
  class(ret) <- "myS3"
  ret
}
out <- my_func(mtcars)

Perfect, now lets implement a print method. Rather than outputting the whole list, we just want to know the most vital information when printing.

print.myS3 <- function(x) {
  cat("Original dataset has", nrow(x$dataset), "rows and",
      ncol(x$dataset), "columns\n", 
      "d is", x$d)
}
out
## Original dataset has 32 rows and 11 columns
##  d is 42

Ha, that is working!. Now we do a mean method, that gives us the mean of the y variable.

mean.myS3 <- function(x) {
  mean(x$y)
}
mean(out)
## [1] 0.2631094

Works too! And finally we do a count_letters method. It takes z from the output and counts how often each letter occurs.

count_letters.myS3 <- function(x) {
  table(out$z)
}
count_letters(out)
## Error in count_letters(out): could not find function "count_letters"

What do you mean “could not find function”? It is right there! Maybe we made a typo. Mmmm, no it doesn’t seem so. Maybe, mmmm, lets look into this…. Half an hour, a bit of swearing and feelings of stupidity later. Pfff, lets not bother about S3, we were happy with just using functions in the first place.

Generics

Now why are print and mean working just fine, but count_letters isn’t? Lets look under the hood of print and mean.

print
## function (x, ...) 
## UseMethod("print")
## 
## 
mean
## function (x, ...) 
## UseMethod("mean")
## 
## 

They look exactly the same! They call the UseMethod function on their own function name. Looking into the help file of UseMethod, it all of a sudden starts to make sense.

“When a function calling UseMethod(“fun”) is applied to an object with class attribute c(“first”, “second”), the system searches for a function called fun.first and, if it finds it, applies it to the object. If no such function is found a function called fun.second is tried. If no class name produces a suitable function, the function fun.default is used, if it exists, or an error results.”

So by calling print and mean on the myS3 object we were not calling the method itself. Rather, we call the general functions print and mean (the generics) and they call the function UseMethod. This function then does the method dispatch: lookup the method belonging to the S3 object the function was called on. We were just lucky the print and mean generics were already in place and called our methods. However, the count_letters function indeed doesn’t exist (as the error message tells us). Only the count_letters method exist, for objects of class myS3. We just learned that methods cannot get called directly, but are invoked by generics. All we need to do, thus, is build a generic for count_letters and we are all set.

count_letters <- function(x) {
  UseMethod("count_letters")
}
count_letters(out)
## 
## a b c 
## 2 1 1
  1. It is actually ill-advised to assign a S3 class directly to an output. Rather use a constructor, see 16.3.1 of Advanced R for the how and why. 

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