R: How to truly remove an S4 slot from an S4 object (Solution attached!)

Question

Let's say I define an S4 class 'foo' with two slots 'a' and 'b', and define an object x of class 'foo',

setClass(Class = 'foo', slots = c(
  a = 'numeric',
  b = 'character'
))
x <- new('foo', a = rnorm(1e3L), b = rep('A', times = 1e3L))
format(object.size(x), units = 'auto') # "16.5 Kb"

Then I want to remove slot 'a' from the definition of 'foo'

setClass(Class = 'foo', slots = c(
  b = 'character'
))
slotNames(x) # slot 'a' automatically removed!! wow!!!

I see that R automatically take cares my object x and have the slot 'a' removed. Nice! But wait, the size of object x is not reduced.

format(object.size(x), units = 'auto') # still "16.5 Kb"
format(object.size(new(Class = 'foo', x)), units = 'auto') # still "16.5 Kb"

Right.. Somehow 'a' is still there but I just cannot do anything to it

head(x@a) # `'a'` is still there
rm(x@a) # error
x@a <- NULL # error

So question: how can I really remove slot 'a' from x and have its size reduced (which is my primary concern)?

---

My deepest gratitude to all answers!

The following solution is inspired by dww

trimS4slot <- function(x) {
  nm0 <- names(attributes(x))
  nm1 <- names(getClassDef(class(x))@slots) # ?methods::.slotNames
  if (any(id <- is.na(match(nm0, table = c(nm1, 'class'))))) attributes(x)[nm0[id]] <- NULL  # ?base::setdiff
  return(x)
}
format(object.size(y1 <- trimS4slot(x)), units = 'auto') # "8.5 Kb"

The following solution is inspired by Robert Hijmans

setClass('foo1', contains = 'foo')
format(object.size(y2 <- as(x, 'foo1')), units = 'auto') # "8.5 Kb"

method::as probably does some comprehensive checks, so it's quite slow though

library(microbenchmark)
microbenchmark(trimS4slot(x), as(x, 'foo1')) # ?methods::as 10 times slower

Ceiling

Excellent question. I will save it for a rainy day. – Holzer

Rather than editing your question title to say "solution attached", please post the solution as an answer and "accept" the answer - that's the way everyone in this community is used to seeing solutions, and the formatting of the question will show that an answer has been accepted. Or, if Robert Hijman's answer is basically the solution you chose, accept his answer by clicking the checkmark in the left margin. – Haarlem

With this example, microbenchmarks shows that as takes 79 microseconds (about 12,500 runs per second) --- how is that "quite slow"? The other method is faster, but is saving 70 microseconds relevant to you? If it does, then perhaps use the fastest (by a small margin) and cleanest solution: x@b <- "" – Consensual

Thanks again for your suggestion Robert! I am updating thousands of saved simulation results on hard drive (readRDS, remove slot(s), saveRDS), so time really matters. Also this is only for package under development (i.e. only user is me), and I have removed the definition and usage of the said slot universally. Thanks again! – Ceiling

Answer 1

What @dww suggests is nifty, and answers your question. But isn't the point of a class that you are guaranteed that its members (the slots) will always be there? If you don't care about that you can use the anything goes S3 classes instead? With S4, I would suggest a more formal approach like this:

setClass(Class = 'bar', slots = c(b = 'character'))

setClass(Class = 'foo', contains='bar', slots = c(a = 'numeric'))

x <- new('foo', a = rnorm(1e3L), b = rep('A', times = 1e3L))
format(object.size(x), units = 'auto')
#[1] "16.5 Kb"

x <- as(x, "bar")  
format(object.size(x), units = 'auto')
#[1] "8.5 Kb"

And if this is just about size, why not just do

x <- new('foo', a = rnorm(1e3L), b = rep('A', times = 1e3L))
x@b <- ""
format(object.size(x), units = 'auto')
#[1] "8.7 Kb"

To me this is clearly the best solution because of its simplicity.

Consensual

Thank you very much! I have put your answer in the end of my question. – Ceiling

Answer 2

Slots are stored as attributes. We have a couple of options for converting a slot to NULL.

Option 1: You can use the check=FALSE argument in slot<- to assign a slot as NULL without triggering an error.

slot(x, 'a', check=FALSE) <- NULL
setClass(Class = 'foo', slots = c(b = 'character'))
format(object.size(x), units = 'auto') 
# [1] "8.7 Kb"

However, the attribute is not completely removed (it still exists with a value of \001NULL\001). This happens because of a line in the C function R_do_slot_assign, which has: if(isNull(value)) value = pseudo_NULL; where pseudo_NULL is "an object that is ...used to represent slots that are NULL (which an attribute can not be)".

One should also take notice of the advice in ?slot that "User's should not set check=FALSE in normal use, since the resulting object can be invalid." It should not cause any issues in this instance, since the slot is being removed immediately after. Nonetheless it is good to be cautious about using the check=False flag unless you are sure you understand what you are doing.

Option 2: A more complete removal can be achieved by directly removing the attribute after removing the slot from the class definition:

setClass(Class = 'foo', slots = c(
  b = 'character'
))
attr(x, 'a') <- NULL
format(object.size(x), units = 'auto') 
# [1] "8.7 Kb"

But, is removing slots even a good idea?

Removing slots is something of a hack that could cause errors later, e.g. if a method is called that assumes the existence of the slot. You might get away with doing this for a specific use case on your own machine. But releasing this into the wild as production code would not be a good idea. In that case, the approach in @RobertHijmans' answer would be the way to go.

Marriage

Thank you very much! I have put your answer in the end of my question. – Ceiling

Thanks for the note! Yes this is for developer (my own) use only. I will not do this for a published package. Thanks again! – Ceiling