我应该在我的 package 中使用 S3 数据帧吗？

Question

I have a package which uses a data.frame based S4 class:

setClass(Class="foobar",
  slots=c(a="character", b="character", c="character"),
  contains="data.frame")

Works as intended. However, I observe weird warnings when combining with tidyverse:

df <- data.frame(ID=1:5)
df2 <- new("foobar", df)
as_tibble(df2)

The last statement incites a warning message:

Warning message:
In class(x) <- c(subclass, tibble_class) :
  Setting class(x) to multiple strings ("tbl_df", "tbl", ...); result will no longer be an S4 object

This is because tidyverse does not support S4 data frames . This can be circumvented in downstream code by using asS3(df) . However, users of my package may be puzzled if they see these warnings. I am now faced with the following choices and I don't really know which would be the most reasonable and correct:

• Keep the S4 model and hope that the users won't mind seeing this warning each time they pass my data frames into something else.
• Use S3. However, I already have another S4 class defined in published versions of my package. I am afraid that I would break someones code.
• Mix S3 and S4. Is it even allowed?

Is there another solution I might be overlooking?

Answer 1

There is no brilliant solution to this which is entirely within your control.

The tidyverse package may call class<- on any data-frame-like object given to it, and as you have seen this will destroy the S4 nature of any object. This can't be worked around by (for instance) defining a method for coerce or calling setAs , as class<- doesn't use that mechanism. ( class<- isn't generic either, you can't set a method for it.) The only way to make tidyverse support S4 is for tidyverse 's author to alter the code to use as or similar, and it doesn't look like that is top of their to-do-list.

You are correct to be worried about dramatically altering the way your class works when you have released a version of your package already with an S4 class.

If:

• your package is quite new and doesn't yet have many users;
• you can do all you need to do with S3; and
• you don't know of another package which has built new classes on top of yours

then it may be best to redefine it as S3, and include a message when your package is installed or loaded to say

thanks for installing myPackage v2. Code may be incompatible with v1.2 or earlier; see help(blah) for details

otherwise, stick with S4.

You can't exactly mix S3 and S4 for class definitions (you can for method definitions). The closest you can come is setOldClass which registers a S3 class as an S4 one (whereas you wanted the opposite). Still, that may help you achieve "you can do all you need to do with S3" above.

One other possibility is to define your own version of class<- which checks to see if an object of S4 class foobar is attempting to be coerced to S3 and calls the ordinary class<- if not. The cure is probably worse than the disease in this case; this will slow down all future S3 class conversions (since class<- is now an ordinary function call, not a primitive) but it should work in principle. Another reason that it is not recommended is that you are relying on no other package higher in the search path doing something similar (what if another package author had the same issue and wanted to do the same trick? Then the results would depend on which package was higher up the search path!)