R seems duplicated() to select the wrong duplicates - r

Question

I've noticed a couple of times now that when I'm using R to identify duplicates, sometimes it seems to identify the wrong cases.
Here's a data frame that has three columns, each which may be holding duplicate values. I want to isolate the cases that are duplicates of another case on all three variables.
set.seed(100)
test <- data.frame(id = sample(1:15, 20, replace = TRUE),
cat1 = sample(letters[1:2], 20, replace = TRUE),
cat2 = sample(letters[1:2], 20, replace = TRUE))
Which gives me:
id cat1 cat2
1 5 b a
2 4 b b
3 9 b b
4 1 b b
5 8 a b
6 8 a a
7 13 b b
8 6 b b
9 9 b a
10 3 a a
11 10 a a
12 14 b a
13 5 a a
14 6 b a
15 12 b b
16 11 b a
17 4 a a
18 6 b a
19 6 b b
20 11 a a
I've tried this a couple of ways, such as:
duplicated(test$id) & duplicated(test$cat1) & duplicated(test$cat2)
But this just results in the same as duplicated(test$id):
[1] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE
[17] TRUE TRUE TRUE TRUE
So instead I tried duplicated(test$id, test$cat1, test$cat2), which produces different results:
[1] TRUE TRUE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE
[17] FALSE TRUE FALSE FALSE
But is still incorrect - if I call these cases from the data frame we get:
> test[which(duplicated(test$id, test$cat1, test$cat2)),]
id cat1 cat2
1 5 b a
2 4 b b
3 9 b b
5 8 a b
8 6 b b
14 6 b a
16 11 b a
18 6 b a
As you can see these are not the rows we should be getting (were it doing what I'd have thought it would do), which should be (as far as I can see):
18 6 b a
19 6 b b
Does anyone know why it's coming up with these results, and where I'm going wrong using it? Is there a simple (ideally non-verbose) way of doing this?

Answer 1

We need to apply duplicated on a data.frame or matrix or vector
i1 <- duplicated(test[c('id', 'cat1')])
i2 <- duplicated(cbind(test$id, test$cat1))
identical(i1, i2)
#[1] TRUE
and not on more than one data.frame or matrix or vector
i3 <- duplicated(test$id, test$cat1)
identical(i1, i3)
#[1] FALSE
It is specified in the documents of ?duplicated
duplicated(x, incomparables = FALSE, ...)
where
x a vector or a data frame or an array or NULL.
and not 'x1', 'x2', etc..
As #Aaron mentioned in the comments, to subset the duplicates from the OP's data
test[duplicated(test),]
and if we wanted only the duplicates, then
test[duplicated(test)|duplicated(test, fromLast = TRUE),]

Answer 2

Taking duplicates of columns separately is not the same as taking duplicates of a data frame or matrix. This example makes it more clear:
df = data.frame(x = c(1,2,1),
y = c(1,3,3))
df$dupe = duplicated(df$x) & duplicated(df$y)
df$dupe2 = duplicated(df[,c("x","y")])
df
Using your method, duplicated says "When I hit the third row, x already had a 1 so it's duplicated. y already had a 3 so it's duplicated." This doesn't mean that it already saw a row where x = 1 and y = 3.