You can use the duplicated()
function to find the unique combinations:
> df[!duplicated(df[1:3]),]
v1 v2 v3 v4 v5
1 7 1 A 100 98
2 7 2 A 98 97
3 8 1 C NA 80
6 9 3 C 75 75
To get only the duplicates, you can check it in both directions:
> df[duplicated(df[1:3]) | duplicated(df[1:3], fromLast=TRUE),]
v1 v2 v3 v4 v5
3 8 1 C NA 80
4 8 1 C 78 75
5 8 1 C 50 62