I am trying to use a data.table within a function, and I am trying to understand why my code is failing. I have a data.table as follows:
DT <- data.table(my_name=c("A","B","C","D","E","F"),my_id=c(2,2,3,3,4,4))
> DT
my_name my_id
1: A 2
2: B 2
3: C 3
4: D 3
5: E 4
6: F 4
I am trying to create all pairs of "my_name" with different values of "my_id", which for DT would be:
Var1 Var2
A C
A D
A E
A F
B C
B D
B E
B F
C E
C F
D E
D F
I have a function to return all pairs of "my_name" for a given pair of values of "my_id" which works as expected.
get_pairs <- function(id1,id2,tdt) {
return(expand.grid(tdt[my_id==id1,my_name],tdt[my_id==id2,my_name]))
}
> get_pairs(2,3,DT)
Var1 Var2
1 A C
2 B C
3 A D
4 B D
Now, I want to execute this function for all pairs of ids, which I try to do by finding all pairs of ids and then using mapply with the get_pairs function.
> combn(unique(DT$my_id),2)
[,1] [,2] [,3]
[1,] 2 2 3
[2,] 3 4 4
tid1 <- combn(unique(DT$my_id),2)[1,]
tid2 <- combn(unique(DT$my_id),2)[2,]
mapply(get_pairs, tid1, tid2, DT)
Error in expand.grid(tdt[my_id == id1, my_name], tdt[my_id == id2, my_name]) :
object 'my_id' not found
Again, if I try to do the same thing without an mapply, it works.
get_pairs3(tid1[1],tid2[1],DT)
Var1 Var2
1 A C
2 B C
3 A D
4 B D
Why does this function fail only when used within an mapply? I think this has something to do with the scope of data.table names, but I'm not sure.
Alternatively, is there a different/more efficient way to accomplish this task? I have a large data.table with a third id "sample" and I need to get all of these pairs for each sample (e.g. operating on DT[sample=="sample_id",] ). I am new to the data.table package, and I may not be using it in the most efficient way.
The reason the function is failing has nothing to do with scoping in this case.
mapply
vectorizes the function, it takes each element of each parameter and passes to the function. So, in your case, thedata.table
elements are its columns, somapply
is passing the columnmy_name
instead of the completedata.table
.If you want to pass the complete
data.table
tomapply
, you should use theMoreArgs
parameter. Then your function will work: