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How can I get all the combinations of a list with duplicates. By duplicates I mean an element with itself. I am building a symmetric matrix.

names.list<-c("A","B","C")
as.data.frame(t(combn(names.list,2)))

Result is:

   V1  V2
1   A   B
2   A   C
3   B   C

When I want:

   V1  V2
1   A   A
2   A   B
3   A   C
4   B   B
5   B   C
6   C   C

Or even:

   V1  V2
1   A   A
2   A   B
3   A   C
4   B   A
5   B   B
6   B   C
7   C   A
8   C   B
9   C   C

But my matrices are large so I would like to keep combinations to a minimum (so preferably the second result), since more combinations = more computations = larger run times..

Thanks.

Travis Liew
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1 Answers1

2

It sounds like you're looking for expand.grid instead of combn:

expand.grid(names.list, names.list)
#   Var1 Var2
# 1    A    A
# 2    B    A
# 3    C    A
# 4    A    B
# 5    B    B
# 6    C    B
# 7    A    C
# 8    B    C
# 9    C    C

Update

There's also combinations from "gtools" which would give you your preferred output.

library(gtools)
combinations(3, 2, names.list, repeats = TRUE)
#     [,1] [,2]
# [1,] "A"  "A" 
# [2,] "A"  "B" 
# [3,] "A"  "C" 
# [4,] "B"  "B" 
# [5,] "B"  "C" 
# [6,] "C"  "C"
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    Thanks for your reply. Any way to use `expand.grid` to compute only unique permutations so that `A,B` and `B,A` do not both appear? This way I only need to calculate once for that combination, since I am building a symmetric matrix. – Travis Liew Feb 14 '14 at 02:34