# Combinatorics

## Install required packages

wants <- c("e1071", "permute")
has   <- wants %in% rownames(installed.packages())
if(any(!has)) install.packages(wants[!has])

## Combinations

### Number of $$k$$-combinations

$${n \choose k}$$

myN <- 5
myK <- 4
choose(myN, myK)
[1] 5
factorial(myN) / (factorial(myK)*factorial(myN-myK))
[1] 5

### Enumerate all combinations

combn(c("a", "b", "c", "d", "e"), myK)
     [,1] [,2] [,3] [,4] [,5]
[1,] "a"  "a"  "a"  "a"  "b"
[2,] "b"  "b"  "b"  "c"  "c"
[3,] "c"  "c"  "d"  "d"  "d"
[4,] "d"  "e"  "e"  "e"  "e" 
combn(c(1, 2, 3, 4), 3)
     [,1] [,2] [,3] [,4]
[1,]    1    1    1    2
[2,]    2    2    3    3
[3,]    3    4    4    4
combn(c(1, 2, 3, 4), 3, sum)
[1] 6 7 8 9
combn(c(1, 2, 3, 4), 3, weighted.mean, w=c(0.5, 0.2, 0.3))
[1] 1.8 2.1 2.3 2.8

## Permutations

### Number of permutations

factorial(7)
[1] 5040

### Random permutation

set.seed(123)
set <- LETTERS[1:10]
sample(set, length(set), replace=FALSE)
 [1] "C" "J" "B" "H" "F" "I" "A" "G" "E" "D"
library(permute)
shuffle(length(set))
 [1] 10  5  3  8  1  4  6  9  7  2

### Enumerate all permutations

#### All permutations at once

set <- LETTERS[1:3]
len <- length(set)
library(e1071)
(mat <- permutations(len))
     [,1] [,2] [,3]
[1,]    1    2    3
[2,]    2    1    3
[3,]    2    3    1
[4,]    1    3    2
[5,]    3    1    2
[6,]    3    2    1
apply(mat, 1, function(x) set[x])
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,] "A"  "B"  "B"  "A"  "C"  "C"
[2,] "B"  "A"  "C"  "C"  "A"  "B"
[3,] "C"  "C"  "A"  "B"  "B"  "A" 

#### Each permutation individually

(grp <- rep(letters[1:3], each=3))
[1] "a" "a" "a" "b" "b" "b" "c" "c" "c"
N      <- length(grp)
nPerms <- 100
library(permute)
pCtrl <- how(nperm=nPerms, complete=FALSE)
for(i in 1:5) {
perm <- permute(i, n=N, control=pCtrl)
print(grp[perm])
}
[1] "c" "a" "c" "c" "a" "b" "a" "b" "b"
[1] "a" "a" "c" "b" "b" "c" "a" "c" "b"
[1] "c" "a" "a" "a" "b" "c" "b" "b" "c"
[1] "b" "a" "a" "b" "c" "b" "a" "c" "c"
[1] "a" "c" "a" "c" "b" "c" "b" "b" "a"

#### Restricted permutations

Permute group membership in a two-way ANOVA design. Here: artificially low number of permutations.

Njk    <- 4              ## cell size
P      <- 2              ## levels factor A
Q      <- 3              ## levels factor B
N      <- Njk*P*Q
nPerms <- 10             ## number of permutations
id     <- 1:(Njk*P*Q)
IV1    <- factor(rep(1:P,  each=Njk*Q))  ## factor A
IV2    <- factor(rep(1:Q, times=Njk*P))  ## factor B
(myDf  <- data.frame(id, IV1, IV2))
   id IV1 IV2
1   1   1   1
2   2   1   2
3   3   1   3
4   4   1   1
5   5   1   2
6   6   1   3
7   7   1   1
8   8   1   2
9   9   1   3
10 10   1   1
11 11   1   2
12 12   1   3
13 13   2   1
14 14   2   2
15 15   2   3
16 16   2   1
17 17   2   2
18 18   2   3
19 19   2   1
20 20   2   2
21 21   2   3
22 22   2   1
23 23   2   2
24 24   2   3
# choose permutation schemes for tests of factor A and B
library(permute)         ## for how(), permute()

## only permute across A (within B)
pCtrlA <- how(plots=Plots(strata=IV2), complete=FALSE, nperm=nPerms)

## only permute across B (within A)
pCtrlB <- how(plots=Plots(strata=IV1), complete=FALSE, nperm=nPerms)

Get permutations for test of factor A

for(i in 1:3) {
perm <- permute(i, n=N, control=pCtrlA)
print(myDf[perm, ])
# not shown
}

Get permutations for test of factor B

for(i in 1:3) {
perm <- permute(i, n=N, control=pCtrlB)
print(myDf[perm, ])
# not shown
}

## Enumerate all $$n$$-tuples

All combinations of elements from $$n$$ different sets (cartesian product)

IV1 <- c("control", "treatment")
IV2 <- c("f", "m")
IV3 <- c(1, 2)
expand.grid(IV1, IV2, IV3)
       Var1 Var2 Var3
1   control    f    1
2 treatment    f    1
3   control    m    1
4 treatment    m    1
5   control    f    2
6 treatment    f    2
7   control    m    2
8 treatment    m    2

## Apply a function to all pairs of elements from two sets

outer(1:5, 1:5, FUN="*")
     [,1] [,2] [,3] [,4] [,5]
[1,]    1    2    3    4    5
[2,]    2    4    6    8   10
[3,]    3    6    9   12   15
[4,]    4    8   12   16   20
[5,]    5   10   15   20   25

## Detach (automatically) loaded packages (if possible)

try(detach(package:e1071))
try(detach(package:permute))