I would like to convert a 4-dimensional array into a 2-dimensional data set.  I present code for two approaches that do that: one approach using a brute force method involving cbind and rbind and a second approach using nested for-loops.  Nevertheless, I am thinking there is likely a better way.  Thank you for any suggestions.
R <- 3    # regions
M <- 5    # sites
J <- 2    # samples
T <- 4    # years
# 4-dim example array
y <- array(NA, dim = c(M, J, T, R))
# region 1
y[,1,1,1] =  1; y[,2,1,1] =  2; 
y[,1,2,1] =  3; y[,2,2,1] =  4; 
y[,1,3,1] =  5; y[,2,3,1] =  6;
y[,1,4,1] =  7; y[,2,4,1] =  8;
# region 2
y[,1,1,2] =  9; y[,2,1,2] = 10; 
y[,1,2,2] = 11; y[,2,2,2] = 12; 
y[,1,3,2] = 13; y[,2,3,2] = 14;
y[,1,4,2] = 15; y[,2,4,2] = 16;
# region 3
y[,1,1,3] = 17; y[,2,1,3] = 18; 
y[,1,2,3] = 19; y[,2,2,3] = 20; 
y[,1,3,3] = 21; y[,2,3,3] = 22;
y[,1,4,3] = 23; y[,2,4,3] = 24;
# desired two-dimensional data set
z = read.table(text = "
 1  2  3  4  5  6  7  8
 1  2  3  4  5  6  7  8
 1  2  3  4  5  6  7  8
 1  2  3  4  5  6  7  8
 1  2  3  4  5  6  7  8
 9 10 11 12 13 14 15 16
 9 10 11 12 13 14 15 16
 9 10 11 12 13 14 15 16
 9 10 11 12 13 14 15 16
 9 10 11 12 13 14 15 16
17 18 19 20 21 22 23 24
17 18 19 20 21 22 23 24
17 18 19 20 21 22 23 24
17 18 19 20 21 22 23 24
17 18 19 20 21 22 23 24
", sep = "", header = FALSE)
# using cbind and rbind to convert 4-dimensional array to 2-dimensional data set
r1 <- cbind(y[,,1,1], y[,,2,1], y[,,3,1], y[,,4,1])
r2 <- cbind(y[,,1,2], y[,,2,2], y[,,3,2], y[,,4,2])
r3 <- cbind(y[,,1,3], y[,,2,3], y[,,3,3], y[,,4,3])
my.data <- rbind(r1,r2,r3)
my.data
# using nested for-loops to convert 4-dimensional array to 2-dimensional data set
m2 <- matrix(NA, nrow = M*R, ncol= J*T)
for(i in 1:R) {
for(j in 1:T) {
m2[(M*(i-1) + (1:M)), (J*(j-1) + (1:J))] = y[,,j,i]
}
}
m2
# basis for nested for-loops above
m3 <- matrix(NA, nrow = M*R, ncol= J*T)
m3[(M*0 + (1:M)), (J*0 + (1:J))] = y[,,1,1]
m3[(M*0 + (1:M)), (J*1 + (1:J))] = y[,,2,1]
m3[(M*0 + (1:M)), (J*2 + (1:J))] = y[,,3,1]
m3[(M*0 + (1:M)), (J*3 + (1:J))] = y[,,4,1]
m3[(M*1 + (1:M)), (J*0 + (1:J))] = y[,,1,2]
m3[(M*1 + (1:M)), (J*1 + (1:J))] = y[,,2,2]
m3[(M*1 + (1:M)), (J*2 + (1:J))] = y[,,3,2]
m3[(M*1 + (1:M)), (J*3 + (1:J))] = y[,,4,2]
m3[(M*2 + (1:M)), (J*0 + (1:J))] = y[,,1,3]
m3[(M*2 + (1:M)), (J*1 + (1:J))] = y[,,2,3]
m3[(M*2 + (1:M)), (J*2 + (1:J))] = y[,,3,3]
m3[(M*2 + (1:M)), (J*3 + (1:J))] = y[,,4,3]
m3
                It took a couple of tries, but:
matrix(aperm(y,c(1,4,2,3)),15)
or more generally
matrix(aperm(y,c(1,4,2,3)),prod(dim(y)[c(1,4)]))
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