distance matrix

dis_multi <- function(x, y) rowSums(x != y)
dis <- function(x, y) sum(x != y)
x <- matrix(rbinom(30000, 3, 0.7), 3000, 10)

st <- proc.time()
distMat <- matrix(0, nrow(x), nrow(x))
for (i in 1:(nrow(x)-2))
  distMat[i, (i+1):nrow(x)] <- dis_multi(x[(i+1):nrow(x), ], t(matrix(x[i,], ncol(x), nrow(x)-i)))
distMat[nrow(x), nrow(x)-1] <- dis(x[nrow(x)-1, ], x[nrow(x), ])
distMat <- distMat + t(distMat)
proc.time() - st
#   user  system elapsed
#   1.10    0.04    1.16

st <- proc.time()
distMat2 <- matrix(0, nrow(x), nrow(x))
for (i in 1:(nrow(x)-1))
{
  for (z in (i+1):nrow(x))
  {
    distMat2[i, z] <- dis(x[i, ], x[z, ])
  }
}
distMat2 <- distMat2 + t(distMat2)
proc.time() - st
#   user  system elapsed
#  14.45    0.16   15.07

all.equal(distMat, distMat2) # TRUE

library(Rcpp)
library(RcppArmadillo)
sourceCpp(code = '
// [[Rcpp::depends(RcppArmadillo)]]
#include <RcppArmadillo.h>
using namespace Rcpp;
using namespace arma;

// [[Rcpp::export]]
mat dis_cal_f(mat x) {
  mat distMat(x.n_rows, x.n_rows);
  for (uword i = 0; i < x.n_rows-1; i++)
  {
    for (uword j = i+1; j < x.n_rows; j++)
      distMat(i, j) = sum(x.row(i) != x.row(j));
  }
  return symmatu(distMat);
}')

st <- proc.time()
distMat3 <- dis_cal_f(x)
proc.time() - st
#   user  system elapsed
#   0.22    0.01    0.24

all.equal(distMat, distMat3) # TRUE