count_cpp

# data generation
set.seed(100)
numData = 1e4
dat = replicate(numData, as.integer(sample(1:100, 10)))
# method 1
st = proc.time()
count = vector('integer', numData)
for (i in 1:ncol(dat))
  count[i] = sum(colSums(matrix(dat %in% dat[,i], 10)) >= 5) - 1
proc.time() - st
#   user  system elapsed
#  22.84    0.91   23.74

# method 2 by Rcpp
library(Rcpp)
library(RcppArmadillo)
sourceCpp(code = '
// [[Rcpp::depends(RcppArmadillo)]]
#define ARMA_DONT_USE_CXX11
#include <RcppArmadillo.h>
using namespace Rcpp;
using namespace arma;

// [[Rcpp::export]]
Col<int> count_cpp(IntegerMatrix xr) {
 Mat<int> x(xr.begin(), xr.nrow(), xr.ncol(), false);
 Col<int> out = zeros< Col<int> >(xr.ncol());
 int count;
 for (uword i = 0; i < x.n_cols; i++)
 {
   for (uword j = 0; j < x.n_cols; j++)
   {
     count = 0;
     for (uword k = 0; k < x.n_rows; k++)
       for (uword l = 0; l < x.n_rows; l++)
         if (x(k, j) == x(l, i))
           count++;
     if (count >= 5)
       out(i)++;
   }
 }
 return out;
}')
st = proc.time()
count2 = count_cpp(dat) - 1
proc.time() - st
#   user  system elapsed
#  7.28    0.01    7.30

# method 3 by Rcpp and RcppParallel
library(Rcpp)
library(RcppArmadillo)
library(RcppParallel)
sourceCpp(code = '
// [[Rcpp::depends(RcppArmadillo, RcppParallel)]]
// [[Rcpp::plugins("cpp11")]]
#include <RcppArmadillo.h>
#include <RcppParallel.h>
using namespace Rcpp;
using namespace arma;
using namespace RcppParallel;

struct CountWorker: public Worker {
  Mat<int>& tableMat;
  Mat<int>& data;
  Col<int>& output;
  CountWorker(Mat<int>& tableMat, Mat<int>& data, Col<int>& output) :
     tableMat(tableMat), data(data), output(output) {}
  void operator()(std::size_t begin, std::size_t end) {
    for (std::size_t i = begin; i < end; i++)
    {
      uvec tmp = find(sum(tableMat.cols(conv_to<uvec>::from(data.col(i))-1), 1) >= 5);
      output(i) = tmp.n_elem;
    }
  }
};

// [[Rcpp::export]]
Col<int> count_cpp(IntegerMatrix xr, IntegerVector tableVecr) {
  Mat<int> x(xr.begin(), xr.nrow(), xr.ncol(), false);
  Col<int> tableVec(tableVecr.begin(), tableVecr.size(), false);
  Mat<int> tableMat = zeros< Mat<int> >(x.n_cols, tableVec.n_elem);
  Col<int> output = zeros< Col<int> >(x.n_cols);
  for (uword i = 0; i < x.n_cols; i++)
    for (uword j = 0; j < x.n_rows; j++)
      tableMat(i, x(j, i)-1)++;
  CountWorker countWorker(tableMat, x, output);
  parallelFor(0, x.n_cols, countWorker);
  return output;
}')
st = proc.time()
tmp = unique(sort(dat))
count3 = count_cpp(dat, tmp) - 1
proc.time() - st
#   user  system elapsed
#   1.16    0.06    0.28

# method 4 modified version of the codes written by Edster
st = proc.time()
Y = unique(sort(dat))
Z = matrix(0, ncol(dat), length(Y))
count4 = vector('numeric', ncol(dat))
for(i in 1:ncol(dat))
  for(j in 1:10)
    Z[i, dat[j, i]] = 1
for(i in 1:ncol(dat))
  count4[i] = sum(rowSums(Z[, dat[,i]]) >= 5) - 1
proc.time() - st
#   user  system elapsed
#   7.10    1.31    8.47

all.equal(count, as.vector(count2))
all.equal(count, as.vector(count3))
all.equal(count, as.vector(count4))