encode = (array) => {
  // crude array equality function
  arrayEquals = (...arr) => {
    return arr[0].map(x => {
      return JSON.stringify(x);
    }).every((x, _, a) => {
      return x === a[0];
    });
  };

  let result = [],
    count = -1,
    len = array.length;

  array.reduce((acc, val, i) => {
    if (!arrayEquals([acc, val])) {
      // if current value differs from last
      if (i !== len - 1) {
        // push the count and data to the result
        result.push([++count, acc]);
        count = 0; // reset the count
      } else { // last iteration
        // push the (n - 1)th  value
        result.push([++count, acc]);
        // now push the nth value
        result.push([1, val]);
      }
    } else {
      // if current value equals the last, increment counter and continue
      count++;
      if (i === len - 1) { // last iteration
        // push regardless 
        count === 1 ? result.push([++count, val]) : result.push([count, val]);
      }
    }
    return val;
  }, array[0]);

  return result;
};

console.log(encode([1, 1, 2, 2, 3, 3, 4]));
console.log(encode([
  [1, 2, 3],
  [4, 5, 6],
  [7, 8, 9],
  [10, 11, 12]
]));
console.log(encode([
  [1, 2, 3],
  [1, 2, 3],
  [4, 5, 6]
]));
console.log(encode([
  [0],
  [0],
  [1],
  [2, 3],
  [4, 5, 6],
  [],
  []
]));