The alert prevents the event from happening. What you could do instead is trigger this function manually, because it happens anyways.
var keyupfunction = function(e){
alert('up');
console.log('up');
}
window.addEventListener('keyup', keyupfunction);
window.addEventListener('keydown', function(e) {
if (i++ % 2) alert('down');
console.log('down');
keyupfunction(e);
});
But really, you shouldn't be using alerts. It prevents these events, but who knows what else it might break. Use something custom instead.