[eluser]TheFuzzy0ne[/eluser]
Welcome to the CodeIgniter forums!
You didn't mention what the problem was.
I assume you're having trouble with CodeIgniter escaping your SELECT clause? You can pass FALSE into $this->db->select() as the second parameter to prevent that.
Code:
$this->db->select('count(DISTINCT source)', FALSE);
$this->db->from('comment c','evaluation e');
$this->db->where('c.evaluation_id','e.id');
$this->db->where('e.department_id', $department_id);