function [pop] = mutate(pop,mu,nElite)
% MUTATE - Implements mutation on the genetic population
% 
% Inputs: 
%   pop
%   mu
%   nElite = number of "elite" chromosomes (population members we will not mutate) 
%   
% Outputs:
% 
% Written by:
% -- 
% John L. Weatherwax                2006-08-28
% 
% email: wax@alum.mit.edu
% 
% Please send comments and especially bug reports to the
% above email address.
% 
%-----

[N_pop,N_var] = size(pop);

if nargin<3 
  nElite = 1;
else
  nElite = min(nElite,N_pop-1); % we mutate at least *one* chromosome
end

num_of_mutations = ceil( mu * ( N_pop - nElite ) * N_var ); % -nElite => we don't mutate nElite of our best chromosome
mrow = ceil( rand(1,num_of_mutations)*( N_pop - nElite ) ) + nElite;
ncol = ceil( rand(1,num_of_mutations)*N_var );
pop(mrow,ncol) = rand(num_of_mutations,num_of_mutations); % replace with a new random variable