Documentation of recombin

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Function Synopsis

NewChrom = recombin(REC_F, Chrom, RecOpt, VLUB, SUBPOP);

Help text

 high level RECOMBINation function

 This function performs recombination between pairs of individuals
 and returns the new individuals after mating. The function handles
 multiple populations and calls the low level recombination function
 for the actual recombination process.
 Different size of every subpopulation is supported.

 Syntax:  NewChrom = recombin(REC_F, OldChrom, RecOpt, VLUB, SUBPOP)

 Input parameters:
    REC_F     - String containing the name of the recombination or
                recombination function
    Chrom     - Matrix containing the chromosomes of the old
                population. Each row corresponds to one individual
    RecOpt    - (optional) Scalar containing the probability of 
                recombination ocurring between pairs of individuals.
                if omitted or NaN, 1 is assumed
    VLUB      - (optional) matrix containing lower and upper
                bounds of all variables, only for 'reclinex' needed
    SUBPOP    - (optional) Vector/scalar containing number of individuals
                per subpopulation/number of subpopulations
                if omitted or NaN, 1 subpopulation is assumed

 Output parameter:
    NewChrom  - Matrix containing the chromosomes of the population
                after recombination in the same format as OldChrom.

 See also: recdis, recint, reclin, recmut, recsp, recdp, recsh, migrate, mutate, selection

Cross-Reference Information

Listing of function recombin

%  Author:  Hartmut Pohlheim
%  History: 18.05.94    file created
%           07.08.95    multi strategy support added
%                          parameter checking shortened
%           13.03.96    test for recnone added
%           29.04.96    call of recombination function with eval changed,
%                          made problem with error
%           31.07.96    new format for SUBPOP introduced, vector contains now
%                          number of individuals for every subpopulation
%           12.02.97    calling syntax changed, VLUB is now 4th parameter
%                          and RecOpt is 3rd parameter,
%                       calling of reclinex (former recmut) changed, is now
%                          identical to all rec/xov functions except the
%                          additional boundaries
%           04.02.98    RecOpt can contain multiple values now, used for 
%                          different RecRate for every subpopulation
%           25.05.99    eval replaced by feval
%                       test for recnone/reclinex simpler now


function NewChrom = recombin(REC_F, Chrom, RecOpt, VLUB, SUBPOP);

% include recombination functions for compilation
%#function recdis reclin reclinex recint recgp recpm recmp recdp recdprs recsh recshrs recsp recsprs 

% Check parameter consistency
   if nargin < 2, error('Not enough input parameter'); end

   % Identify the population size
   [Nind, Nvar] = size(Chrom);
 
   if nargin < 5, SUBPOP = []; end
   SUBPOP = compdiv('checksubpop', SUBPOP, Nind);
   NumSUBPOP = length(SUBPOP);

   if nargin < 3, RecOpt = []; end
   if isnan(RecOpt), RecOpt = []; end
   if isempty(RecOpt), RecOpt = 1; end
   if any([any(RecOpt < 0), any(RecOpt > 1)]), error('RecOpt must contain values in [0, 1]'); end

   if all([size(REC_F,1)  == 1, NumSUBPOP > 1]), REC_F  = repmat(REC_F,  [NumSUBPOP, 1]); end
   if all([size(RecOpt,1) == 1, NumSUBPOP > 1]), RecOpt = repmat(RecOpt, [NumSUBPOP, 1]); end

   if nargin < 4, VLUB = []; end
   if isnan(VLUB), VLUB = []; end

% Select individuals of one subpopulation and call low level function
   NewChrom = [];
   for irun = 1:NumSUBPOP,
      % Get number of individuals in actual subpopulation
      Nind = SUBPOP(irun);
      RecOptIntern = RecOpt(irun,:);

      % Copy individuals of actual subpopulation
      ChromSub = Chrom(sum(SUBPOP(1:irun-1))+1:sum(SUBPOP(1:irun)),:);

      % Test for special case 'recnone': no recombination
      if strcmp(lower(deblank(REC_F(irun,:))), 'recnone'),
         NewChromSub = ChromSub;
      % Test for special case 'reclinex': extended line recombination
      elseif strcmp(lower(deblank(REC_F(irun,:))), 'reclinex'),
         if isempty(VLUB), error('For reclinex boundaries (VLUB) are needed!'); end
         NewChromSub = feval(deblank(REC_F(irun,:)), ChromSub, RecOptIntern, VLUB);
      else     % all other rec* functions
         NewChromSub = feval(deblank(REC_F(irun,:)), ChromSub, RecOptIntern);
      end
      NewChrom=[NewChrom; NewChromSub];
   end


% End of function