function out=legTrackerD2DBS(data)
%legTrackerD2DBS resamples data recorded from day-to-day experiments to
%determine the distribution of distances between flies under a null
%hypothesis that intra-fly distance measures are no different than
%inter-fly distance measures. Output is resampled mean intra-fly distances.
%Usage:
%out=legTrackerD2DBS(data)
%data = n x k array. n is number of flies, k is number of metrics. E.g. k=2
%in analysis of the intra- and inter-fly distance in the first and second
%principle components of Figs 3c and 3e.

% vector of fly identities (length n). Used for its length. Values are used
% to sort shuffled arrays.
flies=[1;1;1;2;2;3;3;4;4;5;5;6;6;6;7;7;8;8];

% number of resampling replicates
n=50000;

%allocate output in memory
out=zeros(n,1);

%for resampling replicates
for i=1:n
    
    % randomly re-order fly identity
    newFlies=flies(randperm(length(flies)));
    newData=[data newFlies];
    
    % sort data for new resampled identities
    newData=sortrows(newData,size(data,2)+1);
    
    % pairwise dist between all flies
    dist=squareform(pdist(newData));
    
    % get intra-fly distances
    d=[dist(2,1) dist(3,1) dist(3,2) dist(5,4)  dist(7,6) dist(9,8) dist(11,9) dist(13,12)  dist(14,12)  dist(14,13) dist(15,16) dist(17,18)];
    d=mean(d);
    out(i)=d;
    
end

%optional metrics to display to command window buffer:

% dist=squareform(pdist(data(:,1:2)));
% intraCluster=mean([dist(2,1) dist(3,1) dist(3,2) dist(5,4)  dist(7,6) dist(9,8) dist(11,9) dist(13,12)  dist(14,12)  dist(14,13) dist(15,16) dist(17,18)])
% meanOut=mean(out)
% stdOut=std(out)