Added source Matlab code for reference
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Waldir Leoncio
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b8af977117
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186 changed files with 61405 additions and 1 deletions
366
matlab/spatial/private/model_search_parallel.m
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366
matlab/spatial/private/model_search_parallel.m
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function [partition, logml, partitionSummary, logmldiff] = model_search_parallel(c, partition, orig_dist, roundTypes)
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% This function clusters DNA alignment using "codon" model in Corander and Tang's
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% paper: Bayesian analysis of population structure based on linked
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% molecular information (2007), Mathematical Biosciences
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% c: preprocessed data for the sequence alignment
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% partition: initial partition of the individuals
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% origdist: hamming distance between individuals, indexed by
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% (1,2)(1,3)(14)...(2,3)(2,4).....(3,4)...(n-1,n)
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% roundTypes: array of operation types
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% Lu Cheng
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% 15.12.2012
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interactive = false;
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global PARTITION;
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global CQ_COUNTS;global SUM_CQ_COUNTS;
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global SP_COUNTS;global SUM_SP_COUNTS;
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global CQ_PRIOR; global SP_PRIOR;
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global LOGML_TABLE;
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global ADDITION_DIFFERENCE;
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global REMOVAL_DIFFERENCE;
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global JOIN_DIFFERENCE;
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global LOC_SP_COUNTS;
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global LOC_CQ_COUNTS;
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clearGlobalVars;
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nPOPS = length(unique(partition));
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% PRIOR VALUES:
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CQ_PRIOR = c.cqPrior;
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SP_PRIOR = c.spPrior;
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% Initialize PARTITION, **_COUNTS, SUM_**_COUNTS, alnMat
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[sumCqCounts, cqCounts] = initialCounts2(partition, c.cqData, nPOPS, c.nMaxCqCodes);
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[sumSpCounts, spCounts] = initialCounts2(partition, c.spData, nPOPS, c.nMaxSpCodes);
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CQ_COUNTS = cqCounts; SUM_CQ_COUNTS = sumCqCounts;
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SP_COUNTS = spCounts; SUM_SP_COUNTS = sumSpCounts;
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PARTITION = partition;
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[cliqcounts, sepcounts] = computeCounts(c.locCliques, c.locSeparators, nPOPS);
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LOC_CQ_COUNTS = cliqcounts;
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LOC_SP_COUNTS = sepcounts;
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% alnMat = c.alnMat;
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partitionSummary = -Inf*ones(30,2,nPOPS); % Tiedot 30 parhaasta partitiosta (npops ja logml)
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partitionSummary(:,1,:) = zeros(30,1,nPOPS);
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worstLogml = -Inf*ones(1, nPOPS); worstIndex = ones(1, nPOPS);
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clear partition cqCounts sumCqCounts spCounts sumSpCounts
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% Initialize LOGML_TABLE:
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nINDS = c.nSeq;
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LOGML_TABLE = zeros(nPOPS,1);
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updateLogmlTable(1:nPOPS);
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REMOVAL_DIFFERENCE = zeros(nINDS,1);
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REMOVAL_DIFFERENCE(:,:) = nan;
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ADDITION_DIFFERENCE = zeros(nINDS,nPOPS);
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ADDITION_DIFFERENCE(:,:) = nan;
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JOIN_DIFFERENCE = zeros(nPOPS, nPOPS);
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JOIN_DIFFERENCE(:,:) = nan;
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% ***********Doc:********************
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% REMOVAL_DIFFERENCE(ind) tells the change in logml if ind is removed from
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% its cluster. nan, if the cluster has changed, since the value was last
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% calculated.
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%
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% ADDITION_DIFFERENCE(ind, pop) tells the change in logml if ind is added
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% to cluster pop. nan, if the cluster has changed since the value was last
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% calculated. Always nan, if pop is ind's own cluster.
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%
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% JOIN_DIFFERENCE(pop1,pop2) = tells the change in logml if pop1 and pop2
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% are combined. nan, if either cluster has changed since the value was last
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% calculated.
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% ***********Doc end*****************
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logml = computeTotalLogml;
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disp('The beginning:');
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% disp(['Partition: ' num2str(PARTITION')]);
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disp(['Nclusters: ' num2str(length(unique(PARTITION)))]);
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disp(['Log(ml*prior): ' num2str(logml)]);
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disp(' ');
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nnotEmptyPops = length(unique(PARTITION));
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if logml>worstLogml(nnotEmptyPops);
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[partitionSummary(:,:,nnotEmptyPops), added] = addToSummary(logml, ...
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partitionSummary(:,:,nnotEmptyPops), worstIndex(nnotEmptyPops));
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if (added==1)
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[worstLogml(nnotEmptyPops), worstIndex(nnotEmptyPops)] = ...
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min(partitionSummary(:,2,nnotEmptyPops));
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end
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end
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% START SEARCH OF THE BEST PARTITION:
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vipu = zeros(1,14);
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if interactive
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roundTypes = input('Input steps: ');
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if ischar(roundTypes), roundTypes = str2num(roundTypes); end
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end
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ready = 0;
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while ready ~= 1
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% disp(['Performing steps: ' num2str(roundTypes)]);
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for n = 1:length(roundTypes)
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round = roundTypes(n);
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moveCounter = 0;
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if round==1 && vipu(1)==0 % move an individual to another population
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% inds = randperm(nINDS);
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inds = getMoveInds(orig_dist,nINDS); % get inds to be moved
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for ind = inds(:)'
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update_difference_tables(ind, c.cqData, c.nMaxCqCodes, ...
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c.spData, c.nMaxSpCodes, c.locCliques, c.locSeparators, logml);
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tmpDiff = REMOVAL_DIFFERENCE(ind) + ADDITION_DIFFERENCE(ind,:);
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tmpDiff(PARTITION(ind)) = 0;
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[maxChange, maxIndex] = max(tmpDiff);
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if maxChange>1e-5
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updateGlobalVariables(ind, maxIndex, c.cqData, c.nMaxCqCodes, ...
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c.spData, c.nMaxSpCodes, c.locCliques, c.locSeparators);
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% fprintf('moving from %d to %d.\n',PARTITION(ind),maxIndex)
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logml = computeTotalLogml();
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moveCounter = moveCounter+1;
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vipu = zeros(1,14);
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nnotEmptyPops = length(unique(PARTITION));
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if logml>worstLogml(nnotEmptyPops);
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[partitionSummary(:,:,nnotEmptyPops), added] = addToSummary(logml, ...
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partitionSummary(:,:,nnotEmptyPops), worstIndex(nnotEmptyPops));
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if (added==1)
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[worstLogml(nnotEmptyPops), worstIndex(nnotEmptyPops)] = ...
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min(partitionSummary(:,2,nnotEmptyPops));
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end
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end
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end
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end
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if moveCounter==0, vipu(1)=1; end
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disp(['Step 1: ' num2str(moveCounter) ' individuals were moved.']);
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elseif round==2 && vipu(2)==0 % join two populations
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update_join_difference(c.cqData, c.nMaxCqCodes, ...
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c.spData, c.nMaxSpCodes, c.locCliques, c.locSeparators, logml);
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[maxChange, aux] = max(JOIN_DIFFERENCE(:));
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[i1, i2] = ind2sub([nPOPS,nPOPS],aux);
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if maxChange>1e-5
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tmpInds = find(PARTITION==i1);
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updateGlobalVariables(tmpInds, i2, c.cqData, c.nMaxCqCodes, ...
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c.spData, c.nMaxSpCodes, c.locCliques, c.locSeparators);
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logml = computeTotalLogml;
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disp(['Step 2: Clusters ' num2str(i1) ' and ' num2str(i2) ' combined.']);
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vipu = zeros(1,14);
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nnotEmptyPops = length(unique(PARTITION));
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if logml>worstLogml(nnotEmptyPops);
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[partitionSummary(:,:,nnotEmptyPops), added] = addToSummary(logml, ...
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partitionSummary(:,:,nnotEmptyPops), worstIndex(nnotEmptyPops));
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if (added==1)
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[worstLogml(nnotEmptyPops), worstIndex(nnotEmptyPops)] = ...
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min(partitionSummary(:,2,nnotEmptyPops));
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end
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end
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else
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disp('Step 2: no changes.');
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vipu(2)=1;
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end
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elseif ismember(round, 3:4) && vipu(round)==0 % Split a population, and move one subpopulation to another population
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pops = randperm(nPOPS);
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splitFlags = zeros(nPOPS,1);
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for pop = pops(:)'
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maxChange = 0;
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indsToBeMoved = [];
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inds2 = find(PARTITION==pop);
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ninds2 = length(inds2);
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if ninds2>4
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if round==3
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dist3 = getDistance(inds2, orig_dist, nINDS);
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npops2 = min(20, floor(ninds2 / 5)); %Moneenko osaan jaetaan
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elseif round==4
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dist3 = getDistance(inds2, orig_dist, nINDS);
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npops2 = 2;
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end
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Z3 = linkage(dist3);
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T3 = cluster_own(Z3, npops2);
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for i = 1:npops2
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indsX = inds2(T3==i); indsX = indsX';
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tmpChanges = calcLogmlChanges(indsX, c.cqData, c.nMaxCqCodes, ...
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c.spData, c.nMaxSpCodes, c.locCliques, c.locSeparators, logml);
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[tmpMaxChange, tmpMaxPop] = max(tmpChanges);
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if tmpMaxChange>maxChange
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maxChange = tmpMaxChange;
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% i1 = pop;
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i2 = tmpMaxPop;
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indsToBeMoved = indsX;
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end
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end
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if maxChange>1e-5
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updateGlobalVariables(indsToBeMoved, i2, c.cqData, c.nMaxCqCodes, ...
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c.spData, c.nMaxSpCodes, c.locCliques, c.locSeparators);
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logml = computeTotalLogml;
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splitFlags(pop)=1;
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nnotEmptyPops = length(unique(PARTITION));
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if logml>worstLogml(nnotEmptyPops);
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[partitionSummary(:,:,nnotEmptyPops), added] = addToSummary(logml, ...
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partitionSummary(:,:,nnotEmptyPops), worstIndex(nnotEmptyPops));
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if (added==1)
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[worstLogml(nnotEmptyPops), worstIndex(nnotEmptyPops)] = ...
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min(partitionSummary(:,2,nnotEmptyPops));
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end
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end
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end
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end
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end
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if any(splitFlags)
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disp(['Step ' num2str(round) ': ' num2str(sum(splitFlags)) ' populations were split.']);
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vipu = zeros(1,14);
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else
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disp(['Step ' num2str(round) ': no changes.']);
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vipu(round)=1;
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end
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end
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end
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if interactive
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roundTypes = input('Input extra steps: ');
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if ischar(roundTypes), roundTypes = str2num(roundTypes); end
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else
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roundTypes = [];
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end
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if isempty(roundTypes)
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ready = 1;
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end
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end
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%disp(' ');
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disp('BEST PARTITION: ');
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%disp(['Partition: ' num2str(PARTITION')]);
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disp(['Nclusters: ' num2str(length(unique(PARTITION)))]);
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disp(['Log(ml): ' num2str(logml)]);
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disp(' ');
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nPOPS= rmEmptyPopulation(c.locCliques, c.locSeparators);
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ADDITION_DIFFERENCE(:) = NaN;
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REMOVAL_DIFFERENCE(:) = NaN;
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logmldiff = zeros(nINDS,nPOPS); % the change of logml if individual i is moved to group j
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for i=1:nINDS
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update_difference_tables(i, c.cqData, c.nMaxCqCodes, ...
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c.spData, c.nMaxSpCodes, c.locCliques, c.locSeparators, logml);
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logmldiff(i,:) = REMOVAL_DIFFERENCE(i)+ADDITION_DIFFERENCE(i,:);
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if all(isnan(logmldiff(i,:)))
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keyboard
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end
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end
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logmldiff(isnan(logmldiff))=0;
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partition = PARTITION;
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%----------------------------------------------------------------------------
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function [dist2, dind1, dind2] = getDistance(inds2, dist_orig, ninds)
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% pick out the distrances between samples in "inds2" from "dist_orig"
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% dist_orig specifies the distances of (1,2),(1,3),(1,4)......(ninds-1,ninds)
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% Lu Cheng, 22.06.2011
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if ~issorted(inds2)
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error('inds2 is not in ascending order!');
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end
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ninds2 = length(inds2);
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apu = zeros(nchoosek(ninds2,2),2);
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irow = 1;
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for i=1:ninds2-1
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for j=i+1:ninds2
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apu(irow, 1) = inds2(i);
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apu(irow, 2) = inds2(j);
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irow = irow+1;
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end
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end
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dind1 = apu(:,1);
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dind2 = apu(:,2);
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apu = (apu(:,1)-1).*ninds - apu(:,1) ./ 2 .* (apu(:,1)-1) + (apu(:,2)-apu(:,1));
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dist2 = dist_orig(apu);
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%---------------------------------------------------------------
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function inds = getMoveInds(dist_orig, ninds)
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% get individual indexs to be moved to another cluster
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% we always take the 30% individuals of each cluster which are most distant
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% to each other
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% Lu Cheng, 25.05.2011
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global PARTITION;
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pops = unique(PARTITION);
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inds = [];
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for tmpPop = pops(:)'
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tmpInds = find(PARTITION == tmpPop)';
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if(length(tmpInds)<20)
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inds = [inds tmpInds(:)']; %#ok<AGROW>
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continue;
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end
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[tmpDist, dind1, dind2] = getDistance(tmpInds,dist_orig,ninds);
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tmpSDist = sort(tmpDist,'Descend');
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tmpInds2 = find(tmpDist>tmpSDist(round(length(tmpSDist)*0.3)));
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tmpInds3 = union(unique(dind1(tmpInds2)), unique(dind2(tmpInds2)));
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inds = [inds tmpInds3(:)']; %#ok<AGROW>
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end
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% ------------------------------------------------------------
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function [partitionSummary, added] = addToSummary(logml, partitionSummary, worstIndex)
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% Tiedetään, ett?annettu logml on isompi kuin huonoin arvo
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% partitionSummary taulukossa. Jos partitionSummary:ss?ei viel?ole
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% annettua logml arvoa, niin lisätään worstIndex:in kohtaan uusi logml ja
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% nykyist?partitiota vastaava nclusters:in arvo. Muutoin ei tehd?mitään.
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global PARTITION;
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apu = find(abs(partitionSummary(:,2)-logml)<1e-5);
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if isempty(apu)
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% Nyt löydetty partitio ei ole viel?kirjattuna summaryyn.
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npops = length(unique(PARTITION));
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partitionSummary(worstIndex,1) = npops;
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partitionSummary(worstIndex,2) = logml;
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added = 1;
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else
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added = 0;
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end
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