moved code from all laskeMuutokset to same R file
This commit is contained in:
Waldir Leoncio
parent
95598800fe
commit
f381207950
2 changed files with 236 additions and 204 deletions
204
R/indMix.R
204
R/indMix.R
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@ -678,57 +678,6 @@ indMix <- function(c, npops, dispText) {
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# %------------------------------------------------------------------------------------
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# function [muutokset, diffInCounts] = ...
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# laskeMuutokset(ind, globalRows, data, adjprior, priorTerm)
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# % Palauttaa npops*1 taulun, jossa i:s alkio kertoo, mik<69> olisi
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# % muutos logml:ss<73>, mik<69>li yksil<69> ind siirret<65><74>n koriin i.
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# % diffInCounts on poistettava COUNTS:in siivusta i1 ja lis<69>tt<74>v<EFBFBD>
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# % COUNTS:in siivuun i2, mik<69>li muutos toteutetaan.
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# %
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# % Lis<69>ys 25.9.2007:
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# % Otettu k<>ytt<74><74>n globaali muuttuja LOGDIFF, johon on tallennettu muutokset
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# % logml:ss<73> siirrett<74>ess<73> yksil<69>it<69> toisiin populaatioihin.
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# global COUNTS; global SUMCOUNTS;
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# global PARTITION; global POP_LOGML;
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# global LOGDIFF;
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# npops = size(COUNTS,3);
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# muutokset = LOGDIFF(ind,:);
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# i1 = PARTITION(ind);
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# i1_logml = POP_LOGML(i1);
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# muutokset(i1) = 0;
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# rows = globalRows(ind,1):globalRows(ind,2);
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# diffInCounts = computeDiffInCounts(rows, size(COUNTS,1), size(COUNTS,2), data);
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# diffInSumCounts = sum(diffInCounts);
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# COUNTS(:,:,i1) = COUNTS(:,:,i1)-diffInCounts;
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# SUMCOUNTS(i1,:) = SUMCOUNTS(i1,:)-diffInSumCounts;
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# new_i1_logml = computePopulationLogml(i1, adjprior, priorTerm);
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# COUNTS(:,:,i1) = COUNTS(:,:,i1)+diffInCounts;
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# SUMCOUNTS(i1,:) = SUMCOUNTS(i1,:)+diffInSumCounts;
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# i2 = find(muutokset==-Inf); % Etsit<69><74>n populaatiot jotka muuttuneet viime kerran j<>lkeen.
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# i2 = setdiff(i2,i1);
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# i2_logml = POP_LOGML(i2);
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# ni2 = length(i2);
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# COUNTS(:,:,i2) = COUNTS(:,:,i2)+repmat(diffInCounts, [1 1 ni2]);
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# SUMCOUNTS(i2,:) = SUMCOUNTS(i2,:)+repmat(diffInSumCounts,[ni2 1]);
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# new_i2_logml = computePopulationLogml(i2, adjprior, priorTerm);
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# COUNTS(:,:,i2) = COUNTS(:,:,i2)-repmat(diffInCounts, [1 1 ni2]);
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# SUMCOUNTS(i2,:) = SUMCOUNTS(i2,:)-repmat(diffInSumCounts,[ni2 1]);
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# muutokset(i2) = new_i1_logml - i1_logml ...
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# + new_i2_logml - i2_logml;
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# LOGDIFF(ind,:) = muutokset;
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# %----------------------------------------------------------------------
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# function diffInCounts = computeDiffInCounts(rows, max_noalle, nloci, data)
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# % Muodostaa max_noalle*nloci taulukon, jossa on niiden alleelien
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@ -781,62 +730,6 @@ indMix <- function(c, npops, dispText) {
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# %--------------------------------------------------------------------------
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# %--
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# %------------------------------------------------------------------------------------
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# function [muutokset, diffInCounts] = laskeMuutokset2( ...
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# i1, globalRows, data, adjprior, priorTerm);
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# % Palauttaa npops*1 taulun, jossa i:s alkio kertoo, mik<69> olisi
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# % muutos logml:ss<73>, mik<69>li korin i1 kaikki yksil<69>t siirret<65><74>n
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# % koriin i.
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# global COUNTS; global SUMCOUNTS;
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# global PARTITION; global POP_LOGML;
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# npops = size(COUNTS,3);
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# muutokset = zeros(npops,1);
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# i1_logml = POP_LOGML(i1);
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# inds = find(PARTITION==i1);
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# ninds = length(inds);
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# if ninds==0
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# diffInCounts = zeros(size(COUNTS,1), size(COUNTS,2));
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# return;
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# end
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# rows = [];
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# for i = 1:ninds
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# ind = inds(i);
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# lisa = globalRows(ind,1):globalRows(ind,2);
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# rows = [rows; lisa'];
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# %rows = [rows; globalRows{ind}'];
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# end
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# diffInCounts = computeDiffInCounts(rows', size(COUNTS,1), size(COUNTS,2), data);
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# diffInSumCounts = sum(diffInCounts);
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# COUNTS(:,:,i1) = COUNTS(:,:,i1)-diffInCounts;
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# SUMCOUNTS(i1,:) = SUMCOUNTS(i1,:)-diffInSumCounts;
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# new_i1_logml = computePopulationLogml(i1, adjprior, priorTerm);
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# COUNTS(:,:,i1) = COUNTS(:,:,i1)+diffInCounts;
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# SUMCOUNTS(i1,:) = SUMCOUNTS(i1,:)+diffInSumCounts;
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# i2 = [1:i1-1 , i1+1:npops];
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# i2_logml = POP_LOGML(i2);
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# COUNTS(:,:,i2) = COUNTS(:,:,i2)+repmat(diffInCounts, [1 1 npops-1]);
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# SUMCOUNTS(i2,:) = SUMCOUNTS(i2,:)+repmat(diffInSumCounts,[npops-1 1]);
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# new_i2_logml = computePopulationLogml(i2, adjprior, priorTerm);
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# COUNTS(:,:,i2) = COUNTS(:,:,i2)-repmat(diffInCounts, [1 1 npops-1]);
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# SUMCOUNTS(i2,:) = SUMCOUNTS(i2,:)-repmat(diffInSumCounts,[npops-1 1]);
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# muutokset(i2) = new_i1_logml - i1_logml ...
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# + new_i2_logml - i2_logml;
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# %---------------------------------------------------------------------------------
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# function updateGlobalVariables2( ...
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# i1, i2, diffInCounts, adjprior, priorTerm);
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@ -864,103 +757,6 @@ indMix <- function(c, npops, dispText) {
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# inx = [find(PARTITION==i1); find(PARTITION==i2)];
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# LOGDIFF(inx,:) = -Inf;
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# %--------------------------------------------------------------------------
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# %----
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# function muutokset = laskeMuutokset3(T2, inds2, globalRows, ...
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# data, adjprior, priorTerm, i1)
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# % Palauttaa length(unique(T2))*npops taulun, jossa (i,j):s alkio
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# % kertoo, mik<69> olisi muutos logml:ss<73>, jos populaation i1 osapopulaatio
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# % inds2(find(T2==i)) siirret<65><74>n koriin j.
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# global COUNTS; global SUMCOUNTS;
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# global PARTITION; global POP_LOGML;
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# npops = size(COUNTS,3);
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# npops2 = length(unique(T2));
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# muutokset = zeros(npops2, npops);
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# i1_logml = POP_LOGML(i1);
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# for pop2 = 1:npops2
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# inds = inds2(find(T2==pop2));
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# ninds = length(inds);
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# if ninds>0
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# rows = [];
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# for i = 1:ninds
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# ind = inds(i);
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# lisa = globalRows(ind,1):globalRows(ind,2);
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# rows = [rows; lisa'];
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# %rows = [rows; globalRows{ind}'];
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# end
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# diffInCounts = computeDiffInCounts(rows', size(COUNTS,1), size(COUNTS,2), data);
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# diffInSumCounts = sum(diffInCounts);
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# COUNTS(:,:,i1) = COUNTS(:,:,i1)-diffInCounts;
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# SUMCOUNTS(i1,:) = SUMCOUNTS(i1,:)-diffInSumCounts;
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# new_i1_logml = computePopulationLogml(i1, adjprior, priorTerm);
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# COUNTS(:,:,i1) = COUNTS(:,:,i1)+diffInCounts;
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# SUMCOUNTS(i1,:) = SUMCOUNTS(i1,:)+diffInSumCounts;
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# i2 = [1:i1-1 , i1+1:npops];
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# i2_logml = POP_LOGML(i2)';
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# COUNTS(:,:,i2) = COUNTS(:,:,i2)+repmat(diffInCounts, [1 1 npops-1]);
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# SUMCOUNTS(i2,:) = SUMCOUNTS(i2,:)+repmat(diffInSumCounts,[npops-1 1]);
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# new_i2_logml = computePopulationLogml(i2, adjprior, priorTerm)';
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# COUNTS(:,:,i2) = COUNTS(:,:,i2)-repmat(diffInCounts, [1 1 npops-1]);
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# SUMCOUNTS(i2,:) = SUMCOUNTS(i2,:)-repmat(diffInSumCounts,[npops-1 1]);
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# muutokset(pop2,i2) = new_i1_logml - i1_logml ...
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# + new_i2_logml - i2_logml;
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# end
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# end
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# %------------------------------------------------------------------------------------
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# function muutokset = laskeMuutokset5(inds, globalRows, data, adjprior, ...
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# priorTerm, i1, i2)
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# % Palauttaa length(inds)*1 taulun, jossa i:s alkio kertoo, mik<69> olisi
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# % muutos logml:ss<73>, mik<69>li yksil<69> i vaihtaisi koria i1:n ja i2:n v<>lill<6C>.
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# global COUNTS; global SUMCOUNTS;
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# global PARTITION; global POP_LOGML;
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# ninds = length(inds);
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# muutokset = zeros(ninds,1);
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# i1_logml = POP_LOGML(i1);
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# i2_logml = POP_LOGML(i2);
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# for i = 1:ninds
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# ind = inds(i);
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# if PARTITION(ind)==i1
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# pop1 = i1; %mist<73>
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# pop2 = i2; %mihin
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# else
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# pop1 = i2;
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# pop2 = i1;
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# end
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# rows = globalRows(ind,1):globalRows(ind,2);
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# diffInCounts = computeDiffInCounts(rows, size(COUNTS,1), size(COUNTS,2), data);
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# diffInSumCounts = sum(diffInCounts);
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# COUNTS(:,:,pop1) = COUNTS(:,:,pop1)-diffInCounts;
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# SUMCOUNTS(pop1,:) = SUMCOUNTS(pop1,:)-diffInSumCounts;
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# COUNTS(:,:,pop2) = COUNTS(:,:,pop2)+diffInCounts;
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# SUMCOUNTS(pop2,:) = SUMCOUNTS(pop2,:)+diffInSumCounts;
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# new_logmls = computePopulationLogml([i1 i2], adjprior, priorTerm);
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# muutokset(i) = sum(new_logmls);
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# COUNTS(:,:,pop1) = COUNTS(:,:,pop1)+diffInCounts;
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# SUMCOUNTS(pop1,:) = SUMCOUNTS(pop1,:)+diffInSumCounts;
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# COUNTS(:,:,pop2) = COUNTS(:,:,pop2)-diffInCounts;
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# SUMCOUNTS(pop2,:) = SUMCOUNTS(pop2,:)-diffInSumCounts;
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# end
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# muutokset = muutokset - i1_logml - i2_logml;
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# %------------------------------------------------------------------------------------
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236
R/laskeMuutokset12345.R
Normal file
236
R/laskeMuutokset12345.R
Normal file
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@ -0,0 +1,236 @@
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#' @title Calculate changes?
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#' @description Palauttaa npops*npops taulun, jonka alkio (i,j) kertoo, mik?on
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#' muutos logml:ss? mikäli populaatiosta i siirretään osuuden verran
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#' todennäköisyysmassaa populaatioon j. Mikäli populaatiossa i ei ole mitään
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#' siirrettävää, on vastaavassa kohdassa rivi nollia.
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#' @param osuus Percentages?
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#' @param omaFreqs own Freqs?
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#' @param osuusTaulu Percentage table?
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#' @param logml log maximum likelihood
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#' @param COUNTS COUNTS
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#' @export
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laskeMuutokset4 <- function (osuus, osuusTaulu, omaFreqs, logml,
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COUNTS = matrix(0)) {
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npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3])
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notEmpty <- which(osuusTaulu > 0.005)
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muutokset <- zeros(npops)
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empties <- !notEmpty
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for (i1 in notEmpty) {
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osuusTaulu[i1] <- osuusTaulu[i1] - osuus
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for (i2 in c(colon(1, i1 - 1), colon(i1 + 1, npops))) {
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osuusTaulu[i2] <- osuusTaulu[i2] + osuus
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loggis <- computeIndLogml(omaFreqs, osuusTaulu)
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# Work around Matlab OOB bug
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if (i1 > nrow(muutokset)) {
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muutokset <- rbind(muutokset, muutokset * 0)
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}
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if (i2 > ncol(muutokset)) {
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muutokset <- cbind(muutokset, muutokset * 0)
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}
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muutokset[i1, i2] <- loggis - logml
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osuusTaulu[i2] <- osuusTaulu[i2] - osuus
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}
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osuusTaulu[i1] <- osuusTaulu[i1] + osuus
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}
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return (muutokset)
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}
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laskeMuutokset <- function(ind, globalRows, data, adjprior, priorTerm) {
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# % Palauttaa npops*1 taulun, jossa i:s alkio kertoo, mik<69> olisi
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# % muutos logml:ss<73>, mik<69>li yksil<69> ind siirret<65><74>n koriin i.
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# % diffInCounts on poistettava COUNTS:in siivusta i1 ja lis<69>tt<74>v<EFBFBD>
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# % COUNTS:in siivuun i2, mik<69>li muutos toteutetaan.
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# %
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# % Lis<69>ys 25.9.2007:
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# % Otettu k<>ytt<74><74>n globaali muuttuja LOGDIFF, johon on tallennettu muutokset
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# % logml:ss<73> siirrett<74>ess<73> yksil<69>it<69> toisiin populaatioihin.
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# global COUNTS; global SUMCOUNTS;
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# global PARTITION; global POP_LOGML;
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# global LOGDIFF;
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# npops = size(COUNTS,3);
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# muutokset = LOGDIFF(ind,:);
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# i1 = PARTITION(ind);
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# i1_logml = POP_LOGML(i1);
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# muutokset(i1) = 0;
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# rows = globalRows(ind,1):globalRows(ind,2);
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# diffInCounts = computeDiffInCounts(rows, size(COUNTS,1), size(COUNTS,2), data);
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# diffInSumCounts = sum(diffInCounts);
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# COUNTS(:,:,i1) = COUNTS(:,:,i1)-diffInCounts;
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# SUMCOUNTS(i1,:) = SUMCOUNTS(i1,:)-diffInSumCounts;
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# new_i1_logml = computePopulationLogml(i1, adjprior, priorTerm);
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# COUNTS(:,:,i1) = COUNTS(:,:,i1)+diffInCounts;
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# SUMCOUNTS(i1,:) = SUMCOUNTS(i1,:)+diffInSumCounts;
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# i2 = find(muutokset==-Inf); % Etsit<69><74>n populaatiot jotka muuttuneet viime kerran j<>lkeen.
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# i2 = setdiff(i2,i1);
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# i2_logml = POP_LOGML(i2);
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# ni2 = length(i2);
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# COUNTS(:,:,i2) = COUNTS(:,:,i2)+repmat(diffInCounts, [1 1 ni2]);
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# SUMCOUNTS(i2,:) = SUMCOUNTS(i2,:)+repmat(diffInSumCounts,[ni2 1]);
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# new_i2_logml = computePopulationLogml(i2, adjprior, priorTerm);
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# COUNTS(:,:,i2) = COUNTS(:,:,i2)-repmat(diffInCounts, [1 1 ni2]);
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# SUMCOUNTS(i2,:) = SUMCOUNTS(i2,:)-repmat(diffInSumCounts,[ni2 1]);
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# muutokset(i2) = new_i1_logml - i1_logml ...
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# + new_i2_logml - i2_logml;
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# LOGDIFF(ind,:) = muutokset;
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return(list(muutokset = muutokset, diffInCounts = diffInCounts))
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}
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# %------------------------------------------------------------------------------------
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laskeMuutokset2 <- function(i1, globalRows, data, adjprior, priorTerm) {
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# % Palauttaa npops*1 taulun, jossa i:s alkio kertoo, mik<69> olisi
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# % muutos logml:ss<73>, mik<69>li korin i1 kaikki yksil<69>t siirret<65><74>n
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# % koriin i.
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# global COUNTS; global SUMCOUNTS;
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# global PARTITION; global POP_LOGML;
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# npops = size(COUNTS,3);
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# muutokset = zeros(npops,1);
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# i1_logml = POP_LOGML(i1);
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# inds = find(PARTITION==i1);
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# ninds = length(inds);
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# if ninds==0
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# diffInCounts = zeros(size(COUNTS,1), size(COUNTS,2));
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# return;
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# end
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# rows = [];
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# for i = 1:ninds
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# ind = inds(i);
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# lisa = globalRows(ind,1):globalRows(ind,2);
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# rows = [rows; lisa'];
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# %rows = [rows; globalRows{ind}'];
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# end
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# diffInCounts = computeDiffInCounts(rows', size(COUNTS,1), size(COUNTS,2), data);
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# diffInSumCounts = sum(diffInCounts);
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# COUNTS(:,:,i1) = COUNTS(:,:,i1)-diffInCounts;
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# SUMCOUNTS(i1,:) = SUMCOUNTS(i1,:)-diffInSumCounts;
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# new_i1_logml = computePopulationLogml(i1, adjprior, priorTerm);
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# COUNTS(:,:,i1) = COUNTS(:,:,i1)+diffInCounts;
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# SUMCOUNTS(i1,:) = SUMCOUNTS(i1,:)+diffInSumCounts;
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# i2 = [1:i1-1 , i1+1:npops];
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# i2_logml = POP_LOGML(i2);
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# COUNTS(:,:,i2) = COUNTS(:,:,i2)+repmat(diffInCounts, [1 1 npops-1]);
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# SUMCOUNTS(i2,:) = SUMCOUNTS(i2,:)+repmat(diffInSumCounts,[npops-1 1]);
|
||||
# new_i2_logml = computePopulationLogml(i2, adjprior, priorTerm);
|
||||
# COUNTS(:,:,i2) = COUNTS(:,:,i2)-repmat(diffInCounts, [1 1 npops-1]);
|
||||
# SUMCOUNTS(i2,:) = SUMCOUNTS(i2,:)-repmat(diffInSumCounts,[npops-1 1]);
|
||||
|
||||
# muutokset(i2) = new_i1_logml - i1_logml ...
|
||||
# + new_i2_logml - i2_logml;
|
||||
return(list(muutokset = muutokset, diffInCounts = diffInCounts))
|
||||
}
|
||||
|
||||
|
||||
laskeMuutokset3 <- function(T2, inds2, globalRows, data, adjprior, priorTerm, i1) {
|
||||
# % Palauttaa length(unique(T2))*npops taulun, jossa (i,j):s alkio
|
||||
# % kertoo, mik<69> olisi muutos logml:ss<73>, jos populaation i1 osapopulaatio
|
||||
# % inds2(find(T2==i)) siirret<65><74>n koriin j.
|
||||
|
||||
# global COUNTS; global SUMCOUNTS;
|
||||
# global PARTITION; global POP_LOGML;
|
||||
# npops = size(COUNTS,3);
|
||||
# npops2 = length(unique(T2));
|
||||
# muutokset = zeros(npops2, npops);
|
||||
|
||||
# i1_logml = POP_LOGML(i1);
|
||||
# for pop2 = 1:npops2
|
||||
# inds = inds2(find(T2==pop2));
|
||||
# ninds = length(inds);
|
||||
# if ninds>0
|
||||
# rows = [];
|
||||
# for i = 1:ninds
|
||||
# ind = inds(i);
|
||||
# lisa = globalRows(ind,1):globalRows(ind,2);
|
||||
# rows = [rows; lisa'];
|
||||
# %rows = [rows; globalRows{ind}'];
|
||||
# end
|
||||
# diffInCounts = computeDiffInCounts(rows', size(COUNTS,1), size(COUNTS,2), data);
|
||||
# diffInSumCounts = sum(diffInCounts);
|
||||
|
||||
# COUNTS(:,:,i1) = COUNTS(:,:,i1)-diffInCounts;
|
||||
# SUMCOUNTS(i1,:) = SUMCOUNTS(i1,:)-diffInSumCounts;
|
||||
# new_i1_logml = computePopulationLogml(i1, adjprior, priorTerm);
|
||||
# COUNTS(:,:,i1) = COUNTS(:,:,i1)+diffInCounts;
|
||||
# SUMCOUNTS(i1,:) = SUMCOUNTS(i1,:)+diffInSumCounts;
|
||||
|
||||
# i2 = [1:i1-1 , i1+1:npops];
|
||||
# i2_logml = POP_LOGML(i2)';
|
||||
|
||||
# COUNTS(:,:,i2) = COUNTS(:,:,i2)+repmat(diffInCounts, [1 1 npops-1]);
|
||||
# SUMCOUNTS(i2,:) = SUMCOUNTS(i2,:)+repmat(diffInSumCounts,[npops-1 1]);
|
||||
# new_i2_logml = computePopulationLogml(i2, adjprior, priorTerm)';
|
||||
# COUNTS(:,:,i2) = COUNTS(:,:,i2)-repmat(diffInCounts, [1 1 npops-1]);
|
||||
# SUMCOUNTS(i2,:) = SUMCOUNTS(i2,:)-repmat(diffInSumCounts,[npops-1 1]);
|
||||
|
||||
# muutokset(pop2,i2) = new_i1_logml - i1_logml ...
|
||||
# + new_i2_logml - i2_logml;
|
||||
# end
|
||||
# end
|
||||
return(muutokset)
|
||||
}
|
||||
|
||||
laskeMuutokset5 <- function(inds, globalRows, data, adjprior, priorTerm, i1, i2) {
|
||||
# % Palauttaa length(inds)*1 taulun, jossa i:s alkio kertoo, mik<69> olisi
|
||||
# % muutos logml:ss<73>, mik<69>li yksil<69> i vaihtaisi koria i1:n ja i2:n v<>lill<6C>.
|
||||
|
||||
# global COUNTS; global SUMCOUNTS;
|
||||
# global PARTITION; global POP_LOGML;
|
||||
|
||||
# ninds = length(inds);
|
||||
# muutokset = zeros(ninds,1);
|
||||
|
||||
# i1_logml = POP_LOGML(i1);
|
||||
# i2_logml = POP_LOGML(i2);
|
||||
|
||||
# for i = 1:ninds
|
||||
# ind = inds(i);
|
||||
# if PARTITION(ind)==i1
|
||||
# pop1 = i1; %mist<73>
|
||||
# pop2 = i2; %mihin
|
||||
# else
|
||||
# pop1 = i2;
|
||||
# pop2 = i1;
|
||||
# end
|
||||
# rows = globalRows(ind,1):globalRows(ind,2);
|
||||
# diffInCounts = computeDiffInCounts(rows, size(COUNTS,1), size(COUNTS,2), data);
|
||||
# diffInSumCounts = sum(diffInCounts);
|
||||
|
||||
# COUNTS(:,:,pop1) = COUNTS(:,:,pop1)-diffInCounts;
|
||||
# SUMCOUNTS(pop1,:) = SUMCOUNTS(pop1,:)-diffInSumCounts;
|
||||
# COUNTS(:,:,pop2) = COUNTS(:,:,pop2)+diffInCounts;
|
||||
# SUMCOUNTS(pop2,:) = SUMCOUNTS(pop2,:)+diffInSumCounts;
|
||||
|
||||
# new_logmls = computePopulationLogml([i1 i2], adjprior, priorTerm);
|
||||
# muutokset(i) = sum(new_logmls);
|
||||
|
||||
# COUNTS(:,:,pop1) = COUNTS(:,:,pop1)+diffInCounts;
|
||||
# SUMCOUNTS(pop1,:) = SUMCOUNTS(pop1,:)+diffInSumCounts;
|
||||
# COUNTS(:,:,pop2) = COUNTS(:,:,pop2)-diffInCounts;
|
||||
# SUMCOUNTS(pop2,:) = SUMCOUNTS(pop2,:)-diffInSumCounts;
|
||||
# end
|
||||
|
||||
# muutokset = muutokset - i1_logml - i2_logml;
|
||||
return(muutokset)
|
||||
}
|
||||
Loading…
Add table
Reference in a new issue