Translate spatialPopMixture functions to R

[wleoncio]

• [ ] spatialPopMixture()
• [x] clearGlobalVars
• [x] computeRows(rowsFromInd, inds, ninds)
• [x] addToSummary(logml, partitionSummary, worstIndex)
• [x] arvoSeuraavaTila(muutokset, logml)
• [x] rand_disc(CDF)
• [x] updateGlobalVariables(ind, i2, diffInCounts, ...
• [x] updateGlobalVariables2(i1, i2, diffInCounts, ...
• [x] updateGlobalVariables3(muuttuvat, diffInCounts, ...
• [x] returnInOrder(inds, pop, globalRows, data, ...
• [ ] laskeMuutokset(ind, globalRows, ...
• [ ] laskeMuutokset2(i1, globalRows, ...
• [ ] laskeMuutokset3(T2, inds2, globalRows, ...
• [ ] laskeMuutokset5(inds, globalRows, data, ...
• [x] computeDiffInCounts(rows, max_noalle, nloci, data)
• [x] computePopulationLogml(pops, adjprior, priorTerm)
• [x] poistaTyhjatPopulaatiot(npops)
• [x] admixture_initialization(data_matrix,nclusters,Z)
• [x] cluster_own(Z,nclust)
• [x] clusternum(X, T, k, c)
• [x] handleData(raw_data)
• [x] newGetDistances(data, initRows)
• [x] getDistances(data_matrix,nclusters)
• [x] linkage(Y, method)
• [x] initPopNames(nameFile)
• [ ] computeCounts(cliques, separators, npops, PARTITION)
• [ ] computeDiffInCliqCounts(cliques, inds)
• [ ] computeLogml(adjprior,priorTerm, ...
• [ ] initializeGammaln(ninds, rowsFromInd, maxSize)
• [x] laskeOsaDist(inds2, dist, ninds)
• [x] testaaGenePopData(tiedostonNimi)
• [x] lueGenePopData(tiedostonNimi)
• [x] lueNimi(line)
• [x] selvitaDigitFormat(line)
• [x] rivinSisaltamienMjonojenLkm(line)
• [x] testaaPop(rivi)
• [x] addAlleles(data, ind, line, divider)
• [x] writeMixtureInfo(logml, globalRows, data, adjprior, ...
• [x] dispLine;
• [x] takeLine(description,width)
• [x] omaRound(num)
• [x] palautaYks(num,yks)
• [x] kldiv2str(div)
• [x] testaaOnkoKunnollinenBapsData(data)
• [ ] testFastaData(inFile)
• [ ] handleCoords(coordinates)
• [ ] laskeKlikit(M, maxCliqSize,maxSepSize)
• [ ] mysetdiff(A,B)
• [ ] checkLogml(priorTerm, adjprior, cliques, separators)
• [x] findEmptyPop(npops)
• [ ] testaaKoordinaatit(ninds, coordinates)
• [x] initialCounts(partition, data, npops, noalle)
• [ ] findOutRowsFromInd(popnames, rows)
• [ ] fiksaaPartitioYksiloTasolle(rows, rowsFromInd)