Translate spatialPopMixture functions to R

[wleoncio]

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