226 lines
No EOL
7.6 KiB
R
226 lines
No EOL
7.6 KiB
R
#' @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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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(
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rows, size(COUNTS, 1), size(COUNTS, 2), data
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)
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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, c(1, 1, ni2))
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SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] + repmat(diffInSumCounts, c(ni2, 1))
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new_i2_logml <- computePopulationLogml(i2, adjprior, priorTerm)
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COUNTS[, , i2] <- COUNTS[, , i2] - repmat(diffInCounts, c(1, 1, ni2))
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SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] - repmat(diffInSumCounts, c(ni2, 1))
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muutokset[i2] <- new_i1_logml - i1_logml + 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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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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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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}
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rows = list()
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for (i in 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 <- c(rows, t(lisa))
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}
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diffInCounts <- computeDiffInCounts(
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t(rows), size(COUNTS, 1), size(COUNTS, 2), data
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)
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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 <- c(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, c(1, 1, npops - 1))
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SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] + repmat(diffInSumCounts, c(npops - 1, 1))
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new_i2_logml <- computePopulationLogml(i2, adjprior, priorTerm)
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COUNTS[, , i2] <- COUNTS[, , i2] - repmat(diffInCounts, c(1, 1, npops - 1))
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SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] - repmat(diffInSumCounts, c(npops - 1, 1))
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muutokset[i2] <- new_i1_logml - i1_logml + new_i2_logml - i2_logml
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return(list(muutokset = muutokset, diffInCounts = diffInCounts))
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}
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laskeMuutokset3 <- function(T2, inds2, globalRows, 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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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 in 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 <- list()
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for (i in 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 <- c(rows, t(lisa))
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}
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diffInCounts <- computeDiffInCounts(
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t(rows), size(COUNTS, 1), size(COUNTS, 2), data
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)
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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 <- c(1:i1-1, i1+1:npops)
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i2_logml <- t(POP_LOGML[i2])
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COUNTS[, , i2] <- COUNTS[, , i2] + repmat(diffInCounts, c(1, 1, npops - 1))
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SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] + repmat(diffInSumCounts, c(npops - 1, 1))
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new_i2_logml <- t(computePopulationLogml(i2, adjprior, priorTerm))
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COUNTS[, , i2] <- COUNTS[, , i2] - repmat(diffInCounts, c(1, 1, npops - 1))
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SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] - repmat(diffInSumCounts, c(npops - 1, 1))
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muutokset[pop2, i2] <- new_i1_logml - i1_logml + new_i2_logml - i2_logml
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}
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}
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return(muutokset)
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}
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laskeMuutokset5 <- function(inds, globalRows, data, adjprior, 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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return(muutokset)
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} |