Merge branch 'refactor-laskeMuutokset' into develop
This commit is contained in:
Waldir Leoncio
commit
ea0a5fb344
11 changed files with 563 additions and 221 deletions
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@ -40,4 +40,4 @@ RoxygenNote: 7.2.1
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Suggests:
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testthat (>= 2.1.0)
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Imports:
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methods, ape, vcfR, Rsamtools, adegenet, matlab2r
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methods, ape, vcfR, Rsamtools, adegenet, matlab2r, R6
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@ -15,7 +15,6 @@ export(greedyPopMix)
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export(handleData)
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export(handlePopData)
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export(initPopNames)
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export(laskeMuutokset4)
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export(learn_partition_modified)
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export(learn_simple_partition)
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export(linkage)
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@ -40,6 +39,7 @@ export(testaaOnkoKunnollinenBapsData)
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export(testaaPop)
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export(writeMixtureInfo)
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export(writeMixtureInfoPop)
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importFrom(R6,R6Class)
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importFrom(Rsamtools,scanBam)
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importFrom(adegenet,.readExt)
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importFrom(adegenet,read.genepop)
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@ -8,7 +8,8 @@
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etsiParas <- function(osuus, osuusTaulu, omaFreqs, logml) {
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ready <- 0
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while (ready != 1) {
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muutokset <- laskeMuutokset4(osuus, osuusTaulu, omaFreqs, logml)
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muutokset <- admix1_muutokset$new()
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muutokset <- muutokset$laskeMuutokset4(osuus, osuusTaulu, omaFreqs, logml)
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# Work around R's base::max() limitation on complex numbers
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if (any(vapply(muutokset, class, vector("character", 1)) == "complex")) {
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22
R/indMix.R
22
R/indMix.R
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@ -142,8 +142,9 @@ indMix <- function(c, npops, dispText = TRUE) {
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for (ind in inds) {
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i1 <- PARTITION[ind]
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muutokset_diffInCounts <- laskeMuutokset(
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# FIXME: using 100-length global variables instead of the ones in this function
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muutokset_diffInCounts <- greedyMix_muutokset$new()
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# FIXME: using 100-length global variables instead of the ones in this function
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muutokset_diffInCounts <- muutokset_diffInCounts$laskeMuutokset(
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ind, rows, data, adjprior, priorTerm
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)
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muutokset <- muutokset_diffInCounts$muutokset
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@ -190,7 +191,8 @@ indMix <- function(c, npops, dispText = TRUE) {
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} else if (round == 2) { # Populaation yhdist<73>minen toiseen.
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maxMuutos <- 0
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for (pop in 1:npops) {
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muutokset_diffInCounts <- laskeMuutokset2(
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muutokset_diffInCounts <- greedyMix_muutokset$new()
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muutokset_diffInCounts <- muutokset_diffInCounts$laskeMuutokset2(
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pop, rows, data, adjprior, priorTerm
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)
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muutokset <- muutokset_diffInCounts$muutokset
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@ -244,7 +246,8 @@ indMix <- function(c, npops, dispText = TRUE) {
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npops2 <- 2 # Moneenko osaan jaetaan
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}
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T2 <- cluster_own(Z2, npops2)
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muutokset <- laskeMuutokset3(
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muutokset_diffInCounts <- greedyMix_muutokset$new()
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muutokset <- muutokset_diffInCounts$laskeMuutokset3(
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T2, inds2, rows, data, adjprior, priorTerm, pop
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)
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isoin <- matlab2r::max(muutokset)[[1]]
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@ -326,8 +329,8 @@ indMix <- function(c, npops, dispText = TRUE) {
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while (length(inds) > 0 & i < length(inds)) {
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i <- i + 1
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ind <- inds[i]
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muutokset_diffInCounts <- laskeMuutokset(
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muutokset_diffInCounts <- greedyMix_muutokset$new()
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muutokset_diffInCounts <- muutokset_diffInCounts$laskeMuutokset(
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ind, rows, data, adjprior, priorTerm
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)
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muutokset <- muutokset_diffInCounts$muutokset
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@ -411,8 +414,8 @@ indMix <- function(c, npops, dispText = TRUE) {
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Z2 <- linkage(t(dist2))
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T2 <- cluster_own(Z2, 2)
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muuttuvat <- inds2[matlab2r::find(T2 == 1)]
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muutokset <- laskeMuutokset3(
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muutokset <- greedyMix_muutokset$new()
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muutokset <- muutokset$laskeMuutokset3(
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T2, inds2, rows, data, adjprior, priorTerm, pop
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)
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totalMuutos <- muutokset(1, emptyPop)
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@ -436,7 +439,8 @@ indMix <- function(c, npops, dispText = TRUE) {
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while (muutettu == 1) {
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muutettu <- 0
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# Siirret<65><74>n yksil<69>it<69> populaatioiden v<>lill<6C>
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muutokset <- laskeMuutokset5(
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muutokset <- greedyMix_muutokset$new()
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muutokset <- muutokset$laskeMuutokset5(
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inds2, rows, data, adjprior, priorTerm,
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pop, emptyPop
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)
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@ -1,161 +1,153 @@
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#' @title Calculate changes (?)
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#' @title Calculate changes (spatial mixture class)
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spatialMixture_muutokset <- R6Class(
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classname = "spatialMixture_muutokset",
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public = list(
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#' @param ind ind
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#' @param rowsFromInd rowsFromInd
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#' @param data data
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#' @param adjprior adjprior
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#' @param priorTerm priorTerm
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#' @param logml logml
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#' @param cliques cliques
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#' @param separators separators
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laskeMuutokset = function(
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ind, rowsFromInd, data, adjprior, priorTerm, logml, cliques, separators
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) {
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stop("Not yet implemented") # TODO: implement
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}
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)
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)
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#' @title Calculate changes (admix1 class)
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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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#' @export
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laskeMuutokset4 <- function(osuus, osuusTaulu, omaFreqs, logml) {
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if (isGlobalEmpty(COUNTS)) {
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npops <- 1
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} else {
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npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3])
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}
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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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#' @importFrom R6 R6Class
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admix1_muutokset <- R6Class(
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classname = "admix1_muutokset",
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public = list(
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#' @param osuus Percentages?
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#' @param osuusTaulu Percentage table?
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#' @param omaFreqs own Freqs?
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#' @param logml log maximum likelihood
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laskeMuutokset4 = function(osuus, osuusTaulu, omaFreqs, logml) {
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if (isGlobalEmpty(COUNTS)) {
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npops <- 1
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} else {
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npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3])
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}
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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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muutokset[i1, i2] <- loggis - logml
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osuusTaulu[i2] <- osuusTaulu[i2] - osuus
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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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osuusTaulu[i1] <- osuusTaulu[i1] + osuus
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}
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return(muutokset)
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}
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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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laskeMuutokset <- function(ind, globalRows, data, adjprior, priorTerm) {
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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 <- colSums(diffInCounts)
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)
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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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#' @title Calculate changes (greedyMix class)
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#' @description 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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greedyMix_muutokset <- R6Class(
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classname = "greedyMix_muutokset",
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public = list(
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#' @param ind ind
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#' @param globalRows globalRows
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#' @param data data
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#' @param adjprior adjprior
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#' @param priorTerm priorTerm
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laskeMuutokset = function(ind, globalRows, data, adjprior, priorTerm) {
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npops <- size(COUNTS, 3)
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muutokset <- LOGDIFF[ind, ]
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i2 <- matlab2r::find(muutokset == -Inf) # Etsit<69><74>n populaatiot jotka muuttuneet viime kerran j<>lkeen. (Searching for populations that have changed since the last time)
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i2 <- setdiff(i2, i1)
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i2_logml <- POP_LOGML[i2]
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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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ni2 <- length(i2)
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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 <- colSums(diffInCounts)
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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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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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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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i2 <- matlab2r::find(muutokset == -Inf) # Etsit<69><74>n populaatiot jotka muuttuneet viime kerran j<>lkeen. (Searching for populations that have changed since the last time)
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i2 <- setdiff(i2, i1)
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i2_logml <- POP_LOGML[i2]
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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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ni2 <- length(i2)
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npops <- size(COUNTS, 3)
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muutokset <- zeros(npops, 1)
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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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i1_logml <- POP_LOGML[i1]
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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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#' @param i1 i1
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#' @param globalRows globalRows
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#' @param data data
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#' @param adjprior adjprior
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#' @param priorTerm priorTerm
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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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inds <- matlab2r::find(PARTITION == i1)
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ninds <- length(inds)
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npops <- size(COUNTS, 3)
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muutokset <- zeros(npops, 1)
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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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i1_logml <- POP_LOGML[i1]
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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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inds <- matlab2r::find(PARTITION == i1)
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ninds <- length(inds)
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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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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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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))
|
||||
SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] - repmat(diffInSumCounts, c(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(matlab2r::find(T2==i)) siirret<65><74>n koriin j.
|
||||
|
||||
npops <- size(COUNTS, 3)
|
||||
npops2 <- length(unique(T2))
|
||||
muutokset <- zeros(npops2, npops)
|
||||
|
||||
i1_logml <- POP_LOGML[i1]
|
||||
for (pop2 in 1:npops2) {
|
||||
inds <- inds2[matlab2r::find(T2 == pop2)]
|
||||
ninds <- length(inds)
|
||||
if (ninds > 0) {
|
||||
rows <- list()
|
||||
for (i in 1:ninds) {
|
||||
ind <- inds[i]
|
||||
lisa <- globalRows[ind, 1]:globalRows[ind, 2]
|
||||
ind <- inds(i)
|
||||
lisa <- globalRows(ind, 1):globalRows(ind, 2)
|
||||
rows <- c(rows, t(lisa))
|
||||
}
|
||||
|
||||
diffInCounts <- computeDiffInCounts(
|
||||
t(rows), size(COUNTS, 1), size(COUNTS, 2), data
|
||||
)
|
||||
|
|
@ -168,61 +160,121 @@ laskeMuutokset3 <- function(T2, inds2, globalRows, data, adjprior, priorTerm, i1
|
|||
SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] + diffInSumCounts
|
||||
|
||||
i2 <- c(1:i1 - 1, i1 + 1:npops)
|
||||
i2_logml <- t(POP_LOGML[i2])
|
||||
i2_logml <- POP_LOGML[i2]
|
||||
|
||||
COUNTS[, , i2] <- COUNTS[, , i2] + repmat(diffInCounts, c(1, 1, npops - 1))
|
||||
SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] + repmat(diffInSumCounts, c(npops - 1, 1))
|
||||
new_i2_logml <- t(computePopulationLogml(i2, adjprior, priorTerm))
|
||||
new_i2_logml <- computePopulationLogml(i2, adjprior, priorTerm)
|
||||
COUNTS[, , i2] <- COUNTS[, , i2] - repmat(diffInCounts, c(1, 1, npops - 1))
|
||||
SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] - repmat(diffInSumCounts, c(npops - 1, 1))
|
||||
|
||||
muutokset[pop2, i2] <- new_i1_logml - i1_logml + new_i2_logml - i2_logml
|
||||
muutokset[i2] <- new_i1_logml - i1_logml + new_i2_logml - i2_logml
|
||||
return(list(muutokset = muutokset, diffInCounts = diffInCounts))
|
||||
},
|
||||
#' @param T2 T2
|
||||
#' @param inds2 inds2
|
||||
#' @param globalRows globalRows
|
||||
#' @param data data
|
||||
#' @param adjprior adjprior
|
||||
#' @param priorTerm priorTerm
|
||||
#' @param i1 i1
|
||||
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(matlab2r::find(T2==i)) siirret<65><74>n koriin j.
|
||||
|
||||
npops <- size(COUNTS, 3)
|
||||
npops2 <- length(unique(T2))
|
||||
muutokset <- zeros(npops2, npops)
|
||||
|
||||
i1_logml <- POP_LOGML[i1]
|
||||
for (pop2 in 1:npops2) {
|
||||
inds <- inds2[matlab2r::find(T2 == pop2)]
|
||||
ninds <- length(inds)
|
||||
if (ninds > 0) {
|
||||
rows <- list()
|
||||
for (i in 1:ninds) {
|
||||
ind <- inds[i]
|
||||
lisa <- globalRows[ind, 1]:globalRows[ind, 2]
|
||||
rows <- c(rows, t(lisa))
|
||||
}
|
||||
diffInCounts <- computeDiffInCounts(
|
||||
t(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 <- c(1:i1 - 1, i1 + 1:npops)
|
||||
i2_logml <- t(POP_LOGML[i2])
|
||||
|
||||
COUNTS[, , i2] <- COUNTS[, , i2] + repmat(diffInCounts, c(1, 1, npops - 1))
|
||||
SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] + repmat(diffInSumCounts, c(npops - 1, 1))
|
||||
new_i2_logml <- t(computePopulationLogml(i2, adjprior, priorTerm))
|
||||
COUNTS[, , i2] <- COUNTS[, , i2] - repmat(diffInCounts, c(1, 1, npops - 1))
|
||||
SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] - repmat(diffInSumCounts, c(npops - 1, 1))
|
||||
|
||||
muutokset[pop2, i2] <- new_i1_logml - i1_logml + new_i2_logml - i2_logml
|
||||
}
|
||||
}
|
||||
return(muutokset)
|
||||
},
|
||||
#' @param inds inds
|
||||
#' @param globalRows globalRows
|
||||
#' @param data data
|
||||
#' @param adjprior adjprior
|
||||
#' @param priorTerm priorTerm
|
||||
#' @param i1 i1
|
||||
#' @param i2 i2
|
||||
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>.
|
||||
|
||||
ninds <- length(inds)
|
||||
muutokset <- zeros(ninds, 1)
|
||||
|
||||
i1_logml <- POP_LOGML[i1]
|
||||
i2_logml <- POP_LOGML[i2]
|
||||
|
||||
for (i in 1:ninds) {
|
||||
ind <- inds[i]
|
||||
if (PARTITION[ind] == i1) {
|
||||
pop1 <- i1 # mist<73>
|
||||
pop2 <- i2 # mihin
|
||||
} else {
|
||||
pop1 <- i2
|
||||
pop2 <- i1
|
||||
}
|
||||
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(c(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
|
||||
}
|
||||
|
||||
muutokset <- muutokset - i1_logml - i2_logml
|
||||
return(muutokset)
|
||||
}
|
||||
}
|
||||
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>.
|
||||
|
||||
ninds <- length(inds)
|
||||
muutokset <- zeros(ninds, 1)
|
||||
|
||||
i1_logml <- POP_LOGML[i1]
|
||||
i2_logml <- POP_LOGML[i2]
|
||||
|
||||
for (i in 1:ninds) {
|
||||
ind <- inds[i]
|
||||
if (PARTITION[ind] == i1) {
|
||||
pop1 <- i1 # mist<73>
|
||||
pop2 <- i2 # mihin
|
||||
} else {
|
||||
pop1 <- i2
|
||||
pop2 <- i1
|
||||
}
|
||||
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(c(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
|
||||
}
|
||||
|
||||
muutokset <- muutokset - i1_logml - i2_logml
|
||||
return(muutokset)
|
||||
}
|
||||
)
|
||||
)
|
||||
|
|
|
|||
13
R/laskeVarmuus.R
Normal file
13
R/laskeVarmuus.R
Normal file
|
|
@ -0,0 +1,13 @@
|
|||
laskeVarmuus <- function(
|
||||
rowsFromInd, data, adjprior, priorTerm, logml, cliques, separators, ninds
|
||||
) {
|
||||
varmuus <- zeros(ninds, 1)
|
||||
for (ind in 1:ninds) {
|
||||
muutokset <- spatialMixture_muutokset$new()
|
||||
muutokset <- muutokset$laskeMuutokset(
|
||||
ind, rowsFromInd, data, adjprior, priorTerm, logml, cliques, separators
|
||||
)
|
||||
varmuus[ind] <- 1 / sum(exp(muutokset))
|
||||
}
|
||||
return(varmuus)
|
||||
}
|
||||
58
man/admix1_muutokset.Rd
Normal file
58
man/admix1_muutokset.Rd
Normal file
|
|
@ -0,0 +1,58 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/laskeMuutokset12345.R
|
||||
\name{admix1_muutokset}
|
||||
\alias{admix1_muutokset}
|
||||
\title{Calculate changes (admix1 class)}
|
||||
\description{
|
||||
Palauttaa npops*npops taulun, jonka alkio (i,j) kertoo, mik?on
|
||||
muutos logml:ss? mikäli populaatiosta i siirretään osuuden verran
|
||||
todennäköisyysmassaa populaatioon j. Mikäli populaatiossa i ei ole mitään
|
||||
siirrettävää, on vastaavassa kohdassa rivi nollia.
|
||||
}
|
||||
\section{Methods}{
|
||||
\subsection{Public methods}{
|
||||
\itemize{
|
||||
\item \href{#method-admix1_muutokset-laskeMuutokset4}{\code{admix1_muutokset$laskeMuutokset4()}}
|
||||
\item \href{#method-admix1_muutokset-clone}{\code{admix1_muutokset$clone()}}
|
||||
}
|
||||
}
|
||||
\if{html}{\out{<hr>}}
|
||||
\if{html}{\out{<a id="method-admix1_muutokset-laskeMuutokset4"></a>}}
|
||||
\if{latex}{\out{\hypertarget{method-admix1_muutokset-laskeMuutokset4}{}}}
|
||||
\subsection{Method \code{laskeMuutokset4()}}{
|
||||
\subsection{Usage}{
|
||||
\if{html}{\out{<div class="r">}}\preformatted{admix1_muutokset$laskeMuutokset4(osuus, osuusTaulu, omaFreqs, logml)}\if{html}{\out{</div>}}
|
||||
}
|
||||
|
||||
\subsection{Arguments}{
|
||||
\if{html}{\out{<div class="arguments">}}
|
||||
\describe{
|
||||
\item{\code{osuus}}{Percentages?}
|
||||
|
||||
\item{\code{osuusTaulu}}{Percentage table?}
|
||||
|
||||
\item{\code{omaFreqs}}{own Freqs?}
|
||||
|
||||
\item{\code{logml}}{log maximum likelihood}
|
||||
}
|
||||
\if{html}{\out{</div>}}
|
||||
}
|
||||
}
|
||||
\if{html}{\out{<hr>}}
|
||||
\if{html}{\out{<a id="method-admix1_muutokset-clone"></a>}}
|
||||
\if{latex}{\out{\hypertarget{method-admix1_muutokset-clone}{}}}
|
||||
\subsection{Method \code{clone()}}{
|
||||
The objects of this class are cloneable with this method.
|
||||
\subsection{Usage}{
|
||||
\if{html}{\out{<div class="r">}}\preformatted{admix1_muutokset$clone(deep = FALSE)}\if{html}{\out{</div>}}
|
||||
}
|
||||
|
||||
\subsection{Arguments}{
|
||||
\if{html}{\out{<div class="arguments">}}
|
||||
\describe{
|
||||
\item{\code{deep}}{Whether to make a deep clone.}
|
||||
}
|
||||
\if{html}{\out{</div>}}
|
||||
}
|
||||
}
|
||||
}
|
||||
163
man/greedyMix_muutokset.Rd
Normal file
163
man/greedyMix_muutokset.Rd
Normal file
|
|
@ -0,0 +1,163 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/laskeMuutokset12345.R
|
||||
\name{greedyMix_muutokset}
|
||||
\alias{greedyMix_muutokset}
|
||||
\title{Calculate changes (greedyMix class)}
|
||||
\description{
|
||||
Palauttaa npops*1 taulun, jossa i:s alkio kertoo, mik<69> olisi
|
||||
muutos logml:ss<73>, mik<69>li yksil<69> ind siirret<65><74>n koriin i.
|
||||
diffInCounts on poistettava COUNTS:in siivusta i1 ja lis<69>tt<74>v<EFBFBD>
|
||||
COUNTS:in siivuun i2, mik<69>li muutos toteutetaan.
|
||||
|
||||
Lis<EFBFBD>ys 25.9.2007:
|
||||
Otettu k<>ytt<74><74>n globaali muuttuja LOGDIFF, johon on tallennettu muutokset
|
||||
logml:ss<73> siirrett<74>ess<73> yksil<69>it<69> toisiin populaatioihin.
|
||||
}
|
||||
\section{Methods}{
|
||||
\subsection{Public methods}{
|
||||
\itemize{
|
||||
\item \href{#method-greedyMix_muutokset-laskeMuutokset}{\code{greedyMix_muutokset$laskeMuutokset()}}
|
||||
\item \href{#method-greedyMix_muutokset-laskeMuutokset2}{\code{greedyMix_muutokset$laskeMuutokset2()}}
|
||||
\item \href{#method-greedyMix_muutokset-laskeMuutokset3}{\code{greedyMix_muutokset$laskeMuutokset3()}}
|
||||
\item \href{#method-greedyMix_muutokset-laskeMuutokset5}{\code{greedyMix_muutokset$laskeMuutokset5()}}
|
||||
\item \href{#method-greedyMix_muutokset-clone}{\code{greedyMix_muutokset$clone()}}
|
||||
}
|
||||
}
|
||||
\if{html}{\out{<hr>}}
|
||||
\if{html}{\out{<a id="method-greedyMix_muutokset-laskeMuutokset"></a>}}
|
||||
\if{latex}{\out{\hypertarget{method-greedyMix_muutokset-laskeMuutokset}{}}}
|
||||
\subsection{Method \code{laskeMuutokset()}}{
|
||||
\subsection{Usage}{
|
||||
\if{html}{\out{<div class="r">}}\preformatted{greedyMix_muutokset$laskeMuutokset(ind, globalRows, data, adjprior, priorTerm)}\if{html}{\out{</div>}}
|
||||
}
|
||||
|
||||
\subsection{Arguments}{
|
||||
\if{html}{\out{<div class="arguments">}}
|
||||
\describe{
|
||||
\item{\code{ind}}{ind}
|
||||
|
||||
\item{\code{globalRows}}{globalRows}
|
||||
|
||||
\item{\code{data}}{data}
|
||||
|
||||
\item{\code{adjprior}}{adjprior}
|
||||
|
||||
\item{\code{priorTerm}}{priorTerm}
|
||||
}
|
||||
\if{html}{\out{</div>}}
|
||||
}
|
||||
}
|
||||
\if{html}{\out{<hr>}}
|
||||
\if{html}{\out{<a id="method-greedyMix_muutokset-laskeMuutokset2"></a>}}
|
||||
\if{latex}{\out{\hypertarget{method-greedyMix_muutokset-laskeMuutokset2}{}}}
|
||||
\subsection{Method \code{laskeMuutokset2()}}{
|
||||
\subsection{Usage}{
|
||||
\if{html}{\out{<div class="r">}}\preformatted{greedyMix_muutokset$laskeMuutokset2(i1, globalRows, data, adjprior, priorTerm)}\if{html}{\out{</div>}}
|
||||
}
|
||||
|
||||
\subsection{Arguments}{
|
||||
\if{html}{\out{<div class="arguments">}}
|
||||
\describe{
|
||||
\item{\code{i1}}{i1}
|
||||
|
||||
\item{\code{globalRows}}{globalRows}
|
||||
|
||||
\item{\code{data}}{data}
|
||||
|
||||
\item{\code{adjprior}}{adjprior}
|
||||
|
||||
\item{\code{priorTerm}}{priorTerm}
|
||||
}
|
||||
\if{html}{\out{</div>}}
|
||||
}
|
||||
}
|
||||
\if{html}{\out{<hr>}}
|
||||
\if{html}{\out{<a id="method-greedyMix_muutokset-laskeMuutokset3"></a>}}
|
||||
\if{latex}{\out{\hypertarget{method-greedyMix_muutokset-laskeMuutokset3}{}}}
|
||||
\subsection{Method \code{laskeMuutokset3()}}{
|
||||
\subsection{Usage}{
|
||||
\if{html}{\out{<div class="r">}}\preformatted{greedyMix_muutokset$laskeMuutokset3(
|
||||
T2,
|
||||
inds2,
|
||||
globalRows,
|
||||
data,
|
||||
adjprior,
|
||||
priorTerm,
|
||||
i1
|
||||
)}\if{html}{\out{</div>}}
|
||||
}
|
||||
|
||||
\subsection{Arguments}{
|
||||
\if{html}{\out{<div class="arguments">}}
|
||||
\describe{
|
||||
\item{\code{T2}}{T2}
|
||||
|
||||
\item{\code{inds2}}{inds2}
|
||||
|
||||
\item{\code{globalRows}}{globalRows}
|
||||
|
||||
\item{\code{data}}{data}
|
||||
|
||||
\item{\code{adjprior}}{adjprior}
|
||||
|
||||
\item{\code{priorTerm}}{priorTerm}
|
||||
|
||||
\item{\code{i1}}{i1}
|
||||
}
|
||||
\if{html}{\out{</div>}}
|
||||
}
|
||||
}
|
||||
\if{html}{\out{<hr>}}
|
||||
\if{html}{\out{<a id="method-greedyMix_muutokset-laskeMuutokset5"></a>}}
|
||||
\if{latex}{\out{\hypertarget{method-greedyMix_muutokset-laskeMuutokset5}{}}}
|
||||
\subsection{Method \code{laskeMuutokset5()}}{
|
||||
\subsection{Usage}{
|
||||
\if{html}{\out{<div class="r">}}\preformatted{greedyMix_muutokset$laskeMuutokset5(
|
||||
inds,
|
||||
globalRows,
|
||||
data,
|
||||
adjprior,
|
||||
priorTerm,
|
||||
i1,
|
||||
i2
|
||||
)}\if{html}{\out{</div>}}
|
||||
}
|
||||
|
||||
\subsection{Arguments}{
|
||||
\if{html}{\out{<div class="arguments">}}
|
||||
\describe{
|
||||
\item{\code{inds}}{inds}
|
||||
|
||||
\item{\code{globalRows}}{globalRows}
|
||||
|
||||
\item{\code{data}}{data}
|
||||
|
||||
\item{\code{adjprior}}{adjprior}
|
||||
|
||||
\item{\code{priorTerm}}{priorTerm}
|
||||
|
||||
\item{\code{i1}}{i1}
|
||||
|
||||
\item{\code{i2}}{i2}
|
||||
}
|
||||
\if{html}{\out{</div>}}
|
||||
}
|
||||
}
|
||||
\if{html}{\out{<hr>}}
|
||||
\if{html}{\out{<a id="method-greedyMix_muutokset-clone"></a>}}
|
||||
\if{latex}{\out{\hypertarget{method-greedyMix_muutokset-clone}{}}}
|
||||
\subsection{Method \code{clone()}}{
|
||||
The objects of this class are cloneable with this method.
|
||||
\subsection{Usage}{
|
||||
\if{html}{\out{<div class="r">}}\preformatted{greedyMix_muutokset$clone(deep = FALSE)}\if{html}{\out{</div>}}
|
||||
}
|
||||
|
||||
\subsection{Arguments}{
|
||||
\if{html}{\out{<div class="arguments">}}
|
||||
\describe{
|
||||
\item{\code{deep}}{Whether to make a deep clone.}
|
||||
}
|
||||
\if{html}{\out{</div>}}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -1,23 +0,0 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/laskeMuutokset12345.R
|
||||
\name{laskeMuutokset4}
|
||||
\alias{laskeMuutokset4}
|
||||
\title{Calculate changes (?)}
|
||||
\usage{
|
||||
laskeMuutokset4(osuus, osuusTaulu, omaFreqs, logml)
|
||||
}
|
||||
\arguments{
|
||||
\item{osuus}{Percentages?}
|
||||
|
||||
\item{osuusTaulu}{Percentage table?}
|
||||
|
||||
\item{omaFreqs}{own Freqs?}
|
||||
|
||||
\item{logml}{log maximum likelihood}
|
||||
}
|
||||
\description{
|
||||
Palauttaa npops*npops taulun, jonka alkio (i,j) kertoo, mik?on
|
||||
muutos logml:ss? mikäli populaatiosta i siirretään osuuden verran
|
||||
todennäköisyysmassaa populaatioon j. Mikäli populaatiossa i ei ole mitään
|
||||
siirrettävää, on vastaavassa kohdassa rivi nollia.
|
||||
}
|
||||
74
man/spatialMixture_muutokset.Rd
Normal file
74
man/spatialMixture_muutokset.Rd
Normal file
|
|
@ -0,0 +1,74 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/laskeMuutokset12345.R
|
||||
\name{spatialMixture_muutokset}
|
||||
\alias{spatialMixture_muutokset}
|
||||
\title{Calculate changes (spatial mixture class)}
|
||||
\description{
|
||||
Calculate changes (spatial mixture class)
|
||||
|
||||
Calculate changes (spatial mixture class)
|
||||
}
|
||||
\section{Methods}{
|
||||
\subsection{Public methods}{
|
||||
\itemize{
|
||||
\item \href{#method-spatialMixture_muutokset-laskeMuutokset}{\code{spatialMixture_muutokset$laskeMuutokset()}}
|
||||
\item \href{#method-spatialMixture_muutokset-clone}{\code{spatialMixture_muutokset$clone()}}
|
||||
}
|
||||
}
|
||||
\if{html}{\out{<hr>}}
|
||||
\if{html}{\out{<a id="method-spatialMixture_muutokset-laskeMuutokset"></a>}}
|
||||
\if{latex}{\out{\hypertarget{method-spatialMixture_muutokset-laskeMuutokset}{}}}
|
||||
\subsection{Method \code{laskeMuutokset()}}{
|
||||
\subsection{Usage}{
|
||||
\if{html}{\out{<div class="r">}}\preformatted{spatialMixture_muutokset$laskeMuutokset(
|
||||
ind,
|
||||
rowsFromInd,
|
||||
data,
|
||||
adjprior,
|
||||
priorTerm,
|
||||
logml,
|
||||
cliques,
|
||||
separators
|
||||
)}\if{html}{\out{</div>}}
|
||||
}
|
||||
|
||||
\subsection{Arguments}{
|
||||
\if{html}{\out{<div class="arguments">}}
|
||||
\describe{
|
||||
\item{\code{ind}}{ind}
|
||||
|
||||
\item{\code{rowsFromInd}}{rowsFromInd}
|
||||
|
||||
\item{\code{data}}{data}
|
||||
|
||||
\item{\code{adjprior}}{adjprior}
|
||||
|
||||
\item{\code{priorTerm}}{priorTerm}
|
||||
|
||||
\item{\code{logml}}{logml}
|
||||
|
||||
\item{\code{cliques}}{cliques}
|
||||
|
||||
\item{\code{separators}}{separators}
|
||||
}
|
||||
\if{html}{\out{</div>}}
|
||||
}
|
||||
}
|
||||
\if{html}{\out{<hr>}}
|
||||
\if{html}{\out{<a id="method-spatialMixture_muutokset-clone"></a>}}
|
||||
\if{latex}{\out{\hypertarget{method-spatialMixture_muutokset-clone}{}}}
|
||||
\subsection{Method \code{clone()}}{
|
||||
The objects of this class are cloneable with this method.
|
||||
\subsection{Usage}{
|
||||
\if{html}{\out{<div class="r">}}\preformatted{spatialMixture_muutokset$clone(deep = FALSE)}\if{html}{\out{</div>}}
|
||||
}
|
||||
|
||||
\subsection{Arguments}{
|
||||
\if{html}{\out{<div class="arguments">}}
|
||||
\describe{
|
||||
\item{\code{deep}}{Whether to make a deep clone.}
|
||||
}
|
||||
\if{html}{\out{</div>}}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -147,9 +147,9 @@ test_that("suoritaMuutos works like on Matlab", {
|
|||
})
|
||||
|
||||
test_that("laskeMuutokset4 works like on Matlab", {
|
||||
mx1 <- t(c(.4, 7))
|
||||
x <- admix1_muutokset$new()
|
||||
expect_equivalent(
|
||||
object = laskeMuutokset4(2, mx1, c(8, 2), 3),
|
||||
object = x$laskeMuutokset4(2, t(c(.4, 7)), c(8, 2), 3),
|
||||
expected = t(c(0, .3742)),
|
||||
tol = .0001
|
||||
)
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue