Syntax fixes
This commit is contained in:
Waldir Leoncio
parent
4d9ed9210f
commit
aec2f40c2c
4 changed files with 44 additions and 41 deletions
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@ -4,7 +4,7 @@ computeDiffInCounts <- function(rows, max_noalle, nloci, data) {
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# % riveill<6C> rows. rows pit<69><74> olla vaakavektori.
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diffInCounts <- zeros(max_noalle, nloci)
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for (i in rows) {
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for (i in seq_len(nrow(data)) ) {
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row <- data[i, ]
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notEmpty <- as.matrix(find(row>=0))
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@ -317,7 +317,7 @@ greedyMix <- function(
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# npops <- logml_npops_partitionSummary$npops
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# partitionSummary <- logml_npops_partitionSummary$partitionSummary
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} else {
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logml_npops_partitionSummary <- indMix(c) # TODO: translate
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logml_npops_partitionSummary <- indMix(c)
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logml <- logml_npops_partitionSummary$logml
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npops <- logml_npops_partitionSummary$npops
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partitionSummary <- logml_npops_partitionSummary$partitionSummary
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@ -20,7 +20,7 @@ handleData <- function(raw_data) {
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# koodi pienimm?ksi koodiksi, joka isompi kuin mik??n k?yt?ss?oleva koodi.
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# T?m?n j?lkeen funktio muuttaa alleelikoodit siten, ett?yhden lokuksen j
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# koodit saavat arvoja v?lill?1,...,noalle(j).
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data <- raw_data
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data <- as.matrix(raw_data)
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nloci <- size(raw_data, 2) - 1
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dataApu <- data[, 1:nloci]
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@ -35,26 +35,31 @@ handleData <- function(raw_data) {
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# isoinAlleeli <- []
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noalle <- zeros(1, nloci)
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alleelitLokuksessa <- cell(nloci, 1)
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alleelitLokuksessa <- cell(nloci, 1, expandable=TRUE)
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for (i in 1:nloci) {
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alleelitLokuksessaI <- unique(data[, i])
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alleelitLokuksessaI_pos <- find(alleelitLokuksessaI >= 0)
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alleelitLokuksessa[i, 1] <- ifelse(
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test = length(alleelitLokuksessaI_pos) > 0,
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yes = alleelitLokuksessaI[alleelitLokuksessaI_pos],
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no = 0
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)
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noalle[i] <- length(alleelitLokuksessa[i, 1])
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alleelitLokuksessa[[i]] <- sort(alleelitLokuksessaI[
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find(
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alleelitLokuksessaI >= 0
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)
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])
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noalle[i] <- length(alleelitLokuksessa[[i]])
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}
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alleleCodes <- zeros(max(noalle), nloci)
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for (i in 1:nloci) {
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alleelitLokuksessaI <- alleelitLokuksessa[i, 1]
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alleelitLokuksessaI <- alleelitLokuksessa[[i]]
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puuttuvia <- max(noalle) - length(alleelitLokuksessaI)
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alleleCodes[, i] <- as.matrix(
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c(alleelitLokuksessaI, zeros(puuttuvia, 1))
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)
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}
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for (loc in seq_len(nloci)) {
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for (all in seq_len(noalle[loc])) {
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data[find(data[, loc] == alleleCodes[all, loc]), loc] <- all
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}
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}
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nind <- max(data[, ncol(data)])
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nrows <- size(data, 1)
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ncols <- size(data, 2)
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56
R/indMix.R
56
R/indMix.R
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@ -21,7 +21,6 @@ indMix <- function(c, npops, dispText) {
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rm(c)
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nargin <- length(as.list(match.call())) - 1
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if (nargin < 2) {
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dispText <- 1
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npopstext <- matrix()
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@ -48,7 +47,7 @@ indMix <- function(c, npops, dispText) {
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} else {
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npopsTaulu <- as.numeric(npopstext)
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ykkoset <- find(npopsTaulu == 1)
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npopsTaulu[ykkoset] <- list() # Mik<69>li ykk<6B>si<73> annettu yl<79>rajaksi, ne poistetaan.
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npopsTaulu[ykkoset] <- NA # Mik<69>li ykk<6B>si<73> annettu yl<79>rajaksi, ne poistetaan (if ones are given as an upper limit, they are deleted)
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if (isempty(npopsTaulu)) {
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logml <- 1
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partitionSummary <- 1
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@ -112,7 +111,7 @@ indMix <- function(c, npops, dispText) {
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vaihe <- 1
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if (dispText) {
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cat(
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message(
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paste0(
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'\nMixture analysis started with initial ',
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as.character(npops),
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@ -125,7 +124,7 @@ indMix <- function(c, npops, dispText) {
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muutoksia <- 0
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if (dispText) {
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cat(paste('\nPerforming steps:', as.character(roundTypes)))
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message(paste('\nPerforming steps:', as.character(roundTypes)))
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}
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for (n in 1:length(roundTypes)) {
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@ -151,35 +150,35 @@ indMix <- function(c, npops, dispText) {
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diffInCounts <- muutokset_diffInCounts$diffInCounts
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if (round == 1) {
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maxMuutos <- max_MATLAB(muutokset)[[1]]
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i2 <- max_MATLAB(muutokset)[[2]]
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maxMuutos <- max_MATLAB(muutokset)$max
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i2 <- max_MATLAB(muutokset)$idx
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}
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if (i1 != i2 & maxMuutos > 1e-5) {
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# browser() # TEMP
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# Tapahtui muutos
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muutoksia <- 1
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if (muutosNyt == 0) {
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muutosNyt <- 1
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if (dispText) {
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cat('Action 1')
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}
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if (dispText) message('Action 1')
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}
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kokeiltu <- zeros(nRoundTypes, 1)
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kivaluku <- kivaluku + 1
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updateGlobalVariables(
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ind, i2, diffInCounts, adjprior, priorTerm
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)
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logml <- logml+maxMuutos
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logml <- logml + maxMuutos
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if (logml > worstLogml) {
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partitionSummary_added <- addToSummary(
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temp_addToSum <- addToSummary(
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logml, partitionSummary, worstIndex
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)
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partitionSummary <- partitionSummary_added$partitionSummary
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added <- partitionSummary_added$added
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partitionSummary <- temp_addToSum$partitionSummary
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added <- temp_addToSum$added
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if (added == 1) {
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worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]]
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worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]]
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temp_minMATLAB <- min_MATLAB(
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partitionSummary[, 2]
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)
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worstLogml <- temp_minMATLAB[[1]]
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worstIndex <- temp_minMATLAB[[2]]
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}
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}
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}
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@ -188,7 +187,6 @@ indMix <- function(c, npops, dispText) {
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if (muutosNyt == 0) {
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kokeiltu[round] <- 1
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}
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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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@ -218,11 +216,11 @@ indMix <- function(c, npops, dispText) {
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cat('Action 2')
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}
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if (logml > worstLogml) {
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partitionSummary_added <- addToSummary(
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temp_addToSum <- addToSummary(
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logml, partitionSummary, worstIndex
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)
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partitionSummary <- partitionSummary_added$partitionSummary
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added <- partitionSummary_added$added
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partitionSummary <- temp_addToSum$partitionSummary
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added <- temp_addToSum$added
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if (added==1) {
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worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]]
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worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]]
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@ -287,11 +285,11 @@ indMix <- function(c, npops, dispText) {
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}
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}
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if (logml > worstLogml) {
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partitionSummary_added <- addToSummary(
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temp_addToSum <- addToSummary(
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logml, partitionSummary, worstIndex
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)
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partitionSummary <- partitionSummary_added$partitionSummary
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added <- partitionSummary_added$added
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partitionSummary <- temp_addToSum$partitionSummary
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added <- temp_addToSum$added
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if (added==1) {
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worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]]
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worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]]
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@ -369,11 +367,11 @@ indMix <- function(c, npops, dispText) {
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}
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}
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if (logml > worstLogml) {
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partitionSummary_added <- addToSummary(
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temp_addToSum <- addToSummary(
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logml, partitionSummary, worstIndex
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)
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partitionSummary <- partitionSummary_added$partitionSummary
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added <- partitionSummary_added$added
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partitionSummary <- temp_addToSum$partitionSummary
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added <- temp_addToSum$added
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if (added==1) {
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worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]]
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worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]]
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@ -474,11 +472,11 @@ indMix <- function(c, npops, dispText) {
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muutoksia <- 1
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logml <- logml + totalMuutos
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if (logml > worstLogml) {
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partitionSummary_added <- addToSummary(
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temp_addToSum <- addToSummary(
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logml, partitionSummary, worstIndex
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)
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partitionSummary <- partitionSummary_added$partitionSummary
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added <- partitionSummary_added$added
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partitionSummary <- temp_addToSum$partitionSummary
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added <- temp_addToSum$added
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if (added == 1) {
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worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]]
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worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]]
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