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Syntax fixes

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This commit is contained in:
Waldir Leoncio 2021-03-31 10:28:11 +02:00
parent 4d9ed9210f
commit aec2f40c2c
4 changed files with 44 additions and 41 deletions
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2
R/computeDiffInCounts.R
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@ -4,7 +4,7 @@ computeDiffInCounts <- function(rows, max_noalle, nloci, data) {
# % riveill<6C> rows. rows pit<69><74> olla vaakavektori. # % riveill<6C> rows. rows pit<69><74> olla vaakavektori.
diffInCounts <- zeros(max_noalle, nloci) diffInCounts <- zeros(max_noalle, nloci)
for (i in rows) { for (i in seq_len(nrow(data)) ) {
row <- data[i, ] row <- data[i, ]
notEmpty <- as.matrix(find(row>=0)) notEmpty <- as.matrix(find(row>=0))

2
R/greedyMix.R
View file

@ -317,7 +317,7 @@ greedyMix <- function(
# npops <- logml_npops_partitionSummary$npops # npops <- logml_npops_partitionSummary$npops
# partitionSummary <- logml_npops_partitionSummary$partitionSummary # partitionSummary <- logml_npops_partitionSummary$partitionSummary
} else { } else {
logml_npops_partitionSummary <- indMix(c) # TODO: translate logml_npops_partitionSummary <- indMix(c)
logml <- logml_npops_partitionSummary$logml logml <- logml_npops_partitionSummary$logml
npops <- logml_npops_partitionSummary$npops npops <- logml_npops_partitionSummary$npops
partitionSummary <- logml_npops_partitionSummary$partitionSummary partitionSummary <- logml_npops_partitionSummary$partitionSummary

25
R/handleData.R
View file

@ -20,7 +20,7 @@ handleData <- function(raw_data) {
# koodi pienimm?ksi koodiksi, joka isompi kuin mik??n k?yt?ss?oleva koodi. # koodi pienimm?ksi koodiksi, joka isompi kuin mik??n k?yt?ss?oleva koodi.
# T?m?n j?lkeen funktio muuttaa alleelikoodit siten, ett?yhden lokuksen j # T?m?n j?lkeen funktio muuttaa alleelikoodit siten, ett?yhden lokuksen j
# koodit saavat arvoja v?lill?1,...,noalle(j). # koodit saavat arvoja v?lill?1,...,noalle(j).
data <- raw_data data <- as.matrix(raw_data)
nloci <- size(raw_data, 2) - 1 nloci <- size(raw_data, 2) - 1
dataApu <- data[, 1:nloci] dataApu <- data[, 1:nloci]
@ -35,26 +35,31 @@ handleData <- function(raw_data) {
# isoinAlleeli <- [] # isoinAlleeli <- []
noalle <- zeros(1, nloci) noalle <- zeros(1, nloci)
alleelitLokuksessa <- cell(nloci, 1) alleelitLokuksessa <- cell(nloci, 1, expandable=TRUE)
for (i in 1:nloci) { for (i in 1:nloci) {
alleelitLokuksessaI <- unique(data[, i]) alleelitLokuksessaI <- unique(data[, i])
alleelitLokuksessaI_pos <- find(alleelitLokuksessaI >= 0) alleelitLokuksessa[[i]] <- sort(alleelitLokuksessaI[
alleelitLokuksessa[i, 1] <- ifelse( find(
test = length(alleelitLokuksessaI_pos) > 0, alleelitLokuksessaI >= 0
yes = alleelitLokuksessaI[alleelitLokuksessaI_pos], )
no = 0 ])
) noalle[i] <- length(alleelitLokuksessa[[i]])
noalle[i] <- length(alleelitLokuksessa[i, 1])
} }
alleleCodes <- zeros(max(noalle), nloci) alleleCodes <- zeros(max(noalle), nloci)
for (i in 1:nloci) { for (i in 1:nloci) {
alleelitLokuksessaI <- alleelitLokuksessa[i, 1] alleelitLokuksessaI <- alleelitLokuksessa[[i]]
puuttuvia <- max(noalle) - length(alleelitLokuksessaI) puuttuvia <- max(noalle) - length(alleelitLokuksessaI)
alleleCodes[, i] <- as.matrix( alleleCodes[, i] <- as.matrix(
c(alleelitLokuksessaI, zeros(puuttuvia, 1)) c(alleelitLokuksessaI, zeros(puuttuvia, 1))
) )
} }
for (loc in seq_len(nloci)) {
for (all in seq_len(noalle[loc])) {
data[find(data[, loc] == alleleCodes[all, loc]), loc] <- all
}
}
nind <- max(data[, ncol(data)]) nind <- max(data[, ncol(data)])
nrows <- size(data, 1) nrows <- size(data, 1)
ncols <- size(data, 2) ncols <- size(data, 2)

56
R/indMix.R
View file

@ -21,7 +21,6 @@ indMix <- function(c, npops, dispText) {
rm(c) rm(c)
nargin <- length(as.list(match.call())) - 1 nargin <- length(as.list(match.call())) - 1
if (nargin < 2) { if (nargin < 2) {
dispText <- 1 dispText <- 1
npopstext <- matrix() npopstext <- matrix()
@ -48,7 +47,7 @@ indMix <- function(c, npops, dispText) {
} else { } else {
npopsTaulu <- as.numeric(npopstext) npopsTaulu <- as.numeric(npopstext)
ykkoset <- find(npopsTaulu == 1) ykkoset <- find(npopsTaulu == 1)
npopsTaulu[ykkoset] <- list() # Mik<69>li ykk<6B>si<73> annettu yl<79>rajaksi, ne poistetaan. 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)
if (isempty(npopsTaulu)) { if (isempty(npopsTaulu)) {
logml <- 1 logml <- 1
partitionSummary <- 1 partitionSummary <- 1
@ -112,7 +111,7 @@ indMix <- function(c, npops, dispText) {
vaihe <- 1 vaihe <- 1
if (dispText) { if (dispText) {
cat( message(
paste0( paste0(
'\nMixture analysis started with initial ', '\nMixture analysis started with initial ',
as.character(npops), as.character(npops),
@ -125,7 +124,7 @@ indMix <- function(c, npops, dispText) {
muutoksia <- 0 muutoksia <- 0
if (dispText) { if (dispText) {
cat(paste('\nPerforming steps:', as.character(roundTypes))) message(paste('\nPerforming steps:', as.character(roundTypes)))
} }
for (n in 1:length(roundTypes)) { for (n in 1:length(roundTypes)) {
@ -151,35 +150,35 @@ indMix <- function(c, npops, dispText) {
diffInCounts <- muutokset_diffInCounts$diffInCounts diffInCounts <- muutokset_diffInCounts$diffInCounts
if (round == 1) { if (round == 1) {
maxMuutos <- max_MATLAB(muutokset)[[1]] maxMuutos <- max_MATLAB(muutokset)$max
i2 <- max_MATLAB(muutokset)[[2]] i2 <- max_MATLAB(muutokset)$idx
} }
if (i1 != i2 & maxMuutos > 1e-5) { if (i1 != i2 & maxMuutos > 1e-5) {
# browser() # TEMP
# Tapahtui muutos # Tapahtui muutos
muutoksia <- 1 muutoksia <- 1
if (muutosNyt == 0) { if (muutosNyt == 0) {
muutosNyt <- 1 muutosNyt <- 1
if (dispText) { if (dispText) message('Action 1')
cat('Action 1')
}
} }
kokeiltu <- zeros(nRoundTypes, 1) kokeiltu <- zeros(nRoundTypes, 1)
kivaluku <- kivaluku + 1 kivaluku <- kivaluku + 1
updateGlobalVariables( updateGlobalVariables(
ind, i2, diffInCounts, adjprior, priorTerm ind, i2, diffInCounts, adjprior, priorTerm
) )
logml <- logml+maxMuutos logml <- logml + maxMuutos
if (logml > worstLogml) { if (logml > worstLogml) {
partitionSummary_added <- addToSummary( temp_addToSum <- addToSummary(
logml, partitionSummary, worstIndex logml, partitionSummary, worstIndex
) )
partitionSummary <- partitionSummary_added$partitionSummary partitionSummary <- temp_addToSum$partitionSummary
added <- partitionSummary_added$added added <- temp_addToSum$added
if (added == 1) { if (added == 1) {
worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]] temp_minMATLAB <- min_MATLAB(
worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]] partitionSummary[, 2]
)
worstLogml <- temp_minMATLAB[[1]]
worstIndex <- temp_minMATLAB[[2]]
} }
} }
} }
@ -188,7 +187,6 @@ indMix <- function(c, npops, dispText) {
if (muutosNyt == 0) { if (muutosNyt == 0) {
kokeiltu[round] <- 1 kokeiltu[round] <- 1
} }
} else if (round == 2) { # Populaation yhdist<73>minen toiseen. } else if (round == 2) { # Populaation yhdist<73>minen toiseen.
maxMuutos <- 0 maxMuutos <- 0
for (pop in 1:npops) { for (pop in 1:npops) {
@ -218,11 +216,11 @@ indMix <- function(c, npops, dispText) {
cat('Action 2') cat('Action 2')
} }
if (logml > worstLogml) { if (logml > worstLogml) {
partitionSummary_added <- addToSummary( temp_addToSum <- addToSummary(
logml, partitionSummary, worstIndex logml, partitionSummary, worstIndex
) )
partitionSummary <- partitionSummary_added$partitionSummary partitionSummary <- temp_addToSum$partitionSummary
added <- partitionSummary_added$added added <- temp_addToSum$added
if (added==1) { if (added==1) {
worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]] worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]]
worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]] worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]]
@ -287,11 +285,11 @@ indMix <- function(c, npops, dispText) {
} }
} }
if (logml > worstLogml) { if (logml > worstLogml) {
partitionSummary_added <- addToSummary( temp_addToSum <- addToSummary(
logml, partitionSummary, worstIndex logml, partitionSummary, worstIndex
) )
partitionSummary <- partitionSummary_added$partitionSummary partitionSummary <- temp_addToSum$partitionSummary
added <- partitionSummary_added$added added <- temp_addToSum$added
if (added==1) { if (added==1) {
worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]] worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]]
worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]] worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]]
@ -369,11 +367,11 @@ indMix <- function(c, npops, dispText) {
} }
} }
if (logml > worstLogml) { if (logml > worstLogml) {
partitionSummary_added <- addToSummary( temp_addToSum <- addToSummary(
logml, partitionSummary, worstIndex logml, partitionSummary, worstIndex
) )
partitionSummary <- partitionSummary_added$partitionSummary partitionSummary <- temp_addToSum$partitionSummary
added <- partitionSummary_added$added added <- temp_addToSum$added
if (added==1) { if (added==1) {
worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]] worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]]
worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]] worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]]
@ -474,11 +472,11 @@ indMix <- function(c, npops, dispText) {
muutoksia <- 1 muutoksia <- 1
logml <- logml + totalMuutos logml <- logml + totalMuutos
if (logml > worstLogml) { if (logml > worstLogml) {
partitionSummary_added <- addToSummary( temp_addToSum <- addToSummary(
logml, partitionSummary, worstIndex logml, partitionSummary, worstIndex
) )
partitionSummary <- partitionSummary_added$partitionSummary partitionSummary <- temp_addToSum$partitionSummary
added <- partitionSummary_added$added added <- temp_addToSum$added
if (added == 1) { if (added == 1) {
worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]] worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]]
worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]] worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]]