From e4af251307533cf2759cbaaaa4c5457436a30494 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Tue, 2 Jul 2024 11:23:22 +0200
Subject: [PATCH 1/6] Fixed tests (#24)
---
tests/testthat/test-greedyMix.R | 11 +++++------
1 file changed, 5 insertions(+), 6 deletions(-)
diff --git a/tests/testthat/test-greedyMix.R b/tests/testthat/test-greedyMix.R
index 6a4f2f2..86cf9fb 100644
--- a/tests/testthat/test-greedyMix.R
+++ b/tests/testthat/test-greedyMix.R
@@ -46,11 +46,10 @@ raw_bam <- importFile(
data = file.path(path_inst, "bam_example.bam"),
format = "BAM",
)
-# TODO: uncomment for testing #24
-# raw_baps <- importFile(
-# data = file.path(path_inst, "FASTA_clustering_haploid.fasta"),
-# format = "FASTA"
-# )
+raw_baps <- importFile(
+ data = file.path(path_inst, "FASTA_clustering_haploid.fasta"),
+ format = "FASTA"
+)
test_that("Files are imported correctly", {
expect_equal(dim(raw_fasta), c(5, 99))
@@ -71,7 +70,7 @@ test_that("Files are imported correctly", {
)
})
-test_that("greedyMix() works", {
+test_that("greedyMix() fails successfully", {
expect_error(greedyMix(file.path(path_inst, "vcf_example.vcf")))
expect_error(greedyMix(file.path(path_inst, "bam_example.bam")))
})
From 6aecf382317182bfc977b92e38ab8e38467936bb Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Tue, 2 Jul 2024 12:17:02 +0200
Subject: [PATCH 2/6] Fixed `indMix()` and subfunctions (#24)
---
R/indMix.R | 86 ++++++------
R/laskeMuutokset12345.R | 252 +++++++++++++++++++-----------------
R/laskeOsaDist.R | 4 +-
R/poistaTyhjatPopulaatiot.R | 16 +--
R/returnInOrder.R | 14 +-
5 files changed, 189 insertions(+), 183 deletions(-)
diff --git a/R/indMix.R b/R/indMix.R
index 323c8d0..f868ed7 100644
--- a/R/indMix.R
+++ b/R/indMix.R
@@ -195,9 +195,7 @@ indMix <- function(c, npops, counts = NULL, sumcounts = NULL, max_iter = 100L, d
} else if (round == 2) { # Populaation yhdist�minen toiseen.
maxMuutos <- 0
for (pop in seq_len(npops)) {
- muutokset_diffInCounts <- greedyMix_muutokset$new
- # FIXME: wrong input
- browser() # TEMP. Tip: browserText()
+ muutokset_diffInCounts <- greedyMix_muutokset$new()
muutokset_diffInCounts <- muutokset_diffInCounts$laskeMuutokset2(
pop, rows, data, adjprior, priorTerm
)
@@ -241,7 +239,7 @@ indMix <- function(c, npops, counts = NULL, sumcounts = NULL, max_iter = 100L, d
maxMuutos <- 0
ninds <- size(rows, 1)
for (pop in seq_len(npops)) {
- inds2 <- matlab2r::find(PARTITION == pop)
+ inds2 <- matlab2r::find(globals$PARTITION == pop)
ninds2 <- length(inds2)
if (ninds2 > 2) {
dist2 <- laskeOsaDist(inds2, dist, ninds)
@@ -256,8 +254,8 @@ indMix <- function(c, npops, counts = NULL, sumcounts = NULL, max_iter = 100L, d
muutokset <- muutokset_diffInCounts$laskeMuutokset3(
T2, inds2, rows, data, adjprior, priorTerm, pop
)
- isoin <- matlab2r::max(muutokset)[[1]]
- indeksi <- matlab2r::max(muutokset)[[2]]
+ isoin <- matlab2r::max(c(muutokset))[[1]]
+ indeksi <- matlab2r::max(c(muutokset))[[2]]
if (isoin > maxMuutos) {
maxMuutos <- isoin
muuttuvaPop2 <- indeksi %% npops2
@@ -277,9 +275,9 @@ indMix <- function(c, npops, counts = NULL, sumcounts = NULL, max_iter = 100L, d
rivit <- rbind(rivit, t(lisa))
}
diffInCounts <- computeDiffInCounts(
- t(rivit), size(COUNTS, 1), size(COUNTS, 2), data
+ t(rivit), size(globals$COUNTS, 1), size(globals$COUNTS, 2), data
)
- i1 <- PARTITION[muuttuvat[1]]
+ i1 <- globals$PARTITION[muuttuvat[1]]
updateGlobalVariables3(
muuttuvat, diffInCounts, adjprior, priorTerm, i2
)
@@ -308,26 +306,24 @@ indMix <- function(c, npops, counts = NULL, sumcounts = NULL, max_iter = 100L, d
} else if (round == 5 || round == 6) {
j <- 0
muutettu <- 0
- poplogml <- POP_LOGML
- partition <- PARTITION
- counts <- COUNTS
- sumcounts <- SUMCOUNTS
- logdiff <- LOGDIFF
+ poplogml <- globals$POP_LOGML
+ partition <- globals$PARTITION
+ counts <- globals$COUNTS
+ sumcounts <- globals$SUMCOUNTS
+ logdiff <- globals$LOGDIFF
pops <- sample(npops)
while (j < npops & muutettu == 0) {
j <- j + 1
pop <- pops[j]
totalMuutos <- 0
- inds <- matlab2r::find(PARTITION == pop)
+ inds <- matlab2r::find(globals$PARTITION == pop)
if (round == 5) {
- aputaulu <- c(inds, rand(length(inds), 1))
+ aputaulu <- matrix(c(inds, rand(length(inds), 1)), ncol = 2)
aputaulu <- sortrows(aputaulu, 2)
inds <- aputaulu[, 1]
- } else if (round == 6) {
- inds <- returnInOrder(
- inds, pop, rows, data, adjprior, priorTerm
- )
+ } else if (round == 6 && length(inds) > 0) {
+ inds <- returnInOrder(inds, pop, rows, data, adjprior, priorTerm)
}
i <- 0
@@ -386,12 +382,12 @@ indMix <- function(c, npops, counts = NULL, sumcounts = NULL, max_iter = 100L, d
} else {
# Miss��n vaiheessa tila ei parantunut.
# Perutaan kaikki muutokset.
- PARTITION <- partition
- SUMCOUNTS <- sumcounts
- POP_LOGML <- poplogml
- COUNTS <- counts
+ globals$PARTITION <- partition
+ globals$SUMCOUNTS <- sumcounts
+ globals$POP_LOGML <- poplogml
+ globals$COUNTS <- counts
logml <- logml - totalMuutos
- LOGDIFF <- logdiff
+ globals$LOGDIFF <- logdiff
kokeiltu[round] <- 1
}
}
@@ -401,20 +397,20 @@ indMix <- function(c, npops, counts = NULL, sumcounts = NULL, max_iter = 100L, d
j <- 0
pops <- sample(npops)
muutoksiaNyt <- 0
- if (emptyPop == -1) {
+ if (emptyPop$emptyPop == -1) {
j <- npops
}
while (j < npops) {
j <- j + 1
pop <- pops[j]
- inds2 <- matlab2r::find(PARTITION == pop)
+ inds2 <- matlab2r::find(globals$PARTITION == pop)
ninds2 <- length(inds2)
if (ninds2 > 5) {
- partition <- PARTITION
- sumcounts <- SUMCOUNTS
- counts <- COUNTS
- poplogml <- POP_LOGML
- logdiff <- LOGDIFF
+ partition <- globals$PARTITION
+ sumcounts <- globals$SUMCOUNTS
+ counts <- globals$COUNTS
+ poplogml <- globals$POP_LOGML
+ logdiff <- globals$LOGDIFF
dist2 <- laskeOsaDist(inds2, dist, ninds)
Z2 <- linkage(t(dist2))
@@ -433,7 +429,7 @@ indMix <- function(c, npops, counts = NULL, sumcounts = NULL, max_iter = 100L, d
rivit <- c(rivit, lisa)
}
diffInCounts <- computeDiffInCounts(
- rivit, size(COUNTS, 1), size(COUNTS, 2), data
+ rivit, size(globals$COUNTS, 1), size(globals$COUNTS, 2), data
)
updateGlobalVariables3(
@@ -454,7 +450,7 @@ indMix <- function(c, npops, counts = NULL, sumcounts = NULL, max_iter = 100L, d
maxMuutos <- indeksi <- matlab2r::max(muutokset)
muuttuva <- inds2(indeksi)
- if (PARTITION(muuttuva) == pop) {
+ if (globals$PARTITION(muuttuva) == pop) {
i2 <- emptyPop
} else {
i2 <- pop
@@ -463,7 +459,7 @@ indMix <- function(c, npops, counts = NULL, sumcounts = NULL, max_iter = 100L, d
if (maxMuutos > 1e-5) {
rivit <- rows[muuttuva, 1]:rows[muuttuva, 2]
diffInCounts <- computeDiffInCounts(
- rivit, size(COUNTS, 1), size(COUNTS, 2),
+ rivit, size(globals$COUNTS, 1), size(globals$COUNTS, 2),
data
)
updateGlobalVariables3(
@@ -498,11 +494,11 @@ indMix <- function(c, npops, counts = NULL, sumcounts = NULL, max_iter = 100L, d
j <- npops
} else {
# palutetaan vanhat arvot
- PARTITION <- partition
- SUMCOUNTS <- sumcounts
- COUNTS <- counts
- POP_LOGML <- poplogml
- LOGDIFF <- logdiff
+ globals$PARTITION <- partition
+ globals$SUMCOUNTS <- sumcounts
+ globals$COUNTS <- counts
+ globals$POP_LOGML <- poplogml
+ globals$LOGDIFF <- logdiff
}
}
}
@@ -540,7 +536,7 @@ indMix <- function(c, npops, counts = NULL, sumcounts = NULL, max_iter = 100L, d
# TALLENNETAAN
npops <- poistaTyhjatPopulaatiot(npops)
- POP_LOGML <- computePopulationLogml(seq_len(npops), adjprior, priorTerm)
+ globals$POP_LOGML <- computePopulationLogml(seq_len(npops), adjprior, priorTerm)
if (dispText) {
message("Found partition with ", as.character(npops), " populations.")
message("Log(ml) = ", as.character(logml))
@@ -550,11 +546,11 @@ indMix <- function(c, npops, counts = NULL, sumcounts = NULL, max_iter = 100L, d
# P�ivitet��n parasta l�ydetty� partitiota.
logmlBest <- logml
npopsBest <- npops
- partitionBest <- PARTITION
- countsBest <- COUNTS
- sumCountsBest <- SUMCOUNTS
- pop_logmlBest <- POP_LOGML
- logdiffbest <- LOGDIFF
+ partitionBest <- globals$PARTITION
+ countsBest <- globals$COUNTS
+ sumCountsBest <- globals$SUMCOUNTS
+ pop_logmlBest <- globals$POP_LOGML
+ logdiffbest <- globals$LOGDIFF
}
}
return(
diff --git a/R/laskeMuutokset12345.R b/R/laskeMuutokset12345.R
index 6cff0e1..78c9f5c 100644
--- a/R/laskeMuutokset12345.R
+++ b/R/laskeMuutokset12345.R
@@ -15,9 +15,9 @@ spatialMixture_muutokset <- R6Class(
) {
# Palauttaa npops * 1 taulun, jossa i:s alkio kertoo, mik?olisi
# muutos logml:ss? mikהli yksil?ind siirretההn koriin i.
- # diffInCounts on poistettava COUNTS:in siivusta i1 ja lisהttהv?
- # COUNTS:in siivuun i2, mikהli muutos toteutetaan.
- npops <- size(COUNTS, 3)
+ # diffInCounts on poistettava globals$COUNTS:in siivusta i1 ja lisהttהv?
+ # globals$COUNTS:in siivuun i2, mikהli muutos toteutetaan.
+ npops <- size(globals$COUNTS, 3)
muutokset <- zeros(npops, 1)
emptyPop_pops <- findEmptyPop(npops)
@@ -25,42 +25,42 @@ spatialMixture_muutokset <- R6Class(
pops <- emptyPop_pops$pops
rm(emptyPop_pops)
- i1 <- PARTITION(ind)
+ i1 <- globals$PARTITION(ind)
i2 <- pops[find(pops != i1)]
if (emptyPop > 0) {
i2 <- c(i2, emptyPop)
}
rows <- ((ind - 1) * rowsFromInd + 1):(ind * rowsFromInd)
- diffInCounts <- computeDiffInCounts(rows, size(COUNTS, 1), size(COUNTS, 2), data)
+ diffInCounts <- computeDiffInCounts(rows, size(globals$COUNTS, 1), size(globals$COUNTS, 2), data)
diffInSumCounts <- sum(diffInCounts)
diffInCliqCounts <- computeDiffInCliqCounts(cliques, ind)
diffInSepCounts <- computeDiffInCliqCounts(separators, ind)
- COUNTS[, ,i1] <- COUNTS[, , i1] - diffInCounts
- SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] - diffInSumCounts
- CLIQCOUNTS[, i1] <- CLIQCOUNTS[, i1] - diffInCliqCounts
- SEPCOUNTS[, i1] <- SEPCOUNTS[, i1] - diffInSepCounts
+ globals$COUNTS[, ,i1] <- globals$COUNTS[, , i1] - diffInCounts
+ globals$SUMCOUNTS[i1, ] <- globals$SUMCOUNTS[i1, ] - diffInSumCounts
+ globals$CLIQCOUNTS[, i1] <- globals$CLIQCOUNTS[, i1] - diffInCliqCounts
+ globals$SEPCOUNTS[, i1] <- globals$SEPCOUNTS[, i1] - diffInSepCounts
for (i in i2) {
- CLIQCOUNTS[, i] <- CLIQCOUNTS[, i] + diffInCliqCounts
- SEPCOUNTS[, i] <- SEPCOUNTS[, i] + diffInSepCounts
- COUNTS[, ,i] <- COUNTS[, , i] + diffInCounts
- SUMCOUNTS[i, ] <- SUMCOUNTS[i, ] + diffInSumCounts
+ globals$CLIQCOUNTS[, i] <- globals$CLIQCOUNTS[, i] + diffInCliqCounts
+ globals$SEPCOUNTS[, i] <- globals$SEPCOUNTS[, i] + diffInSepCounts
+ globals$COUNTS[, ,i] <- globals$COUNTS[, , i] + diffInCounts
+ globals$SUMCOUNTS[i, ] <- globals$SUMCOUNTS[i, ] + diffInSumCounts
muutokset[i] <- computeLogml(adjprior, priorTerm) - logml
- CLIQCOUNTS[, i] <- CLIQCOUNTS[, i] - diffInCliqCounts
- SEPCOUNTS[, i] <- SEPCOUNTS[, i] - diffInSepCounts
- COUNTS[, , i] <- COUNTS[, , i] - diffInCounts
- SUMCOUNTS[i, ] <- SUMCOUNTS[i, ] - diffInSumCounts
+ globals$CLIQCOUNTS[, i] <- globals$CLIQCOUNTS[, i] - diffInCliqCounts
+ globals$SEPCOUNTS[, i] <- globals$SEPCOUNTS[, i] - diffInSepCounts
+ globals$COUNTS[, , i] <- globals$COUNTS[, , i] - diffInCounts
+ globals$SUMCOUNTS[i, ] <- globals$SUMCOUNTS[i, ] - diffInSumCounts
}
- COUNTS[, , i1] <- COUNTS[, , i1] + diffInCounts
- SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] + diffInSumCounts
- CLIQCOUNTS[, i1] <- CLIQCOUNTS[, i1] + diffInCliqCounts
- SEPCOUNTS[, i1] <- SEPCOUNTS[, i1] + diffInSepCounts
+ globals$COUNTS[, , i1] <- globals$COUNTS[, , i1] + diffInCounts
+ globals$SUMCOUNTS[i1, ] <- globals$SUMCOUNTS[i1, ] + diffInSumCounts
+ globals$CLIQCOUNTS[, i1] <- globals$CLIQCOUNTS[, i1] + diffInCliqCounts
+ globals$SEPCOUNTS[, i1] <- globals$SEPCOUNTS[, i1] + diffInSepCounts
# Asetetaan muillekin tyhjille populaatioille sama muutos, kuin
# emptyPop:lle
@@ -87,11 +87,11 @@ spatialMixture_muutokset <- R6Class(
# koriin i.
# Laskee muutokset vain yhdelle tyhjהlle populaatiolle, muille tulee
# muutokseksi 0.
- # global COUNTS # global SUMCOUNTS
- # global PARTITION # global POP_LOGML
- # global CLIQCOUNTS # global SEPCOUNTS
+ # global globals$COUNTS # global globals$SUMCOUNTS
+ # global globals$PARTITION # global globals$POP_LOGML
+ # global globals$CLIQCOUNTS # global globals$SEPCOUNTS
- npops <- size(COUNTS, 3)
+ npops <- size(globals$COUNTS, 3)
muutokset <- zeros(npops, 1)
emptyPop <- findEmptyPop(npops)$emptyPop
@@ -102,37 +102,37 @@ spatialMixture_muutokset <- R6Class(
i2 <- c(i2, emptyPop)
}
- inds <- find(PARTITION == i1)
+ inds <- find(globals$PARTITION == i1)
rows <- computeRows(rowsFromInd, inds, length(inds))
- diffInCounts <- computeDiffInCounts(rows, size(COUNTS, 1), size(COUNTS, 2), data)
+ diffInCounts <- computeDiffInCounts(rows, size(globals$COUNTS, 1), size(globals$COUNTS, 2), data)
diffInSumCounts <- sum(diffInCounts)
diffInCliqCounts <- computeDiffInCliqCounts(cliques, inds)
diffInSepCounts <- computeDiffInCliqCounts(separators, inds)
- COUNTS[, ,i1] <- COUNTS[, , i1] - diffInCounts
- SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] - diffInSumCounts
- CLIQCOUNTS[, i1] <- 0
- SEPCOUNTS[, i1] <- 0
+ globals$COUNTS[, ,i1] <- globals$COUNTS[, , i1] - diffInCounts
+ globals$SUMCOUNTS[i1, ] <- globals$SUMCOUNTS[i1, ] - diffInSumCounts
+ globals$CLIQCOUNTS[, i1] <- 0
+ globals$SEPCOUNTS[, i1] <- 0
for (i in i2) {
- CLIQCOUNTS[, i] <- CLIQCOUNTS[, i] + diffInCliqCounts
- SEPCOUNTS[, i] <- SEPCOUNTS[, i] + diffInSepCounts
- COUNTS[, ,i] <- COUNTS[, , i] + diffInCounts
- SUMCOUNTS[i, ] <- SUMCOUNTS[i, ] + diffInSumCounts
+ globals$CLIQCOUNTS[, i] <- globals$CLIQCOUNTS[, i] + diffInCliqCounts
+ globals$SEPCOUNTS[, i] <- globals$SEPCOUNTS[, i] + diffInSepCounts
+ globals$COUNTS[, ,i] <- globals$COUNTS[, , i] + diffInCounts
+ globals$SUMCOUNTS[i, ] <- globals$SUMCOUNTS[i, ] + diffInSumCounts
muutokset[i] <- computeLogml(adjprior, priorTerm) - logml
- CLIQCOUNTS[, i] <- CLIQCOUNTS[, i] - diffInCliqCounts
- SEPCOUNTS[, i] <- SEPCOUNTS[, i] - diffInSepCounts
- COUNTS[, ,i] <- COUNTS[, , i] - diffInCounts
- SUMCOUNTS[i, ] <- SUMCOUNTS[i, ] - diffInSumCounts
+ globals$CLIQCOUNTS[, i] <- globals$CLIQCOUNTS[, i] - diffInCliqCounts
+ globals$SEPCOUNTS[, i] <- globals$SEPCOUNTS[, i] - diffInSepCounts
+ globals$COUNTS[, ,i] <- globals$COUNTS[, , i] - diffInCounts
+ globals$SUMCOUNTS[i, ] <- globals$SUMCOUNTS[i, ] - diffInSumCounts
}
- COUNTS[, ,i1] <- COUNTS[, , i1] + diffInCounts
- SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] + diffInSumCounts
- CLIQCOUNTS[, i1] <- diffInCliqCounts
- SEPCOUNTS[, i1] <- diffInSepCounts
+ globals$COUNTS[, ,i1] <- globals$COUNTS[, , i1] + diffInCounts
+ globals$SUMCOUNTS[i1, ] <- globals$SUMCOUNTS[i1, ] + diffInSumCounts
+ globals$CLIQCOUNTS[, i1] <- diffInCliqCounts
+ globals$SEPCOUNTS[, i1] <- diffInSepCounts
return(list(muutokset = muutokset, diffInCounts = diffInCounts))
},
#' @param T2 T2
@@ -154,11 +154,11 @@ spatialMixture_muutokset <- R6Class(
# inds2(find(T2 == i)) siirretההn koriin j.
# Laskee vain yhden tyhjהn populaation, muita kohden muutokseksi jהה 0.
- # global COUNTS # global SUMCOUNTS
- # global PARTITION # global POP_LOGML
- # global CLIQCOUNTS # global SEPCOUNTS
+ # global globals$COUNTS # global globals$SUMCOUNTS
+ # global globals$PARTITION # global globals$POP_LOGML
+ # global globals$CLIQCOUNTS # global globals$SEPCOUNTS
- npops <- size(COUNTS, 3)
+ npops <- size(globals$COUNTS, 3)
npops2 <- length(unique(T2))
muutokset <- zeros(npops2, npops)
@@ -168,15 +168,15 @@ spatialMixture_muutokset <- R6Class(
if (ninds > 0) {
rows <- computeRows(rowsFromInd, inds, ninds)
- diffInCounts <- computeDiffInCounts(rows, size(COUNTS, 1), size(COUNTS, 2), data)
+ diffInCounts <- computeDiffInCounts(rows, size(globals$COUNTS, 1), size(globals$COUNTS, 2), data)
diffInSumCounts <- sum(diffInCounts)
diffInCliqCounts <- computeDiffInCliqCounts(cliques, inds)
diffInSepCounts <- computeDiffInCliqCounts(separators, inds)
- COUNTS[, ,i1] <- COUNTS[, , i1] - diffInCounts
- SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] - diffInSumCounts
- CLIQCOUNTS[, i1] <- CLIQCOUNTS[, i1] - diffInCliqCounts
- SEPCOUNTS[, i1] <- SEPCOUNTS[, i1] - diffInSepCounts
+ globals$COUNTS[, ,i1] <- globals$COUNTS[, , i1] - diffInCounts
+ globals$SUMCOUNTS[i1, ] <- globals$SUMCOUNTS[i1, ] - diffInSumCounts
+ globals$CLIQCOUNTS[, i1] <- globals$CLIQCOUNTS[, i1] - diffInCliqCounts
+ globals$SEPCOUNTS[, i1] <- globals$SEPCOUNTS[, i1] - diffInSepCounts
emptyPop <- findEmptyPop(npops)$emptyPop
pops <- findEmptyPop(npops)$pops
@@ -186,23 +186,23 @@ spatialMixture_muutokset <- R6Class(
}
for (i in i2) {
- CLIQCOUNTS[, i] <- CLIQCOUNTS[, i] + diffInCliqCounts
- SEPCOUNTS[, i] <- SEPCOUNTS[, i] + diffInSepCounts
- COUNTS[, ,i] <- COUNTS[, , i] + diffInCounts
- SUMCOUNTS[i, ] <- SUMCOUNTS[i, ] + diffInSumCounts
+ globals$CLIQCOUNTS[, i] <- globals$CLIQCOUNTS[, i] + diffInCliqCounts
+ globals$SEPCOUNTS[, i] <- globals$SEPCOUNTS[, i] + diffInSepCounts
+ globals$COUNTS[, ,i] <- globals$COUNTS[, , i] + diffInCounts
+ globals$SUMCOUNTS[i, ] <- globals$SUMCOUNTS[i, ] + diffInSumCounts
muutokset[pop2, i] <- computeLogml(adjprior, priorTerm) - logml
- CLIQCOUNTS[, i] <- CLIQCOUNTS[, i] - diffInCliqCounts
- SEPCOUNTS[, i] <- SEPCOUNTS[, i] - diffInSepCounts
- COUNTS[, ,i] <- COUNTS[, , i] - diffInCounts
- SUMCOUNTS[i, ] <- SUMCOUNTS[i, ] - diffInSumCounts
+ globals$CLIQCOUNTS[, i] <- globals$CLIQCOUNTS[, i] - diffInCliqCounts
+ globals$SEPCOUNTS[, i] <- globals$SEPCOUNTS[, i] - diffInSepCounts
+ globals$COUNTS[, ,i] <- globals$COUNTS[, , i] - diffInCounts
+ globals$SUMCOUNTS[i, ] <- globals$SUMCOUNTS[i, ] - diffInSumCounts
}
- COUNTS[, ,i1] <- COUNTS[, , i1] + diffInCounts
- SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] + diffInSumCounts
- CLIQCOUNTS[, i1] <- CLIQCOUNTS[, i1] + diffInCliqCounts
- SEPCOUNTS[, i1] <- SEPCOUNTS[, i1] + diffInSepCounts
+ globals$COUNTS[, ,i1] <- globals$COUNTS[, , i1] + diffInCounts
+ globals$SUMCOUNTS[i1, ] <- globals$SUMCOUNTS[i1, ] + diffInSumCounts
+ globals$CLIQCOUNTS[, i1] <- globals$CLIQCOUNTS[, i1] + diffInCliqCounts
+ globals$SEPCOUNTS[, i1] <- globals$SEPCOUNTS[, i1] + diffInSepCounts
}
}
return(muutokset)
@@ -224,18 +224,18 @@ spatialMixture_muutokset <- R6Class(
# Palauttaa length(inds) * 1 taulun, jossa i:s alkio kertoo, mik?olisi
# muutos logml:ss? mikהli yksil?i vaihtaisi koria i1:n ja i2:n vהlill?
- # global COUNTS # global SUMCOUNTS
- # global PARTITION
- # global CLIQCOUNTS # global SEPCOUNTS
+ # global globals$COUNTS # global globals$SUMCOUNTS
+ # global globals$PARTITION
+ # global globals$CLIQCOUNTS # global globals$SEPCOUNTS
ninds <- length(inds)
muutokset <- zeros(ninds, 1)
- cliqsize <- size(CLIQCOUNTS, 2)
- sepsize <- size(SEPCOUNTS, 2)
+ cliqsize <- size(globals$CLIQCOUNTS, 2)
+ sepsize <- size(globals$SEPCOUNTS, 2)
for (i in 1:ninds) {
ind <- inds[i]
- if (PARTITION[ind] == i1) {
+ if (globals$PARTITION[ind] == i1) {
pop1 <- i1 # mist?
pop2 <- i2 # mihin
} else {
@@ -244,32 +244,32 @@ spatialMixture_muutokset <- R6Class(
}
rows <- ((ind - 1) * rowsFromInd + 1):(ind * rowsFromInd)
- diffInCounts <- computeDiffInCounts(rows, size(COUNTS, 1), size(COUNTS, 2), data)
+ diffInCounts <- computeDiffInCounts(rows, size(globals$COUNTS, 1), size(globals$COUNTS, 2), data)
diffInSumCounts <- sum(diffInCounts)
diffInCliqCounts <- computeDiffInCliqCounts(cliques, ind)
diffInSepCounts <- computeDiffInCliqCounts(separators, ind)
- COUNTS[, ,pop1] <- COUNTS[, , pop1] - diffInCounts
- SUMCOUNTS[pop1, ] <- SUMCOUNTS[pop1, ] - diffInSumCounts
- COUNTS[, ,pop2] <- COUNTS[, , pop2] + diffInCounts
- SUMCOUNTS[pop2, ] <- SUMCOUNTS[pop2, ] + diffInSumCounts
+ globals$COUNTS[, ,pop1] <- globals$COUNTS[, , pop1] - diffInCounts
+ globals$SUMCOUNTS[pop1, ] <- globals$SUMCOUNTS[pop1, ] - diffInSumCounts
+ globals$COUNTS[, ,pop2] <- globals$COUNTS[, , pop2] + diffInCounts
+ globals$SUMCOUNTS[pop2, ] <- globals$SUMCOUNTS[pop2, ] + diffInSumCounts
- CLIQCOUNTS[, pop1] <- CLIQCOUNTS[, pop1] - diffInCliqCounts
- CLIQCOUNTS[, pop2] <- CLIQCOUNTS[, pop2] + diffInCliqCounts
- SEPCOUNTS[, pop1] <- SEPCOUNTS[, pop1] - diffInSepCounts
- SEPCOUNTS[, pop2] <- SEPCOUNTS[, pop2] + diffInSepCounts
+ globals$CLIQCOUNTS[, pop1] <- globals$CLIQCOUNTS[, pop1] - diffInCliqCounts
+ globals$CLIQCOUNTS[, pop2] <- globals$CLIQCOUNTS[, pop2] + diffInCliqCounts
+ globals$SEPCOUNTS[, pop1] <- globals$SEPCOUNTS[, pop1] - diffInSepCounts
+ globals$SEPCOUNTS[, pop2] <- globals$SEPCOUNTS[, pop2] + diffInSepCounts
muutokset[i] <- computeLogml(adjprior, priorTerm) - logml
- COUNTS[, ,pop1] <- COUNTS[, , pop1] + diffInCounts
- SUMCOUNTS[pop1, ] <- SUMCOUNTS[pop1, ] + diffInSumCounts
- COUNTS[, ,pop2] <- COUNTS[, , pop2] - diffInCounts
- SUMCOUNTS[pop2, ] <- SUMCOUNTS[pop2, ] - diffInSumCounts
+ globals$COUNTS[, ,pop1] <- globals$COUNTS[, , pop1] + diffInCounts
+ globals$SUMCOUNTS[pop1, ] <- globals$SUMCOUNTS[pop1, ] + diffInSumCounts
+ globals$COUNTS[, ,pop2] <- globals$COUNTS[, , pop2] - diffInCounts
+ globals$SUMCOUNTS[pop2, ] <- globals$SUMCOUNTS[pop2, ] - diffInSumCounts
- CLIQCOUNTS[, pop1] <- CLIQCOUNTS[, pop1] + diffInCliqCounts
- CLIQCOUNTS[, pop2] <- CLIQCOUNTS[, pop2] - diffInCliqCounts
- SEPCOUNTS[, pop1] <- SEPCOUNTS[, pop1] + diffInSepCounts
- SEPCOUNTS[, pop2] <- SEPCOUNTS[, pop2] - diffInSepCounts
+ globals$CLIQCOUNTS[, pop1] <- globals$CLIQCOUNTS[, pop1] + diffInCliqCounts
+ globals$CLIQCOUNTS[, pop2] <- globals$CLIQCOUNTS[, pop2] - diffInCliqCounts
+ globals$SEPCOUNTS[, pop1] <- globals$SEPCOUNTS[, pop1] + diffInSepCounts
+ globals$SEPCOUNTS[, pop2] <- globals$SEPCOUNTS[, pop2] - diffInSepCounts
}
return(muutokset)
@@ -327,8 +327,8 @@ admix1_muutokset <- R6Class(
#' @title Calculate changes (greedyMix class)
#' @description Palauttaa npops*1 taulun, jossa i:s alkio kertoo, mik� olisi
#' muutos logml:ss�, mik�li yksil� ind siirret��n koriin i.
-#' diffInCounts on poistettava COUNTS:in siivusta i1 ja lis�tt�v�
-#' COUNTS:in siivuun i2, mik�li muutos toteutetaan.
+#' diffInCounts on poistettava globals$COUNTS:in siivusta i1 ja lis�tt�v�
+#' globals$COUNTS:in siivuun i2, mik�li muutos toteutetaan.
#'
#' Lis�ys 25.9.2007:
#' Otettu k�ytt��n globaali muuttuja LOGDIFF, johon on tallennettu muutokset
@@ -401,11 +401,11 @@ greedyMix_muutokset <- R6Class(
if (ninds == 0) {
diffInCounts <- zeros(size(globals$COUNTS, 1), size(globals$COUNTS, 2))
- return()
+ return(list("muutokset" = muutokset, "diffInCounts" = diffInCounts))
}
rows <- list()
- for (i in 1:ninds) {
+ for (i in seq_len(ninds)) {
ind <- inds[i]
lisa <- globalRows[ind, 1]:globalRows[ind, 2]
rows <- c(rows, t(lisa))
@@ -414,7 +414,7 @@ greedyMix_muutokset <- R6Class(
diffInCounts <- computeDiffInCounts(
t(rows), size(globals$COUNTS, 1), size(globals$COUNTS, 2), data
)
- diffInSumCounts <- sum(diffInCounts)
+ diffInSumCounts <- colSums(diffInCounts)
globals$COUNTS[, , i1] <- globals$COUNTS[, , i1] - diffInCounts
globals$SUMCOUNTS[i1, ] <- globals$SUMCOUNTS[i1, ] - diffInSumCounts
@@ -422,7 +422,11 @@ greedyMix_muutokset <- R6Class(
globals$COUNTS[, , i1] <- globals$COUNTS[, , i1] + diffInCounts
globals$SUMCOUNTS[i1, ] <- globals$SUMCOUNTS[i1, ] + diffInSumCounts
- i2 <- c(1:i1 - 1, i1 + 1:npops)
+ if (i1 < npops) {
+ i2 <- c(1:(i1 - 1), (i1 + 1):npops)
+ } else {
+ i2 <- 1:(i1 - 1)
+ }
i2_logml <- globals$POP_LOGML[i2]
globals$COUNTS[, , i2] <- globals$COUNTS[, , i2] + repmat(diffInCounts, c(1, 1, npops - 1))
@@ -431,7 +435,8 @@ greedyMix_muutokset <- R6Class(
globals$COUNTS[, , i2] <- globals$COUNTS[, , i2] - repmat(diffInCounts, c(1, 1, npops - 1))
globals$SUMCOUNTS[i2, ] <- globals$SUMCOUNTS[i2, ] - repmat(diffInSumCounts, c(npops - 1, 1))
- muutokset[i2] <- new_i1_logml - i1_logml + new_i2_logml - i2_logml
+ i1_diff <- new_i1_logml - i1_logml
+ muutokset[i2] <- rep(i1_diff, length(i2_logml)) + new_i2_logml - i2_logml
return(list(muutokset = muutokset, diffInCounts = diffInCounts))
},
#' @param T2 T2
@@ -448,11 +453,11 @@ greedyMix_muutokset <- R6Class(
# kertoo, mik� olisi muutos logml:ss�, jos populaation i1 osapopulaatio
# inds2(matlab2r::find(T2==i)) siirret��n koriin j.
- npops <- size(COUNTS, 3)
+ npops <- size(globals$COUNTS, 3)
npops2 <- length(unique(T2))
muutokset <- zeros(npops2, npops)
- i1_logml <- POP_LOGML[i1]
+ i1_logml <- globals$POP_LOGML[i1]
for (pop2 in 1:npops2) {
inds <- inds2[matlab2r::find(T2 == pop2)]
ninds <- length(inds)
@@ -464,26 +469,31 @@ greedyMix_muutokset <- R6Class(
rows <- c(rows, t(lisa))
}
diffInCounts <- computeDiffInCounts(
- t(rows), size(COUNTS, 1), size(COUNTS, 2), data
+ t(rows), size(globals$COUNTS, 1), size(globals$COUNTS, 2), data
)
- diffInSumCounts <- sum(diffInCounts)
+ diffInSumCounts <- colSums(diffInCounts)
- COUNTS[, , i1] <- COUNTS[, , i1] - diffInCounts
- SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] - diffInSumCounts
+ globals$COUNTS[, , i1] <- globals$COUNTS[, , i1] - diffInCounts
+ globals$SUMCOUNTS[i1, ] <- globals$SUMCOUNTS[i1, ] - diffInSumCounts
new_i1_logml <- computePopulationLogml(i1, adjprior, priorTerm)
- COUNTS[, , i1] <- COUNTS[, , i1] + diffInCounts
- SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] + diffInSumCounts
+ globals$COUNTS[, , i1] <- globals$COUNTS[, , i1] + diffInCounts
+ globals$SUMCOUNTS[i1, ] <- globals$SUMCOUNTS[i1, ] + diffInSumCounts
- i2 <- c(1:i1 - 1, i1 + 1:npops)
- i2_logml <- t(POP_LOGML[i2])
+ if (i1 < npops) {
+ i2 <- c(1:(i1 - 1), (i1 + 1):npops)
+ } else {
+ i2 <- 1:(i1 - 1)
+ }
+ i2_logml <- t(globals$POP_LOGML[i2])
- COUNTS[, , i2] <- COUNTS[, , i2] + repmat(diffInCounts, c(1, 1, npops - 1))
- SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] + repmat(diffInSumCounts, c(npops - 1, 1))
+ globals$COUNTS[, , i2] <- globals$COUNTS[, , i2] + repmat(diffInCounts, c(1, 1, npops - 1))
+ globals$SUMCOUNTS[i2, ] <- globals$SUMCOUNTS[i2, ] + repmat(diffInSumCounts, c(npops - 1, 1))
new_i2_logml <- t(computePopulationLogml(i2, adjprior, priorTerm))
- COUNTS[, , i2] <- COUNTS[, , i2] - repmat(diffInCounts, c(1, 1, npops - 1))
- SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] - repmat(diffInSumCounts, c(npops - 1, 1))
+ globals$COUNTS[, , i2] <- globals$COUNTS[, , i2] - repmat(diffInCounts, c(1, 1, npops - 1))
+ globals$SUMCOUNTS[i2, ] <- globals$SUMCOUNTS[i2, ] - repmat(diffInSumCounts, c(npops - 1, 1))
- muutokset[pop2, i2] <- new_i1_logml - i1_logml + new_i2_logml - i2_logml
+ i1_diff <- new_i1_logml - i1_logml
+ muutokset[pop2, i2] <- rep(i1_diff, length(i2_logml)) + new_i2_logml - i2_logml
}
}
return(muutokset)
@@ -502,12 +512,12 @@ greedyMix_muutokset <- R6Class(
ninds <- length(inds)
muutokset <- zeros(ninds, 1)
- i1_logml <- POP_LOGML[i1]
- i2_logml <- POP_LOGML[i2]
+ i1_logml <- globals$POP_LOGML[i1]
+ i2_logml <- globals$POP_LOGML[i2]
for (i in 1:ninds) {
ind <- inds[i]
- if (PARTITION[ind] == i1) {
+ if (globals$PARTITION[ind] == i1) {
pop1 <- i1 # mist�
pop2 <- i2 # mihin
} else {
@@ -516,24 +526,24 @@ greedyMix_muutokset <- R6Class(
}
rows <- globalRows[ind, 1]:globalRows[ind, 2]
diffInCounts <- computeDiffInCounts(
- rows, size(COUNTS, 1), size(COUNTS, 2), data
+ rows, size(globals$COUNTS, 1), size(globals$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
+ globals$COUNTS[, , pop1] <- globals$COUNTS[, , pop1] - diffInCounts
+ globals$SUMCOUNTS[pop1, ] <- globals$SUMCOUNTS[pop1, ] - diffInSumCounts
+ globals$COUNTS[, , pop2] <- globals$COUNTS[, , pop2] + diffInCounts
+ globals$SUMCOUNTS[pop2, ] <- globals$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
+ globals$COUNTS[, , pop1] <- globals$COUNTS[, , pop1] + diffInCounts
+ globals$SUMCOUNTS[pop1, ] <- globals$SUMCOUNTS[pop1, ] + diffInSumCounts
+ globals$COUNTS[, , pop2] <- globals$COUNTS[, , pop2] - diffInCounts
+ globals$SUMCOUNTS[pop2, ] <- globals$SUMCOUNTS[pop2, ] - diffInSumCounts
}
muutokset <- muutokset - i1_logml - i2_logml
diff --git a/R/laskeOsaDist.R b/R/laskeOsaDist.R
index 4f76b8b..b6c8570 100644
--- a/R/laskeOsaDist.R
+++ b/R/laskeOsaDist.R
@@ -11,8 +11,8 @@ laskeOsaDist <- function(inds2, dist, ninds) {
ninds2 <- length(inds2)
apu <- zeros(choose(ninds2, 2), 2)
rivi <- 1
- for (i in 1:ninds2 - 1) {
- for (j in i + 1:ninds2) {
+ for (i in 1:(ninds2 - 1)) {
+ for (j in (i + 1):ninds2) {
apu[rivi, 1] <- inds2[i]
apu[rivi, 2] <- inds2[j]
rivi <- rivi + 1
diff --git a/R/poistaTyhjatPopulaatiot.R b/R/poistaTyhjatPopulaatiot.R
index 0635e9a..12eb486 100644
--- a/R/poistaTyhjatPopulaatiot.R
+++ b/R/poistaTyhjatPopulaatiot.R
@@ -1,14 +1,14 @@
poistaTyhjatPopulaatiot <- function(npops) {
- # % Poistaa tyhjentyneet populaatiot COUNTS:ista ja
- # % SUMCOUNTS:ista. P�ivitt�� npops:in ja PARTITION:in.
- notEmpty <- matlab2r::find(apply(SUMCOUNTS, 1, function(x) any(x > 0)))
- COUNTS <- COUNTS[, , notEmpty]
- SUMCOUNTS <- SUMCOUNTS[notEmpty, ]
- LOGDIFF <- LOGDIFF[, notEmpty]
+ # % Poistaa tyhjentyneet populaatiot globals$COUNTS:ista ja
+ # % globals$SUMCOUNTS:ista. P�ivitt�� npops:in ja globals$PARTITION:in.
+ notEmpty <- matlab2r::find(apply(globals$SUMCOUNTS, 1, function(x) any(x > 0)))
+ globals$COUNTS <- globals$COUNTS[, , notEmpty]
+ globals$SUMCOUNTS <- globals$SUMCOUNTS[notEmpty, ]
+ globals$LOGDIFF <- globals$LOGDIFF[, notEmpty]
for (n in 1:length(notEmpty)) {
- apu <- matlab2r::find(PARTITION == notEmpty[n])
- PARTITION[apu] <- n
+ apu <- matlab2r::find(globals$PARTITION == notEmpty[n])
+ globals$PARTITION[apu] <- n
}
npops <- length(notEmpty)
return(npops)
diff --git a/R/returnInOrder.R b/R/returnInOrder.R
index 5287007..4fda453 100644
--- a/R/returnInOrder.R
+++ b/R/returnInOrder.R
@@ -4,21 +4,21 @@ returnInOrder <- function(inds, pop, globalRows, data, adjprior, priorTerm) {
# % arvoa eniten.
ninds <- length(inds)
- apuTaulu <- c(inds, zeros(ninds, 1))
+ apuTaulu <- cbind(inds, zeros(ninds, 1))
for (i in 1:ninds) {
ind <- inds[i]
rows <- globalRows[i, 1]:globalRows[i, 2]
diffInCounts <- computeDiffInCounts(
- rows, size[COUNTS, 1], size[COUNTS, 2], data
+ rows, size(globals$COUNTS, 1), size(globals$COUNTS, 2), data
)
- diffInSumCounts <- sum(diffInCounts)
+ diffInSumCounts <- colSums(diffInCounts)
- COUNTS[, , pop] <- COUNTS[, , pop] - diffInCounts
- SUMCOUNTS[pop, ] <- SUMCOUNTS[pop, ] - diffInSumCounts
+ globals$COUNTS[, , pop] <- globals$COUNTS[, , pop] - diffInCounts
+ globals$SUMCOUNTS[pop, ] <- globals$SUMCOUNTS[pop, ] - diffInSumCounts
apuTaulu[i, 2] <- computePopulationLogml(pop, adjprior, priorTerm)
- COUNTS[, , pop] <- COUNTS[, , pop] + diffInCounts
- SUMCOUNTS[pop, ] <- SUMCOUNTS[pop, ] + diffInSumCounts
+ globals$COUNTS[, , pop] <- globals$COUNTS[, , pop] + diffInCounts
+ globals$SUMCOUNTS[pop, ] <- globals$SUMCOUNTS[pop, ] + diffInSumCounts
}
apuTaulu <- sortrows(apuTaulu, 2)
inds <- apuTaulu[ninds:1, 1]
From e873075ebf5b2c85f4a42f211660390dffb3e3d4 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Tue, 2 Jul 2024 16:39:38 +0200
Subject: [PATCH 3/6] =?UTF-8?q?Fixed=20`greedyMix()`=20for=20BAPS=20files?=
=?UTF-8?q?=20(#24)=20=F0=9F=8D=BE?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
R/writeMixtureInfo.R | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/R/writeMixtureInfo.R b/R/writeMixtureInfo.R
index 65bdbee..79294e5 100644
--- a/R/writeMixtureInfo.R
+++ b/R/writeMixtureInfo.R
@@ -257,8 +257,8 @@ writeMixtureInfo <- function(
}
partitionSummary <- sortrows(partitionSummary, 2)
- partitionSummary <- partitionSummary[size(partitionSummary, 1):1, ]
- partitionSummary <- partitionSummary[matlab2r::find(partitionSummary[, 2] > -1e49), ]
+ partitionSummary <- partitionSummary[size(partitionSummary, 1):1, , drop = FALSE]
+ partitionSummary <- partitionSummary[matlab2r::find(partitionSummary[, 2] > -1e49), , drop = FALSE]
if (size(partitionSummary, 1) > 10) {
vikaPartitio <- 10
} else {
From 95ff2378b1e81e8838908a34742a796250ec7882 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Tue, 2 Jul 2024 16:39:48 +0200
Subject: [PATCH 4/6] Added unit tests (#24)
---
tests/testthat/test-greedyMix.R | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/tests/testthat/test-greedyMix.R b/tests/testthat/test-greedyMix.R
index 86cf9fb..6029c63 100644
--- a/tests/testthat/test-greedyMix.R
+++ b/tests/testthat/test-greedyMix.R
@@ -75,6 +75,13 @@ test_that("greedyMix() fails successfully", {
expect_error(greedyMix(file.path(path_inst, "bam_example.bam")))
})
+test_that("greedyMix() works when it should", {
+ baps_file <- file.path(path_inst, "BAPS_clustering_diploid.txt")
+ greedy_baps <- greedyMix(baps_file, "BAPS")
+ expect_type(greedy_baps, "list")
+ expect_length(greedy_baps, 10L)
+})
+
context("Linkage")
test_that("Linkages are properly calculated", {
From 3ce6659120f84f523330f787303145f1e30970c2 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Tue, 2 Jul 2024 16:53:04 +0200
Subject: [PATCH 5/6] Updated docs
---
man/greedyMix_muutokset.Rd | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/man/greedyMix_muutokset.Rd b/man/greedyMix_muutokset.Rd
index e73eb05..3700a75 100644
--- a/man/greedyMix_muutokset.Rd
+++ b/man/greedyMix_muutokset.Rd
@@ -6,8 +6,8 @@
\description{
Palauttaa npops*1 taulun, jossa i:s alkio kertoo, mik� olisi
muutos logml:ss�, mik�li yksil� ind siirret��n koriin i.
-diffInCounts on poistettava COUNTS:in siivusta i1 ja lis�tt�v�
-COUNTS:in siivuun i2, mik�li muutos toteutetaan.
+diffInCounts on poistettava globals$COUNTS:in siivusta i1 ja lis�tt�v�
+globals$COUNTS:in siivuun i2, mik�li muutos toteutetaan.
Lis�ys 25.9.2007:
Otettu k�ytt��n globaali muuttuja LOGDIFF, johon on tallennettu muutokset
From d861ffb551b94d2f32220f9e237149eb3d450b52 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Tue, 2 Jul 2024 16:53:10 +0200
Subject: [PATCH 6/6] Increment version number to 0.0.0.9028
---
DESCRIPTION | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 53dba3a..a2e2c03 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: rBAPS
Title: Bayesian Analysis of Population Structure
-Version: 0.0.0.9027
+Version: 0.0.0.9028
Date: 2020-11-09
Authors@R:
c(