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Fixed syntax

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This commit is contained in:
Waldir Leoncio 2021-02-01 09:22:58 +01:00
parent bdf512fca7
commit c0d36e2c30
3 changed files with 16 additions and 7 deletions
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2
R/computeDiffInCounts.R
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@ -6,7 +6,7 @@ computeDiffInCounts <- function(rows, max_noalle, nloci, data) {
diffInCounts <- zeros(max_noalle, nloci) diffInCounts <- zeros(max_noalle, nloci)
for (i in rows) { for (i in rows) {
row <- data[i, ] row <- data[i, ]
notEmpty <- find(row>=0) notEmpty <- as.matrix(find(row>=0))
if (length(notEmpty) > 0) { if (length(notEmpty) > 0) {
diffInCounts[row(notEmpty) + (notEmpty - 1) * max_noalle] <- diffInCounts[row(notEmpty) + (notEmpty - 1) * max_noalle] <-

17
R/computePopulationLogml.R
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@ -1,18 +1,26 @@
computePopulationLogml <- function(pops, adjprior, priorTerm) { computePopulationLogml <- function(pops, adjprior, priorTerm = 0) {
# Palauttaa length(pops)*1 taulukon, jossa on laskettu korikohtaiset # Palauttaa length(pops)*1 taulukon, jossa on laskettu korikohtaiset
# ======================================================== #
# Limiting COUNTS size #
# ======================================================== #
COUNTS <- COUNTS[seq_len(nrow(adjprior)), seq_len(ncol(adjprior)), pops, drop=FALSE]
x <- size(COUNTS, 1) x <- size(COUNTS, 1)
y <- size(COUNTS, 2) y <- size(COUNTS, 2)
z <- length(pops) z <- length(pops)
popLogml <- squeeze( # ======================================================== #
# Computation #
# ======================================================== #
term1 <- squeeze(
# FIXME: assumes COUNTS has 3 dims. Where does this come from? # FIXME: assumes COUNTS has 3 dims. Where does this come from?
sum( sum(
sum( sum(
reshape( reshape(
lgamma( lgamma(
repmat(adjprior, c(1, 1, length(pops))) + repmat(adjprior, c(1, 1, length(pops))) +
COUNTS[, , pops] COUNTS[seq_len(nrow(adjprior)), seq_len(ncol(adjprior)), pops, drop=FALSE]
), ),
c(x, y, z) c(x, y, z)
), ),
@ -20,6 +28,7 @@ computePopulationLogml <- function(pops, adjprior, priorTerm) {
), ),
2 2
) )
) - sum(lgamma(1 + SUMCOUNTS[pops, ]), 2) - priorTerm )
popLogml <- term1 - sum(lgamma(1 + SUMCOUNTS[pops, ]), 2) - priorTerm
return(popLogml) return(popLogml)
} }

4
R/indMix.R
View file

@ -137,11 +137,11 @@ indMix <- function(c, npops, dispText) {
round <- roundTypes[n] round <- roundTypes[n]
kivaluku <- 0 kivaluku <- 0
if (kokeiltu(round) == 1) { #Askelta kokeiltu viime muutoksen j<>lkeen if (kokeiltu[round] == 1) { #Askelta kokeiltu viime muutoksen j<>lkeen
} else if (round == 0 | round == 1) { #Yksil<69>n siirt<72>minen toiseen populaatioon. } else if (round == 0 | round == 1) { #Yksil<69>n siirt<72>minen toiseen populaatioon.
inds <- 1:ninds inds <- 1:ninds
aputaulu <- c(t(inds), rand(ninds, 1)) aputaulu <- cbind(inds, rand(ninds, 1))
aputaulu <- sortrows(aputaulu, 2) aputaulu <- sortrows(aputaulu, 2)
inds <- t(aputaulu[, 1]) inds <- t(aputaulu[, 1])
muutosNyt <- 0 muutosNyt <- 0