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Translated remaining code on initialPopCounts

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This commit is contained in:
Waldir Leoncio 2020-11-09 14:34:54 +01:00
parent 71092c4eeb
commit 203835b866
1 changed files with 16 additions and 18 deletions
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34
R/initialPopCounts.R
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@ -1,22 +1,20 @@
initialPopCounts <- function(data, npops, rows, noalle, adjprior) {
# nloci=size(data,2)
# counts <- zeros(max(noalle),nloci,npops)
# sumcounts <- zeros(npops,nloci)
# for (i in 1:npops) {
# for (j in 1:nloci) {
# i_rivit <- rows(i,1):rows(i,2)
# havainnotLokuksessa <- find(data(i_rivit,j)>=0)
# sumcounts(i,j) <- length(havainnotLokuksessa)
# for (k in 1:noalle(j)) {
# alleleCode <- k
# N_ijk <- length(find(data(i_rivit,j)==alleleCode))
# counts(k,j,i) <- N_ijk
# }
# }
# }
# logml <- laskeLoggis(counts, sumcounts, adjprior)
nloci <- size(data, 2)
counts <- zeros(max(noalle), nloci, npops)
sumcounts <- zeros(npops, nloci)
for (i in 1:npops) {
for (j in 1:nloci) {
i_rivit <- rows(i, 1):rows(i, 2)
havainnotLokuksessa <- find(data(i_rivit, j) >= 0)
sumcounts(i, j) <- length(havainnotLokuksessa)
for (k in 1:noalle[j]) {
alleleCode <- k
N_ijk <- length(find(data(i_rivit, j) == alleleCode))
counts(k, j, i) <- N_ijk
}
}
}
logml <- laskeLoggis(counts, sumcounts, adjprior)
return(sumcounts = sumcounts, counts = counts, logml = logml)
}