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Merge branch 'initialCounts' into dev

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This commit is contained in:
Waldir Leoncio 2020-07-14 15:47:44 +02:00
commit 390af9c65a
2 changed files with 25 additions and 32 deletions
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32
R/greedyMix.R
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@ -877,38 +877,6 @@ greedyMix <- function(
# %----------------------------------------------------------------------------------------
# function logml = ...
# initialCounts(partition, data, npops, rows, noalle, adjprior)
# nloci=size(data,2);
# ninds = size(rows, 1);
# koot = rows(:,1) - rows(:,2) + 1;
# maxSize = max(koot);
# counts = zeros(max(noalle),nloci,npops);
# sumcounts = zeros(npops,nloci);
# for i=1:npops
# for j=1:nloci
# havainnotLokuksessa = find(partition==i & data(:,j)>=0);
# sumcounts(i,j) = length(havainnotLokuksessa);
# for k=1:noalle(j)
# alleleCode = k;
# N_ijk = length(find(data(havainnotLokuksessa,j)==alleleCode));
# counts(k,j,i) = N_ijk;
# end
# end
# end
# %initializeGammaln(ninds, maxSize, max(noalle));
# logml = laskeLoggis(counts, sumcounts, adjprior);
# %-----------------------------------------------------------------------
# function logml=computeLogml(counts, sumcounts, noalle, data, rowsFromInd)
# nloci = size(counts,2);
# npops = size(counts,3);

25
R/initialCounts.R Normal file
View file

@ -0,0 +1,25 @@
initialCounts <- function(partition, data, npops, rows, noalle, adjprior) {
nloci <- size(data, 2)
ninds <- size(rows, 1)
koot <- rows[, 1] - rows[, 2] + 1
maxSize <- max(koot)
counts <- zeros(max(noalle), nloci, npops)
sumcounts <- zeros(npops, nloci)
for (i in 1:npops) {
for (j in 1:nloci) {
havainnotLokuksessa <- find(partition == i & data[, j] >= 0)
sumcounts[i, j] <- length(havainnotLokuksessa)
for (k in 1:noalle[j]) {
alleleCode <- k
N_ijk <- length(
find(data[havainnotLokuksessa, j] == alleleCode)
)
counts[k, j, i] <- N_ijk
}
}
}
logml <- laskeLoggis(counts, sumcounts, adjprior)
return(logml)
}